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############################################################### ############################################################### ############################################################### ### CCP4 6.3: MOLREP(ccp4) version 11.1.03 : ## ############################################################### User: Administrator Run date: 10/ 5/2013 Run time: 18:24:56 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.
$TEXT:Reference1: $$ comment $$ MOLREP: an automated program for molecular replacement A.Vagin,A.Teplyakov. J. Appl. Cryst. (1997) 30, 1022-1025. $$ $SUMMARY :Reference1: $$ MOLREP: $$ :TEXT:Reference1: $$ +-----------------------------------------+ | | | --- MOLREP --- | | /Vers 11.1.03; 12.03.2013/ | | | +-----------------------------------------+ OPENED INPUT MTZ FILE Logical Name: C:/SOLVE_REFINE/lizozim/mr-refine-build/lizozim-xds-p43212.mtz Filename: C:/SOLVE_REFINE/lizozim/mr-refine-build/lizozim-xds-p43212.mtz ----------------------------------- --- MTZ file :C:/SOLVE_REFINE/lizozim/mr-refine-build/lizozim-xds-p43212.mtz No Label type 1 H H 2 K H 3 L H 4 FreeR_flag I 5 I J 6 SIGI Q 7 F F 8 SIGF Q ----------------------------------- +===== Input keywords ============================+ | _LABIN F=F SIGF=SIGF | | _SURF Y | | _COMPL 0.95 | | _SIM 0.6 | | _FILE_S C:/SOLVE_REFINE/lizozim/mr-refine-build/193L-csirke-fasta.pir | _RESMAX 3.5 | +=================================================+ Data line--- LABIN F=F SIGF=SIGF OPENED INPUT MTZ FILE Logical Name: C:/SOLVE_REFINE/lizozim/mr-refine-build/lizozim-xds-p43212.mtz Filename: C:/SOLVE_REFINE/lizozim/mr-refine-build/lizozim-xds-p43212.mtz Number of reflections : 24467 Time: 18h 24m 56s Full doc. in: C:/Ccp4Temp\lizozim_7_molrep_molrep.doc Script file : C:/Ccp4Temp\lizozim_7_molrep_molrep.btc Input MODEL_file ::/SOLVE_REFINE/lizozim/mr-refine-build/modell-2ZIL-human.pdb Input SF_file :C:/Ccp4Temp/lizozim_7_molrep_molrep_mtz.cif --- Alignment -- Flag D3,SS,OCC,CORR,DIST:YYNNN read file protein-1 read file protein-2 Number of atoms, N_inside,Nres : 1029 454 130 Percent SS,H,B : 39.2 24.6 14.6 MATRIX (UNIT-1,GOMOLOGY-,HYDROPHOB-H STRUCTURE-S,KODON-K ) :B MATCH MAX,MIN : 1.000 0.063 "0" : 0.312 "12,2" : 1.062 0.437 PENALTY O,E : 0.750 0.125 "0" : 0.312 ------------------------------------------------ NUMBER OF AMINO ACIDS IN 1-ST SEQ= 129 NUMBER OF AMINO ACIDS IN 2-ND SEQ= 130 NUMBER OF ALIGNED AMINO ACIDS = 129 NUMBER OF IDENTICAL AMINO ACIDS = 78 IDENTITY = 60.465 = 0.534 (for 1-st seq) = 0.661 (for 1-st seq),sig = 0.2491 0.0099 = 0.691 N_gap = 1 ------------------------------------------------ ------------------------------------------------------ 11111111112222222222333333333344444444 44 12345678901234567890123456789012345678901234567 89 ss surf 193L:KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNT_DG 2ZIL:KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDR *** ***** ** * * *** ** ** * ** ** ** *** * * ss HHHHHHHHHH HHHHHHHHHH BBBBB surf 24152121131135231331461211111111222131115143325734 11111111112222222222333333333344444444445 12345678901234567890123456789012345678901234567890 ------------------------------------------------------ + +++++ +++ + +++++ + +++ + +++++++++ ++ +++++++++++++++++++++++++++++++++ ++ +++++++++++++++++++++++++++++++++++++++++++++++ ++ ------------------------------------------------------ ------------------------------------------------------ 55555555556666666666777777777788888888889999999999 01234567890123456789012345678901234567890123456789 ss surf 193L:STDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIV 2ZIL:STDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVV ****** ***** ***** *** * * ***** * * *** * ss BBBBB BBB BBB BBB HHHHHHHHHHH surf 11111111111131132541362422151314112344132114111211 1 55555555566666666667777777777888888888899999999990 12345678901234567890123456789012345678901234567890 ------------------------------------------------------ +++++++++++++++++++++ + ++ + + +++++++++++++++++++++++ +++++++++++ ++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------------------------------ ------------------------------------------------------ 111111111111111111111111111111 000000000011111111112222222222 012345678901234567890123456789 ss surf 193L:SDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 2ZIL:RDPQGIRAWVAWRNRCQNRDVRQYVQGCGV * * ********* ** ** ss H surf 326411331411333126441531147163 111111111111111111111111111111 000000000111111111122222222223 123456789012345678901234567890 ------------------------------------------------------ ++++++++++ + + + +++++++++++++++ + ++++++ ++++++++++++++++++++++++++++++ ------------------------------------------------------ ------------------------------------------------ NUMBER OF AMINO ACIDS IN 1-ST SEQ= 129 NUMBER OF AMINO ACIDS IN 2-ND SEQ= 130 NUMBER OF ALIGNED AMINO ACIDS = 129 NUMBER OF IDENTICAL AMINO ACIDS = 78 IDENTITY = 60.465 = 0.534 (for 1-st seq) = 0.661 (for 1-st seq) = 0.2491 = 0.691 IDENT_NEW = 67.389 N_gap = 1 ------------------------------------------------ Alignement: identity = 60.47 --- model was corrected by alignement --- output file: align.pdb Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: C:\CCP4\6.3\lib\data\syminfo.lib -- Model -- INFO: model was corrected (keyword SURF="Y") model was shifted to the origin of coordinate system shift vector : -12.78 -15.31 -29.15 /fract/ : -0.162 -0.195 -0.791 Number of atoms: 917 Natom_inside : 361 INFO: expected number of models : 1 INFO: V_model: 72.2% (of asymm. part of u.c.) -- Structure Factors -- ------------- Fobs: resolution : 19.09 1.36 Completeness of Fobs : 0.971 B_overall of Fobs : 16.388 Optical resolution : 1.163 Anisotropic distribution of Structure Factors: Ratio of Eigen values : 1.0000 0.9993 0.8970 INFO: Anisotropicy will not be used ------------- Resolution will be used : 19.09 3.50 ------------- -- Filters -- ------------- Completeness of model, COMPL = V_model/(V_cell/Nsym) RESMIN ~ Rad_model Rad_model,COMPL : 18.635 0.950 Similarity of model : SIM --> BADD Sim,Badd : 0.600 -10.316 Filters off,add (A) : 19.51 1.74 INFO: Filter off = Highpass filter (corresponds to keyword: RESMIN) INFO: Filter add = Lowpass filter (connected with keywords: SIM, BADD) ------------- Space group : P 43 21 2 No: 96 Sett: 1 Cell: 78.713 78.713 36.840 90.00 90.00 90.00 --- Rotation function --- Radius of gyration : 13.73 WARNING: Radius of integration > 18.42 Radius of integration : 18.42 Resolution : 19.09 3.50 --- rfcoef for model --- --- rfcoef for Fobs --- NCS (from Self rotation Function): 6 NCS_model (from Model Self rotation Function): 1 Program will use NCS_model =: 1 --- Peaks of Rotation Function --- +------------------------------------------+ | theta phi chi Rf/sigma | +------------------------------------------+ | 1 160.59 175.49 62.50 5.60 | | 2 161.02 170.38 62.39 5.41 | | 3 165.48 -178.04 144.44 4.38 | | 4 155.24 -91.90 177.37 3.88 | | 5 66.89 93.55 65.51 3.51 | | 6 75.36 89.08 75.16 3.49 | | 7 163.91 171.35 76.64 3.43 | | 8 144.93 -164.80 73.94 3.42 | | 9 164.48 168.10 77.03 3.37 | | 10 66.61 89.98 87.96 3.21 | | 11 104.81 -176.60 80.81 3.20 | | 12 117.39 175.52 91.75 3.13 | | 13 143.47 -133.33 157.18 3.08 | | 14 17.93 71.78 117.12 3.02 | | 15 40.30 64.15 150.71 2.99 | | 16 68.71 116.99 91.62 2.97 | | 17 69.24 80.32 59.86 2.95 | | 18 67.89 120.11 67.83 2.95 | | 19 39.73 62.99 150.79 2.94 | | 20 134.38 169.08 76.67 2.88 | | 21 82.75 83.14 90.93 2.84 | | 22 28.42 78.64 165.30 2.84 | | 23 145.33 127.61 55.78 2.83 | | 24 136.26 -155.21 124.96 2.82 | | 25 153.72 173.54 118.83 2.81 | | 26 108.30 147.01 88.83 2.79 | | 27 49.38 81.38 96.07 2.78 | | 28 41.65 16.20 173.92 2.76 | | 29 134.08 155.98 52.21 2.75 | | 30 114.24 154.06 67.96 2.74 | | 31 40.18 48.32 167.02 2.73 | | 32 119.63 -168.37 86.74 2.72 | | 33 136.33 -155.15 123.38 2.72 | | 34 114.96 152.11 67.24 2.72 | | 35 177.16 -104.39 158.14 2.69 | | 36 135.97 -141.63 144.40 2.69 | | 37 30.03 47.17 167.49 2.66 | | 38 30.87 48.37 167.23 2.66 | +------------------------------------------+ INFO: Relations between peaks see in molrep.doc ---RF peak similarity --- +------------------------------------------------------------------------+ 1 | 9 8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 2 | 8 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 3 | . . 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 4 | . . . 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 5 | . . . . 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 6 | . . . . . 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 7 | . . . . . . 9 . 8 . . . . . . . . . . . . . . . . . . . . . . . . . . .| 8 | . . . . . . . 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 9 | . . . . . . 8 . 9 . . . . . . . . . . . . . . . . . . . . . . . . . . .| 10 | . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . . . . . . . . .| 11 | . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . . . . . . . .| 12 | . . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . . . . . . .| 13 | . . . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . . . . . .| 14 | . . . . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . . . . .| 15 | . . . . . . . . . . . . . . 9 . . . 8 . . . . . . . . . . . . . . . . .| 16 | . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . . .| 17 | . . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . . .| 18 | . . . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . . . . . . .| 19 | . . . . . . . . . . . . . . 8 . . . 9 . . . . . . . . . . . . . . . . .| 20 | . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . . . . .| 21 | . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . . . .| 22 | . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . . .| 23 | . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . . . . . .| 24 | . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . 8 . . .| 25 | . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . . . .| 26 | . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . . .| 27 | . . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . . .| 28 | . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . . .