Sun 23 Dec 22:22:46 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prr-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-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 22:22:55 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-3.4-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 1882 and 0 Target number of residues in the AU: 1882 Target solvent content: 0.6429 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 73.79 37049 reflections ( 97.55 % complete ) and 0 restraints for refining 21028 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2944 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2395 (Rfree = 0.000) for 21028 atoms. Found 129 (158 requested) and removed 143 (79 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 21575 seeds are put forward NCS extension: 0 residues added, 21575 seeds are put forward Round 1: 1262 peptides, 227 chains. Longest chain 14 peptides. Score 0.387 Round 2: 1441 peptides, 203 chains. Longest chain 31 peptides. Score 0.534 Round 3: 1517 peptides, 202 chains. Longest chain 20 peptides. Score 0.570 Round 4: 1538 peptides, 185 chains. Longest chain 30 peptides. Score 0.612 Round 5: 1528 peptides, 192 chains. Longest chain 25 peptides. Score 0.595 Taking the results from Round 4 Chains 196, Residues 1353, Estimated correctness of the model 32.5 % 12 chains (137 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5739 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1961 (Rfree = 0.000) for 17196 atoms. Found 64 (129 requested) and removed 90 (64 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.1853 (Rfree = 0.000) for 17170 atoms. Found 40 (129 requested) and removed 76 (64 requested) atoms. Cycle 3: After refmac, R = 0.1666 (Rfree = 0.000) for 17134 atoms. Found 28 (129 requested) and removed 95 (64 requested) atoms. Cycle 4: After refmac, R = 0.1639 (Rfree = 0.000) for 17067 atoms. Found 25 (128 requested) and removed 83 (64 requested) atoms. Cycle 5: After refmac, R = 0.1527 (Rfree = 0.000) for 17009 atoms. Found 20 (128 requested) and removed 78 (64 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.19 Search for helices and strands: 0 residues in 0 chains, 17714 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 17740 seeds are put forward Round 1: 1381 peptides, 206 chains. Longest chain 25 peptides. Score 0.498 Round 2: 1526 peptides, 198 chains. Longest chain 26 peptides. Score 0.582 Round 3: 1517 peptides, 180 chains. Longest chain 33 peptides. Score 0.613 Round 4: 1514 peptides, 180 chains. Longest chain 33 peptides. Score 0.611 Round 5: 1517 peptides, 181 chains. Longest chain 33 peptides. Score 0.611 Taking the results from Round 3 Chains 192, Residues 1337, Estimated correctness of the model 32.9 % 11 chains (133 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5658 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1749 (Rfree = 0.000) for 17196 atoms. Found 63 (129 requested) and removed 98 (64 requested) atoms. Cycle 7: After refmac, R = 0.1637 (Rfree = 0.000) for 17161 atoms. Found 36 (129 requested) and removed 79 (64 requested) atoms. Cycle 8: After refmac, R = 0.1525 (Rfree = 0.000) for 17118 atoms. Found 23 (129 requested) and removed 77 (64 requested) atoms. Cycle 9: After refmac, R = 0.1500 (Rfree = 0.000) for 17064 atoms. Found 17 (128 requested) and removed 69 (64 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1458 (Rfree = 0.000) for 17012 atoms. Found 16 (128 requested) and removed 72 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.17 Search for helices and strands: 0 residues in 0 chains, 17704 seeds are put forward NCS extension: 19 residues added (20 deleted due to clashes), 17723 seeds are put forward Round 1: 1425 peptides, 212 chains. Longest chain 30 peptides. Score 0.507 Round 2: 1539 peptides, 196 chains. Longest chain 24 peptides. Score 0.592 Round 3: 1527 peptides, 177 chains. Longest chain 31 peptides. Score 0.622 Round 4: 1487 peptides, 189 chains. Longest chain 23 peptides. Score 0.583 Round 5: 1529 peptides, 183 chains. Longest chain 25 peptides. Score 0.612 Taking the results from Round 3 Chains 183, Residues 1350, Estimated correctness of the model 35.7 % 12 chains (139 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 37049 reflections ( 97.55 % complete ) and 5751 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1760 (Rfree = 0.000) for 17196 atoms. Found 44 (129 requested) and removed 86 (64 requested) atoms. Cycle 12: After refmac, R = 0.1624 (Rfree = 0.000) for 17154 atoms. Found 20 (129 requested) and removed 85 (64 requested) atoms. Cycle 13: After refmac, R = 0.1569 (Rfree = 0.000) for 17089 atoms. Found 29 (129 requested) and removed 73 (64 requested) atoms. Cycle 14: After refmac, R = 0.1530 (Rfree = 0.000) for 17045 atoms. Found 28 (128 requested) and removed 