null Tue 25 Dec 19:27:57 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-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 ============================================================ Tue 25 Dec 19:28:07 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-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 1940 and 0 Target number of residues in the AU: 1940 Target solvent content: 0.6319 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.75 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 3.200 Wilson plot Bfac: 67.47 44474 reflections ( 97.55 % complete ) and 0 restraints for refining 20874 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2903 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2120 (Rfree = 0.000) for 20874 atoms. Found 91 (187 requested) and removed 152 (93 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 21420 seeds are put forward NCS extension: 0 residues added, 21420 seeds are put forward Round 1: 1356 peptides, 231 chains. Longest chain 21 peptides. Score 0.429 Round 2: 1562 peptides, 209 chains. Longest chain 26 peptides. Score 0.576 Round 3: 1611 peptides, 208 chains. Longest chain 27 peptides. Score 0.599 Round 4: 1623 peptides, 185 chains. Longest chain 31 peptides. Score 0.645 Round 5: 1679 peptides, 186 chains. Longest chain 35 peptides. Score 0.664 Taking the results from Round 5 Chains 201, Residues 1493, Estimated correctness of the model 57.2 % 22 chains (317 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 7053 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2114 (Rfree = 0.000) for 17266 atoms. Found 89 (154 requested) and removed 133 (77 requested) atoms. Cycle 2: After refmac, R = 0.1931 (Rfree = 0.000) for 17222 atoms. Found 54 (154 requested) and removed 90 (77 requested) atoms. Cycle 3: After refmac, R = 0.1855 (Rfree = 0.000) for 17186 atoms. Found 26 (154 requested) and removed 85 (77 requested) atoms. Cycle 4: After refmac, R = 0.1814 (Rfree = 0.000) for 17127 atoms. Found 24 (153 requested) and removed 84 (76 requested) atoms. Cycle 5: After refmac, R = 0.1781 (Rfree = 0.000) for 17067 atoms. Found 26 (153 requested) and removed 80 (76 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 17749 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 17767 seeds are put forward Round 1: 1497 peptides, 201 chains. Longest chain 21 peptides. Score 0.564 Round 2: 1632 peptides, 181 chains. Longest chain 33 peptides. Score 0.656 Round 3: 1643 peptides, 166 chains. Longest chain 32 peptides. Score 0.685 Round 4: 1644 peptides, 170 chains. Longest chain 30 peptides. Score 0.678 Round 5: 1652 peptides, 177 chains. Longest chain 31 peptides. Score 0.670 Taking the results from Round 3 Chains 179, Residues 1477, Estimated correctness of the model 61.9 % 21 chains (295 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 6861 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2052 (Rfree = 0.000) for 17266 atoms. Found 69 (154 requested) and removed 108 (77 requested) atoms. Cycle 7: After refmac, R = 0.1909 (Rfree = 0.000) for 17227 atoms. Found 35 (154 requested) and removed 81 (77 requested) atoms. Cycle 8: After refmac, R = 0.1838 (Rfree = 0.000) for 17181 atoms. Found 18 (154 requested) and removed 79 (77 requested) atoms. Cycle 9: After refmac, R = 0.1996 (Rfree = 0.000) for 17120 atoms. Found 87 (153 requested) and removed 81 (76 requested) atoms. Cycle 10: After refmac, R = 0.1772 (Rfree = 0.000) for 17126 atoms. Found 37 (153 requested) and removed 85 (76 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 17740 seeds are put forward NCS extension: 18 residues added (12 deleted due to clashes), 17758 seeds are put forward Round 1: 1516 peptides, 207 chains. Longest chain 23 peptides. Score 0.560 Round 2: 1613 peptides, 181 chains. Longest chain 35 peptides. Score 0.649 Round 3: 1608 peptides, 189 chains. Longest chain 38 peptides. Score 0.633 Round 4: 1598 peptides, 184 chains. Longest chain 35 peptides. Score 0.638 Round 5: 1578 peptides, 171 chains. Longest chain 33 peptides. Score 0.653 Taking the results from Round 5 Chains 187, Residues 1407, Estimated correctness of the model 54.6 % 17 chains (269 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 6529 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2023 (Rfree = 0.000) for 17266 atoms. Found 91 (154 requested) and removed 126 (77 requested) atoms. Cycle 12: After refmac, R = 0.1846 (Rfree = 0.000) for 17231 atoms. Found 23 (154 requested) and removed 82 (77 requested) atoms. Cycle 13: After refmac, R = 0.1802 (Rfree = 0.000) for 17172 atoms. Found 17 (154 requested) and removed 80 (77 requested) atoms. Cycle 14: After refmac, R = 0.1763 (Rfree = 0.000) for 17109 atoms. Found 23 (153 requested) and removed 80 (76 requested) atoms. Cycle 