| 29 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . . . .| 30 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . 8 . .| 31 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . . .| 32 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 . . . .| 33 | . . . . . . . . . . . . . . . . . . . . . . . 8 . . . . . . . . 9 . . .| 34 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 . . . 9 . .| 35 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 .| 36 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9| 37 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 38 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| +------------------------------------------------------------------------+ Time: 18h 25m 5s Elapsed: 0h 0m 9s --- Translation function --- Resolution : 19.09 3.50 NCS model : 1 Time_elapsed: 0h 0m 10s Remained: 0h 0m 37s RF TF TF/sig TFcntrst PFind PF PFmin wRfac Score Cntrst (for) 1 1 10.73 3.961 1.00 1.00 -17.12 0.492 0.459 0.00 ( 0.459) 2 1 9.057 3.553 1.00 1.00 -17.32 0.517 0.401 0.00 ( 0.459) 3 1 3.201 2.551 1.00 1.00 -21.62 0.634 0.136 0.00 ( 0.459) 4 1 2.176 -0.084 1.00 1.00 -13.18 0.652 0.079 7.31 ( 0.459) 5 2 3.351 1.357 1.00 1.00 -20.56 0.642 0.110 8.66 ( 0.459) 6 1 3.511 2.561 1.00 1.00 -17.64 0.634 0.125 8.35 ( 0.459) 7 1 3.214 1.446 1.00 1.00 -16.97 0.636 0.113 8.95 ( 0.459) 8 1 2.970 0.512 1.00 1.00 -15.63 0.653 0.101 9.72 ( 0.459) 9 3 2.736 0.985 1.00 1.00 -17.26 0.637 0.103 9.72 ( 0.459) 10 1 3.844 2.416 1.00 1.00 -18.94 0.641 0.123 9.84 ( 0.459) 11 2 2.862 2.484 1.00 0.94 -17.14 0.625 0.138 9.43 ( 0.459) 12 2 2.110 1.771 1.00 0.93 -16.52 0.647 0.106 9.70 ( 0.459) 13 1 3.039 2.365 1.00 0.88 -13.65 0.648 0.094 9.25 ( 0.459) INFO: Contrast and TF/sig are good enough. Stop this run --- Summary --- +------------------------------------------------------------------------------+ | RF TF theta phi chi tx ty tz TF/sg wRfac Score | +------------------------------------------------------------------------------+ | 1 1 1 160.59 175.49 62.50 0.507 0.244 0.011 10.73 0.492 0.459 | | 2 2 1 161.02 170.38 62.39 0.007 0.745 0.010 9.06 0.517 0.401 | | 3 11 2 104.81 -176.60 80.81 0.694 0.036 0.442 2.86 0.625 0.138 | | 4 3 1 165.48 -178.04 144.44 0.723 0.031 0.400 3.20 0.634 0.136 | | 5 6 1 75.36 89.08 75.16 0.775 0.461 0.430 3.51 0.634 0.125 | | 6 10 1 66.61 89.98 87.96 0.787 0.451 0.231 3.84 0.641 0.123 | | 7 7 1 163.91 171.35 76.64 0.721 0.475 0.080 3.21 0.636 0.113 | | 8 5 2 66.89 93.55 65.51 0.750 0.491 0.433 3.35 0.642 0.110 | | 9 12 2 117.39 175.52 91.75 0.738 0.035 0.481 2.11 0.647 0.106 | | 10 9 3 164.48 168.10 77.03 0.720 0.476 0.083 2.74 0.637 0.103 | | 11 8 1 144.93 -164.80 73.94 0.511 0.221 0.091 2.97 0.653 0.101 | | 12 13 1 143.47 -133.33 157.18 0.732 0.525 0.459 3.04 0.648 0.094 | | 13 4 1 155.24 -91.90 177.37 0.742 0.881 0.218 2.18 0.652 0.079 | +------------------------------------------------------------------------------+ TF/sig = 10.73 Contrast = 9.25 After stick correction: Move closer to origin I_sym_operator : 5 new position(frac): 0.007 0.256 0.239 Nmon RF TF theta phi chi tx ty tz TF/sg wRfac Score 1 1 1 89.21 29.79 160.21 0.007 0.256 0.239 10.73 0.492 0.459 --- convert "molrep.crd" to "molrep.pdb" --- Time: 18h 25m 17s Elapsed: 0h 0m 21s
MOLREP(ccp4): Normal termination Times: User: 0.0s System: 0.0s Elapsed: 0:21
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