76 (64 requested) atoms. Cycle 15: After refmac, R = 0.1478 (Rfree = 0.000) for 16997 atoms. Found 24 (128 requested) and removed 74 (64 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 17710 seeds are put forward NCS extension: 10 residues added (9 deleted due to clashes), 17720 seeds are put forward Round 1: 1318 peptides, 204 chains. Longest chain 23 peptides. Score 0.471 Round 2: 1445 peptides, 183 chains. Longest chain 31 peptides. Score 0.576 Round 3: 1406 peptides, 180 chains. Longest chain 24 peptides. Score 0.565 Round 4: 1467 peptides, 180 chains. Longest chain 27 peptides. Score 0.592 Round 5: 1476 peptides, 182 chains. Longest chain 25 peptides. Score 0.592 Taking the results from Round 5 Chains 188, Residues 1294, Estimated correctness of the model 26.0 % 9 chains (94 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5357 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1767 (Rfree = 0.000) for 17196 atoms. Found 80 (129 requested) and removed 91 (64 requested) atoms. Cycle 17: After refmac, R = 0.1587 (Rfree = 0.000) for 17185 atoms. Found 18 (129 requested) and removed 72 (64 requested) atoms. Cycle 18: After refmac, R = 0.1523 (Rfree = 0.000) for 17131 atoms. Found 16 (129 requested) and removed 71 (64 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1471 (Rfree = 0.000) for 17076 atoms. Found 19 (128 requested) and removed 70 (64 requested) atoms. Cycle 20: After refmac, R = 0.1450 (Rfree = 0.000) for 17025 atoms. Found 18 (128 requested) and removed 67 (64 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 17729 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 17743 seeds are put forward Round 1: 1301 peptides, 212 chains. Longest chain 15 peptides. Score 0.444 Round 2: 1407 peptides, 193 chains. Longest chain 23 peptides. Score 0.539 Round 3: 1448 peptides, 186 chains. Longest chain 27 peptides. Score 0.572 Round 4: 1441 peptides, 185 chains. Longest chain 24 peptides. Score 0.571 Round 5: 1455 peptides, 176 chains. Longest chain 27 peptides. Score 0.594 Taking the results from Round 5 Chains 188, Residues 1279, Estimated correctness of the model 26.7 % 17 chains (179 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5620 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1784 (Rfree = 0.000) for 17196 atoms. Found 61 (129 requested) and removed 85 (64 requested) atoms. Cycle 22: After refmac, R = 0.1640 (Rfree = 0.000) for 17172 atoms. Found 29 (129 requested) and removed 73 (64 requested) atoms. Cycle 23: After refmac, R = 0.1579 (Rfree = 0.000) for 17128 atoms. Found 16 (129 requested) and removed 67 (64 requested) atoms. Cycle 24: After refmac, R = 0.1537 (Rfree = 0.000) for 17077 atoms. Found 18 (128 requested) and removed 67 (64 requested) atoms. Cycle 25: After refmac, R = 0.1505 (Rfree = 0.000) for 17028 atoms. Found 17 (128 requested) and removed 67 (64 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 17701 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 17713 seeds are put forward Round 1: 1257 peptides, 196 chains. Longest chain 18 peptides. Score 0.458 Round 2: 1382 peptides, 187 chains. Longest chain 23 peptides. Score 0.540 Round 3: 1396 peptides, 185 chains. Longest chain 22 peptides. Score 0.550 Round 4: 1417 peptides, 197 chains. Longest chain 22 peptides. Score 0.535 Round 5: 1431 peptides, 188 chains. Longest chain 24 peptides. Score 0.560 Taking the results from Round 5 Chains 197, Residues 1243, Estimated correctness of the model 15.1 % 13 chains (144 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 5335 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1727 (Rfree = 0.000) for 17196 atoms. Found 45 (129 requested) and removed 93 (64 requested) atoms. Cycle 27: After refmac, R = 0.1613 (Rfree = 0.000) for 17148 atoms. Found 29 (129 requested) and removed 75 (64 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1572 (Rfree = 0.000) for 17102 atoms. Found 24 (129 requested) and removed 66 (64 requested) atoms. Cycle 29: After refmac, R = 0.1546 (Rfree = 0.000) for 17060 atoms. Found 28 (128 requested) and removed 68 (64 requested) atoms. Cycle 30: After refmac, R = 0.1511 (Rfree = 0.000) for 17020 atoms. Found 31 (128 requested) and removed 74 (64 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.17 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: 1188 peptides, 210 chains. Longest chain 14 peptides. Score 0.387 Round 2: 1352 peptides, 206 chains. Longest chain 17 peptides. Score 0.484 Round 3: 1351 peptides, 194 chains. Longest chain 23 peptides. Score 0.510 Round 4: 1333 peptides, 194 chains. Longest chain 21 peptides. Score 0.501 Round 5: 1363 peptides, 197 chains. Longest chain 22 peptides. Score 0.509 Taking the results from Round 3 Chains 204, Residues 1157, Estimated correctness of the model 0.0 % 12 chains (107 