null Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prr-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:12 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1816 and 0 Target number of residues in the AU: 1816 Target solvent content: 0.6555 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 119.307 3.600 Wilson plot Bfac: 81.74 31226 reflections ( 97.59 % complete ) and 0 restraints for refining 20853 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3071 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2623 (Rfree = 0.000) for 20853 atoms. Found 133 (133 requested) and removed 100 (66 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 21484 seeds are put forward NCS extension: 0 residues added, 21484 seeds are put forward Round 1: 1224 peptides, 215 chains. Longest chain 16 peptides. Score 0.395 Round 2: 1329 peptides, 174 chains. Longest chain 22 peptides. Score 0.542 Round 3: 1399 peptides, 173 chains. Longest chain 20 peptides. Score 0.576 Round 4: 1397 peptides, 159 chains. Longest chain 27 peptides. Score 0.603 Round 5: 1394 peptides, 165 chains. Longest chain 27 peptides. Score 0.590 Taking the results from Round 4 Chains 168, Residues 1238, Estimated correctness of the model 15.8 % 11 chains (128 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5297 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1947 (Rfree = 0.000) for 17144 atoms. Found 52 (109 requested) and removed 82 (54 requested) atoms. Cycle 2: After refmac, R = 0.1814 (Rfree = 0.000) for 17114 atoms. Found 47 (109 requested) and removed 98 (54 requested) atoms. Cycle 3: After refmac, R = 0.1707 (Rfree = 0.000) for 17063 atoms. Found 24 (109 requested) and removed 90 (54 requested) atoms. Cycle 4: After refmac, R = 0.1617 (Rfree = 0.000) for 16997 atoms. Found 33 (109 requested) and removed 85 (54 requested) atoms. Cycle 5: After refmac, R = 0.1579 (Rfree = 0.000) for 16945 atoms. Found 31 (108 requested) and removed 88 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17647 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 17662 seeds are put forward Round 1: 1239 peptides, 208 chains. Longest chain 18 peptides. Score 0.420 Round 2: 1375 peptides, 187 chains. Longest chain 28 peptides. Score 0.536 Round 3: 1409 peptides, 176 chains. Longest chain 23 peptides. Score 0.574 Round 4: 1418 peptides, 167 chains. Longest chain 30 peptides. Score 0.596 Round 5: 1410 peptides, 164 chains. Longest chain 25 peptides. Score 0.599 Taking the results from Round 5 Chains 169, Residues 1246, Estimated correctness of the model 14.3 % 8 chains (105 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5221 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1791 (Rfree = 0.000) for 17144 atoms. Found 51 (109 requested) and removed 95 (54 requested) atoms. Cycle 7: After refmac, R = 0.1626 (Rfree = 0.000) for 17100 atoms. Found 37 (109 requested) and removed 87 (54 requested) atoms. Cycle 8: After refmac, R = 0.1514 (Rfree = 0.000) for 17050 atoms. Found 36 (109 requested) and removed 78 (54 requested) atoms. Cycle 9: After refmac, R = 0.1241 (Rfree = 0.000) for 17008 atoms. Found 10 (109 requested) and removed 70 (54 requested) atoms. Cycle 10: After refmac, R = 0.1182 (Rfree = 0.000) for 16948 atoms. Found 5 (108 requested) and removed 70 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 17614 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 17652 seeds are put forward Round 1: 1251 peptides, 201 chains. Longest chain 24 peptides. Score 0.443 Round 2: 1406 peptides, 183 chains. Longest chain 26 peptides. Score 0.559 Round 3: 1416 peptides, 178 chains. Longest chain 29 peptides. Score 0.573 Round 4: 1407 peptides, 177 chains. Longest chain 27 peptides. Score 0.571 Round 5: 1404 peptides, 175 chains. Longest chain 41 peptides. Score 0.574 Taking the results from Round 5 Chains 185, Residues 1229, Estimated correctness of the model 4.2 % 13 chains (166 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5385 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1765 (Rfree = 0.000) for 17144 atoms. Found 63 (109 requested) and removed 97 (54 requested) atoms. Cycle 12: After refmac, R = 0.1621 (Rfree = 0.000) for 17110 atoms. Found 39 (109 requested) and removed 79 (54 requested) atoms. Cycle 13: After refmac, R = 0.1553 (Rfree = 0.000) for 17070 atoms. Found 42 (109 requested) and removed 75 (54 requested) atoms. Cycle 14: After refmac, R = 0.1486 (Rfree = 0.000) for 17037 atoms. Found 38 (109 requested) and removed 79 (54 requested) atoms. Cycle 15: After refmac, R = 0.1448 (Rfree = 0.000) for 16996 atoms. Found 42 (109 requested) and removed 85 (54 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 17716 