15: After refmac, R = 0.1729 (Rfree = 0.000) for 17052 atoms. Found 16 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 17675 seeds are put forward NCS extension: 10 residues added (16 deleted due to clashes), 17685 seeds are put forward Round 1: 1406 peptides, 204 chains. Longest chain 29 peptides. Score 0.515 Round 2: 1516 peptides, 186 chains. Longest chain 36 peptides. Score 0.601 Round 3: 1495 peptides, 183 chains. Longest chain 34 peptides. Score 0.598 Round 4: 1548 peptides, 187 chains. Longest chain 29 peptides. Score 0.612 Round 5: 1517 peptides, 178 chains. Longest chain 33 peptides. Score 0.616 Taking the results from Round 5 Chains 196, Residues 1339, Estimated correctness of the model 45.3 % 15 chains (187 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5937 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2025 (Rfree = 0.000) for 17266 atoms. Found 99 (154 requested) and removed 106 (77 requested) atoms. Cycle 17: After refmac, R = 0.1873 (Rfree = 0.000) for 17259 atoms. Found 43 (154 requested) and removed 82 (77 requested) atoms. Cycle 18: After refmac, R = 0.1825 (Rfree = 0.000) for 17220 atoms. Found 25 (154 requested) and removed 81 (77 requested) atoms. Cycle 19: After refmac, R = 0.1780 (Rfree = 0.000) for 17164 atoms. Found 21 (154 requested) and removed 78 (77 requested) atoms. Cycle 20: After refmac, R = 0.1749 (Rfree = 0.000) for 17107 atoms. Found 23 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17710 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 17735 seeds are put forward Round 1: 1364 peptides, 202 chains. Longest chain 22 peptides. Score 0.499 Round 2: 1452 peptides, 184 chains. Longest chain 25 peptides. Score 0.577 Round 3: 1473 peptides, 184 chains. Longest chain 40 peptides. Score 0.587 Round 4: 1432 peptides, 181 chains. Longest chain 23 peptides. Score 0.575 Round 5: 1468 peptides, 192 chains. Longest chain 25 peptides. Score 0.569 Taking the results from Round 3 Chains 197, Residues 1289, Estimated correctness of the model 37.5 % 18 chains (194 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5748 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1905 (Rfree = 0.000) for 17266 atoms. Found 68 (154 requested) and removed 92 (77 requested) atoms. Cycle 22: After refmac, R = 0.1796 (Rfree = 0.000) for 17242 atoms. Found 33 (154 requested) and removed 83 (77 requested) atoms. Cycle 23: After refmac, R = 0.1730 (Rfree = 0.000) for 17192 atoms. Found 20 (154 requested) and removed 80 (77 requested) atoms. Cycle 24: After refmac, R = 0.1694 (Rfree = 0.000) for 17132 atoms. Found 13 (153 requested) and removed 76 (76 requested) atoms. Cycle 25: After refmac, R = 0.1639 (Rfree = 0.000) for 17069 atoms. Found 13 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17717 seeds are put forward NCS extension: 28 residues added (9 deleted due to clashes), 17745 seeds are put forward Round 1: 1269 peptides, 206 chains. Longest chain 24 peptides. Score 0.441 Round 2: 1390 peptides, 191 chains. Longest chain 23 peptides. Score 0.535 Round 3: 1419 peptides, 181 chains. Longest chain 24 peptides. Score 0.569 Round 4: 1434 peptides, 190 chains. Longest chain 29 peptides. Score 0.557 Round 5: 1405 peptides, 179 chains. Longest chain 22 peptides. Score 0.567 Taking the results from Round 3 Chains 191, Residues 1238, Estimated correctness of the model 32.4 % 20 chains (180 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5467 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1855 (Rfree = 0.000) for 17266 atoms. Found 55 (154 requested) and removed 100 (77 requested) atoms. Cycle 27: After refmac, R = 0.1757 (Rfree = 0.000) for 17221 atoms. Found 32 (154 requested) and removed 79 (77 requested) atoms. Cycle 28: After refmac, R = 0.1711 (Rfree = 0.000) for 17174 atoms. Found 23 (154 requested) and removed 79 (77 requested) atoms. Cycle 29: After refmac, R = 0.1687 (Rfree = 0.000) for 17118 atoms. Found 15 (153 requested) and removed 77 (76 requested) atoms. Cycle 30: After refmac, R = 0.1637 (Rfree = 0.000) for 17056 atoms. Found 10 (153 requested) and removed 76 (76 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17678 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 17694 seeds are put forward Round 1: 1241 peptides, 203 chains. Longest chain 16 peptides. Score 0.433 Round 2: 1387 peptides, 190 chains. Longest chain 20 peptides. Score 0.536 Round 3: 1402 peptides, 191 chains. Longest chain 24 peptides. Score 0.541 Round 4: 1416 peptides, 188 chains. Longest chain 35 peptides. Score 0.553 Round 5: 1370 peptides, 189 chains. Longest chain 19 peptides. Score 0.530 Taking the results from Round 4 Chains 193, Residues 1228, Estimated correctness of the model 27.8 % 11 chains (123 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5191 