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 2pc1-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-4.0-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/2pc1-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-4.0-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 22:23:11 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/2pc1-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-4.0-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 122 and 0 Target number of residues in the AU: 122 Target solvent content: 0.6469 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.42 Input MTZ file: 2pc1-4.0-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: 35.480 37.650 41.500 94.220 109.420 113.080 Input sequence file: 2pc1-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.65 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. Conditional restraints will be used 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 Loops will be built when appropriate and at the last cycle Resolution range: 25.956 4.001 Wilson plot Bfac: 75.95 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1442 reflections ( 94.25 % complete ) and 0 restraints for refining 1770 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3092 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1788 (Rfree = 0.000) for 1770 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.98 Search for helices and strands: 0 residues in 0 chains, 1787 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 8 peptides. Score 0.240 Round 2: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.306 Round 3: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.297 Round 4: 77 peptides, 13 chains. Longest chain 14 peptides. Score 0.407 Round 5: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.457 Taking the results from Round 5 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 3591 restraints for refining 1451 atoms. 3324 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2416 (Rfree = 0.000) for 1451 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.1955 (Rfree = 0.000) for 1443 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.1884 (Rfree = 0.000) for 1431 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.1738 (Rfree = 0.000) for 1427 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.1714 (Rfree = 0.000) for 1421 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 4.00 Search for helices and strands: 0 residues in 0 chains, 1448 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.330 Round 2: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.410 Round 3: 77 peptides, 12 chains. Longest chain 14 peptides. Score 0.444 Round 4: 78 peptides, 13 chains. Longest chain 14 peptides. Score 0.416 Round 5: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 3 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 3332 restraints for refining 1379 atoms. 3084 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1843 (Rfree = 0.000) for 1379 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.1781 (Rfree = 0.000) for 1369 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.1789 (Rfree = 0.000) for 1360 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.1837 (Rfree = 0.000) for 1355 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.1903 (Rfree = 0.000) for 1344 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 4.10 Search for helices and strands: 0 residues in 0 chains, 1383 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.274 Round 2: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.306 Round 3: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.326 Round 4: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.284 Round 5: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.301 Taking the results from Round 3 Chains 10, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 3148 restraints for refining 1280 atoms. 2978 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2006 (Rfree = 0.000) for 1280 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.2117 (Rfree = 0.000) for 1269 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.1814 (Rfree = 0.000) for 1268 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.1827 (Rfree = 0.000) for 1261 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.1801 (Rfree = 0.000) for 1258 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 4.21 Search for helices and strands: 0 residues in 0 chains, 1306 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 6 peptides. Score 0.189 Round 2: 54 peptides, 11 chains. Longest chain 10 peptides. Score 0.274 Round 3: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.274 Round 4: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.284 Round 5: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.279 Taking the results from Round 4 Chains 11, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 2678 restraints for refining 1166 atoms. 2513 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1842 (Rfree = 0.000) for 1166 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 17: After refmac, R = 0.1506 (Rfree = 0.000) for 1160 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.1541 (Rfree = 0.000) for 1156 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.1699 (Rfree = 0.000) for 1152 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 20: After refmac, R = 0.1478 (Rfree = 0.000) for 1146 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 4.14 Search for helices and strands: 0 residues in 0 chains, 1181 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.220 Round 2: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.306 Round 3: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.323 Round 4: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.379 Round 5: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.336 Taking the results from Round 4 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 2469 restraints for refining 1156 atoms. 2227 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1685 (Rfree = 0.000) for 1156 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.1527 (Rfree = 0.000) for 1151 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.1639 (Rfree = 0.000) for 1149 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 24: After refmac, R = 0.1553 (Rfree = 0.000) for 1142 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.1460 (Rfree = 0.000) for 1137 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 4.16 Search for helices and strands: 0 residues in 0 chains, 1167 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.280 Round 2: 64 peptides, 13 chains. Longest chain 10 peptides. Score 0.289 Round 3: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.339 Round 4: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.304 Round 5: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 2707 restraints for refining 1175 atoms. 2506 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1628 (Rfree = 0.000) for 1175 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 27: After refmac, R = 0.1532 (Rfree = 0.000) for 1175 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.1526 (Rfree = 0.000) for 1171 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.1539 (Rfree = 0.000) for 1166 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.1520 (Rfree = 0.000) for 1161 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 4.14 Search for helices and strands: 0 residues in 0 chains, 1204 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.279 Round 2: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.345 Round 3: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.320 Round 4: 51 peptides, 9 chains. Longest chain 11 peptides. Score 0.329 Round 5: 54 peptides, 10 chains. Longest chain 7 peptides. Score 0.316 Taking the results from Round 2 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 2652 restraints for refining 1161 atoms. 2474 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1639 (Rfree = 0.000) for 1161 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 32: After refmac, R = 0.1616 (Rfree = 0.000) for 1159 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.1614 (Rfree = 0.000) for 1157 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.1622 (Rfree = 0.000) for 1153 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1600 (Rfree = 0.000) for 1151 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 4.10 Search for helices and strands: 0 residues in 0 chains, 1184 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 7 peptides. Score 0.229 Round 2: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.390 Round 3: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.355 Round 4: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.346 Round 5: 72 peptides, 12 chains. Longest chain 9 peptides. Score 0.402 Taking the results from Round 5 Chains 12, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 2547 restraints for refining 1170 atoms. 2319 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1773 (Rfree = 0.000) for 1170 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 37: After refmac, R = 0.1699 (Rfree = 0.000) for 1168 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.1690 (Rfree = 0.000) for 1166 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.1692 (Rfree = 0.000) for 1162 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1625 (Rfree = 0.000) for 1161 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 4.18 Search for helices and strands: 0 residues in 0 chains, 1186 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.230 Round 2: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.304 Round 3: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.250 Round 4: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.291 Round 5: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.272 Taking the results from Round 2 Chains 11, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 94.25 % complete ) and 2649 restraints for refining 1161 atoms. 2476 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1668 (Rfree = 0.000) for 1161 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.1632 (Rfree = 0.000) for 1158 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1604 (Rfree = 0.000) for 1156 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1611 (Rfree = 0.000) for 1156 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.1624 (Rfree = 0.000) for 1154 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 4.12 Search for helices and strands: 0 residues in 0 chains, 1182 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.231 Round 2: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.329 Round 3: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.222 Round 4: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.256 Round 5: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.269 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pc1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1442 reflections ( 94.25 % complete ) and 2676 restraints for refining 1163 atoms. 2517 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1707 (Rfree = 0.000) for 1163 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1577 (Rfree = 0.000) for 1160 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1587 (Rfree = 0.000) for 1155 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1531 (Rfree = 0.000) for 1152 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:16 GMT 2018 Job finished. TimeTaking 25.25 Used memory is bytes: 20049112