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 17733 seeds are put forward Round 1: 1172 peptides, 196 chains. Longest chain 13 peptides. Score 0.411 Round 2: 1338 peptides, 182 chains. Longest chain 24 peptides. Score 0.529 Round 3: 1330 peptides, 185 chains. Longest chain 18 peptides. Score 0.519 Round 4: 1359 peptides, 180 chains. Longest chain 21 peptides. Score 0.543 Round 5: 1387 peptides, 183 chains. Longest chain 25 peptides. Score 0.550 Taking the results from Round 5 Chains 191, Residues 1204, Estimated correctness of the model 0.0 % 11 chains (105 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 5029 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1778 (Rfree = 0.000) for 17144 atoms. Found 74 (109 requested) and removed 84 (54 requested) atoms. Cycle 17: After refmac, R = 0.1619 (Rfree = 0.000) for 17134 atoms. Found 55 (109 requested) and removed 78 (54 requested) atoms. Cycle 18: After refmac, R = 0.1572 (Rfree = 0.000) for 17111 atoms. Found 41 (109 requested) and removed 80 (54 requested) atoms. Cycle 19: After refmac, R = 0.1221 (Rfree = 0.000) for 17072 atoms. Found 10 (109 requested) and removed 65 (54 requested) atoms. Cycle 20: After refmac, R = 0.1164 (Rfree = 0.000) for 17017 atoms. Found 8 (109 requested) and removed 63 (54 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 17682 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 17700 seeds are put forward Round 1: 1179 peptides, 204 chains. Longest chain 16 peptides. Score 0.396 Round 2: 1310 peptides, 178 chains. Longest chain 25 peptides. Score 0.524 Round 3: 1344 peptides, 179 chains. Longest chain 27 peptides. Score 0.539 Round 4: 1307 peptides, 169 chains. Longest chain 28 peptides. Score 0.542 Round 5: 1317 peptides, 173 chains. Longest chain 24 peptides. Score 0.538 Taking the results from Round 4 Chains 178, Residues 1138, Estimated correctness of the model 0.0 % 13 chains (125 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4851 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1738 (Rfree = 0.000) for 17144 atoms. Found 53 (109 requested) and removed 77 (54 requested) atoms. Cycle 22: After refmac, R = 0.1634 (Rfree = 0.000) for 17120 atoms. Found 55 (109 requested) and removed 65 (54 requested) atoms. Cycle 23: After refmac, R = 0.1290 (Rfree = 0.000) for 17110 atoms. Found 18 (109 requested) and removed 66 (54 requested) atoms. Cycle 24: After refmac, R = 0.1225 (Rfree = 0.000) for 17062 atoms. Found 4 (109 requested) and removed 71 (54 requested) atoms. Cycle 25: After refmac, R = 0.1201 (Rfree = 0.000) for 16995 atoms. Found 4 (109 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17600 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 17614 seeds are put forward Round 1: 1099 peptides, 188 chains. Longest chain 14 peptides. Score 0.390 Round 2: 1213 peptides, 180 chains. Longest chain 21 peptides. Score 0.471 Round 3: 1275 peptides, 174 chains. Longest chain 19 peptides. Score 0.516 Round 4: 1271 peptides, 180 chains. Longest chain 20 peptides. Score 0.501 Round 5: 1253 peptides, 179 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 3 Chains 176, Residues 1101, Estimated correctness of the model 0.0 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4467 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1611 (Rfree = 0.000) for 17144 atoms. Found 43 (109 requested) and removed 73 (54 requested) atoms. Cycle 27: After refmac, R = 0.1578 (Rfree = 0.000) for 17114 atoms. Found 59 (109 requested) and removed 71 (54 requested) atoms. Cycle 28: After refmac, R = 0.1541 (Rfree = 0.000) for 17102 atoms. Found 56 (109 requested) and removed 72 (54 requested) atoms. Cycle 29: After refmac, R = 0.1183 (Rfree = 0.000) for 17086 atoms. Found 10 (109 requested) and removed 63 (54 requested) atoms. Cycle 30: After refmac, R = 0.1126 (Rfree = 0.000) for 17033 atoms. Found 5 (109 requested) and removed 63 (54 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17642 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 17651 seeds are put forward Round 1: 1112 peptides, 201 chains. Longest chain 15 peptides. Score 0.365 Round 2: 1204 peptides, 187 chains. Longest chain 28 peptides. Score 0.450 Round 3: 1242 peptides, 181 chains. Longest chain 23 peptides. Score 0.484 Round 4: 1245 peptides, 177 chains. Longest chain 24 peptides. Score 0.495 Round 5: 1247 peptides, 174 chains. Longest chain 24 peptides. Score 0.502 Taking the results from Round 5 Chains 175, Residues 1073, Estimated correctness of the model 0.0 % 7 chains (81 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4424 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1644 (Rfree = 0.000) for 17144 atoms. Found 54 (109 requested) and