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1853 (Rfree = 0.000) for 17266 atoms. Found 59 (154 requested) and removed 99 (77 requested) atoms. Cycle 32: After refmac, R = 0.1742 (Rfree = 0.000) for 17226 atoms. Found 28 (154 requested) and removed 78 (77 requested) atoms. Cycle 33: After refmac, R = 0.1695 (Rfree = 0.000) for 17176 atoms. Found 22 (154 requested) and removed 81 (77 requested) atoms. Cycle 34: After refmac, R = 0.1639 (Rfree = 0.000) for 17117 atoms. Found 18 (153 requested) and removed 77 (76 requested) atoms. Cycle 35: After refmac, R = 0.1587 (Rfree = 0.000) for 17058 atoms. Found 11 (153 requested) and removed 80 (76 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17650 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 17664 seeds are put forward Round 1: 1241 peptides, 208 chains. Longest chain 38 peptides. Score 0.421 Round 2: 1300 peptides, 181 chains. Longest chain 26 peptides. Score 0.513 Round 3: 1348 peptides, 191 chains. Longest chain 26 peptides. Score 0.515 Round 4: 1345 peptides, 184 chains. Longest chain 24 peptides. Score 0.528 Round 5: 1314 peptides, 186 chains. Longest chain 21 peptides. Score 0.509 Taking the results from Round 4 Chains 189, Residues 1161, Estimated correctness of the model 20.2 % 11 chains (89 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4800 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1793 (Rfree = 0.000) for 17266 atoms. Found 59 (154 requested) and removed 88 (77 requested) atoms. Cycle 37: After refmac, R = 0.1688 (Rfree = 0.000) for 17237 atoms. Found 23 (154 requested) and removed 78 (77 requested) atoms. Cycle 38: After refmac, R = 0.1656 (Rfree = 0.000) for 17182 atoms. Found 20 (154 requested) and removed 80 (77 requested) atoms. Cycle 39: After refmac, R = 0.1639 (Rfree = 0.000) for 17122 atoms. Found 14 (153 requested) and removed 78 (76 requested) atoms. Cycle 40: After refmac, R = 0.1613 (Rfree = 0.000) for 17058 atoms. Found 16 (153 requested) and removed 76 (76 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17656 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 17668 seeds are put forward Round 1: 1123 peptides, 195 chains. Longest chain 16 peptides. Score 0.386 Round 2: 1260 peptides, 195 chains. Longest chain 18 peptides. Score 0.461 Round 3: 1285 peptides, 193 chains. Longest chain 18 peptides. Score 0.479 Round 4: 1307 peptides, 202 chains. Longest chain 20 peptides. Score 0.470 Round 5: 1266 peptides, 189 chains. Longest chain 25 peptides. Score 0.478 Taking the results from Round 3 Chains 194, Residues 1092, Estimated correctness of the model 4.4 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4262 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1753 (Rfree = 0.000) for 17266 atoms. Found 49 (154 requested) and removed 85 (77 requested) atoms. Cycle 42: After refmac, R = 0.1691 (Rfree = 0.000) for 17230 atoms. Found 30 (154 requested) and removed 80 (77 requested) atoms. Cycle 43: After refmac, R = 0.1675 (Rfree = 0.000) for 17180 atoms. Found 26 (154 requested) and removed 79 (77 requested) atoms. Cycle 44: After refmac, R = 0.1663 (Rfree = 0.000) for 17127 atoms. Found 25 (153 requested) and removed 76 (76 requested) atoms. Cycle 45: After refmac, R = 0.1631 (Rfree = 0.000) for 17076 atoms. Found 29 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17660 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 17676 seeds are put forward Round 1: 1061 peptides, 192 chains. Longest chain 15 peptides. Score 0.358 Round 2: 1228 peptides, 188 chains. Longest chain 23 peptides. Score 0.461 Round 3: 1231 peptides, 179 chains. Longest chain 19 peptides. Score 0.483 Round 4: 1220 peptides, 177 chains. Longest chain 24 peptides. Score 0.482 Round 5: 1265 peptides, 173 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 176, Residues 1092, Estimated correctness of the model 15.5 % 11 chains (88 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 176 chains (1092 residues) following loop building 11 chains (88 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 44474 reflections ( 97.55 % complete ) and 4517 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1794 (Rfree = 0.000) for 17266 atoms. Found 0 (154 requested) and removed 22 (77 requested) atoms. Cycle 47: After refmac, R = 0.1731 (Rfree = 0.000) for 17244 atoms. Found 0 (154 requested) and removed 19 (77 requested) atoms. Cycle 48: After refmac, R = 0.1717 (Rfree = 0.000) for 17225 atoms. Found 0 (154 requested) and removed 22 (77 requested) atoms. Cycle 49: After refmac, R = 0.1690 (Rfree = 0.000) for 17203 atoms. Found 0 (154 requested) and removed 25 (77 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:53:56 GMT 2018 Job finished. TimeTaking 205.98 Used memory is bytes: 22439240