removed 78 (54 requested) atoms. Cycle 32: After refmac, R = 0.1531 (Rfree = 0.000) for 17120 atoms. Found 66 (109 requested) and removed 75 (54 requested) atoms. Cycle 33: After refmac, R = 0.1529 (Rfree = 0.000) for 17111 atoms. Found 60 (109 requested) and removed 69 (54 requested) atoms. Cycle 34: After refmac, R = 0.1475 (Rfree = 0.000) for 17102 atoms. Found 64 (109 requested) and removed 72 (54 requested) atoms. Cycle 35: After refmac, R = 0.1419 (Rfree = 0.000) for 17094 atoms. Found 44 (109 requested) and removed 79 (54 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 17740 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 17763 seeds are put forward Round 1: 1001 peptides, 183 chains. Longest chain 13 peptides. Score 0.345 Round 2: 1215 peptides, 185 chains. Longest chain 22 peptides. Score 0.461 Round 3: 1206 peptides, 179 chains. Longest chain 19 peptides. Score 0.470 Round 4: 1166 peptides, 175 chains. Longest chain 13 peptides. Score 0.458 Round 5: 1207 peptides, 175 chains. Longest chain 23 peptides. Score 0.480 Taking the results from Round 5 Chains 176, Residues 1032, Estimated correctness of the model 0.0 % 6 chains (66 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 4255 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1610 (Rfree = 0.000) for 17144 atoms. Found 78 (109 requested) and removed 87 (54 requested) atoms. Cycle 37: After refmac, R = 0.1525 (Rfree = 0.000) for 17135 atoms. Found 62 (109 requested) and removed 71 (54 requested) atoms. Cycle 38: After refmac, R = 0.1478 (Rfree = 0.000) for 17126 atoms. Found 66 (109 requested) and removed 86 (54 requested) atoms. Cycle 39: After refmac, R = 0.1101 (Rfree = 0.000) for 17106 atoms. Found 13 (109 requested) and removed 65 (54 requested) atoms. Cycle 40: After refmac, R = 0.1029 (Rfree = 0.000) for 17054 atoms. Found 7 (109 requested) and removed 63 (54 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17621 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 17640 seeds are put forward Round 1: 977 peptides, 175 chains. Longest chain 17 peptides. Score 0.351 Round 2: 1132 peptides, 172 chains. Longest chain 19 peptides. Score 0.447 Round 3: 1177 peptides, 170 chains. Longest chain 17 peptides. Score 0.476 Round 4: 1164 peptides, 174 chains. Longest chain 15 peptides. Score 0.460 Round 5: 1176 peptides, 174 chains. Longest chain 18 peptides. Score 0.466 Taking the results from Round 3 Chains 170, Residues 1007, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 31226 reflections ( 97.59 % complete ) and 3920 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1486 (Rfree = 0.000) for 17144 atoms. Found 50 (109 requested) and removed 76 (54 requested) atoms. Cycle 42: After refmac, R = 0.1490 (Rfree = 0.000) for 17118 atoms. Found 82 (109 requested) and removed 74 (54 requested) atoms. Cycle 43: After refmac, R = 0.1063 (Rfree = 0.000) for 17126 atoms. Found 12 (109 requested) and removed 62 (54 requested) atoms. Cycle 44: After refmac, R = 0.0995 (Rfree = 0.000) for 17076 atoms. Found 9 (109 requested) and removed 56 (54 requested) atoms. Cycle 45: After refmac, R = 0.0979 (Rfree = 0.000) for 17029 atoms. Found 9 (109 requested) and removed 57 (54 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 17557 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 17572 seeds are put forward Round 1: 962 peptides, 183 chains. Longest chain 18 peptides. Score 0.321 Round 2: 1098 peptides, 175 chains. Longest chain 20 peptides. Score 0.421 Round 3: 1121 peptides, 171 chains. Longest chain 18 peptides. Score 0.444 Round 4: 1151 peptides, 170 chains. Longest chain 23 peptides. Score 0.462 Round 5: 1140 peptides, 162 chains. Longest chain 27 peptides. Score 0.475 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 165, Residues 978, Estimated correctness of the model 0.0 % 8 chains (70 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 165 chains (978 residues) following loop building 8 chains (70 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31226 reflections ( 97.59 % complete ) and 4017 restraints for refining 17144 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1536 (Rfree = 0.000) for 17144 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 47: After refmac, R = 0.1574 (Rfree = 0.000) for 17090 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 48: After refmac, R = 0.1493 (Rfree = 0.000) for 17036 atoms. Found 0 (109 requested) and removed 54 (54 requested) atoms. Cycle 49: After refmac, R = 0.1409 (Rfree = 0.000) for 16982 atoms. Found 0 (108 requested) and removed 54 (54 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:16:06 GMT 2018 Job finished. TimeTaking 173.07 Used memory is bytes: 9735040