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4828 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1656 (Rfree = 0.000) for 17196 atoms. Found 54 (129 requested) and removed 82 (64 requested) atoms. Cycle 32: After refmac, R = 0.1577 (Rfree = 0.000) for 17168 atoms. Found 33 (129 requested) and removed 70 (64 requested) atoms. Cycle 33: After refmac, R = 0.1522 (Rfree = 0.000) for 17131 atoms. Found 19 (129 requested) and removed 71 (64 requested) atoms. Cycle 34: After refmac, R = 0.1468 (Rfree = 0.000) for 17079 atoms. Found 17 (128 requested) and removed 70 (64 requested) atoms. Cycle 35: After refmac, R = 0.1434 (Rfree = 0.000) for 17026 atoms. Found 29 (128 requested) and removed 72 (64 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 17682 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 17691 seeds are put forward Round 1: 1131 peptides, 208 chains. Longest chain 18 peptides. Score 0.359 Round 2: 1267 peptides, 203 chains. Longest chain 18 peptides. Score 0.447 Round 3: 1255 peptides, 186 chains. Longest chain 28 peptides. Score 0.479 Round 4: 1250 peptides, 191 chains. Longest chain 23 peptides. Score 0.465 Round 5: 1280 peptides, 183 chains. Longest chain 23 peptides. Score 0.499 Taking the results from Round 5 Chains 191, Residues 1097, Estimated correctness of the model 0.0 % 15 chains (108 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4576 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1646 (Rfree = 0.000) for 17196 atoms. Found 59 (129 requested) and removed 91 (64 requested) atoms. Cycle 37: After refmac, R = 0.1528 (Rfree = 0.000) for 17164 atoms. Found 34 (129 requested) and removed 71 (64 requested) atoms. Cycle 38: After refmac, R = 0.1509 (Rfree = 0.000) for 17127 atoms. Found 32 (129 requested) and removed 76 (64 requested) atoms. Cycle 39: After refmac, R = 0.1481 (Rfree = 0.000) for 17083 atoms. Found 30 (128 requested) and removed 76 (64 requested) atoms. Cycle 40: After refmac, R = 0.1447 (Rfree = 0.000) for 17037 atoms. Found 31 (128 requested) and removed 65 (64 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 17684 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 17700 seeds are put forward Round 1: 1100 peptides, 211 chains. Longest chain 21 peptides. Score 0.333 Round 2: 1237 peptides, 202 chains. Longest chain 21 peptides. Score 0.433 Round 3: 1211 peptides, 193 chains. Longest chain 18 peptides. Score 0.440 Round 4: 1237 peptides, 194 chains. Longest chain 21 peptides. Score 0.452 Round 5: 1256 peptides, 195 chains. Longest chain 24 peptides. Score 0.459 Taking the results from Round 5 Chains 199, Residues 1061, Estimated correctness of the model 0.0 % 12 chains (108 residues) have been docked in sequence ------------------------------------------------------ 37049 reflections ( 97.55 % complete ) and 4445 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1661 (Rfree = 0.000) for 17196 atoms. Found 71 (129 requested) and removed 79 (64 requested) atoms. Cycle 42: After refmac, R = 0.1575 (Rfree = 0.000) for 17188 atoms. Found 55 (129 requested) and removed 73 (64 requested) atoms. Cycle 43: After refmac, R = 0.1503 (Rfree = 0.000) for 17170 atoms. Found 48 (129 requested) and removed 69 (64 requested) atoms. Cycle 44: After refmac, R = 0.1465 (Rfree = 0.000) for 17149 atoms. Found 47 (129 requested) and removed 70 (64 requested) atoms. Cycle 45: After refmac, R = 0.1422 (Rfree = 0.000) for 17126 atoms. Found 41 (129 requested) and removed 65 (64 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.18 Search for helices and strands: 0 residues in 0 chains, 17766 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 17778 seeds are put forward Round 1: 988 peptides, 196 chains. Longest chain 17 peptides. Score 0.303 Round 2: 1152 peptides, 186 chains. Longest chain 27 peptides. Score 0.425 Round 3: 1126 peptides, 179 chains. Longest chain 19 peptides. Score 0.427 Round 4: 1148 peptides, 188 chains. Longest chain 24 peptides. Score 0.417 Round 5: 1169 peptides, 180 chains. Longest chain 27 peptides. Score 0.448 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 183, Residues 989, Estimated correctness of the model 0.0 % 13 chains (95 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 21 H and 34 H 182 chains (995 residues) following loop building 12 chains (107 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 37049 reflections ( 97.55 % complete ) and 4156 restraints for refining 17196 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1689 (Rfree = 0.000) for 17196 atoms. Found 0 (129 requested) and removed 44 (64 requested) atoms. Cycle 47: After refmac, R = 0.1615 (Rfree = 0.000) for 17152 atoms. Found 0 (129 requested) and removed 49 (64 requested) atoms. Cycle 48: After refmac, R = 0.1547 (Rfree = 0.000) for 17103 atoms. Found 0 (129 requested) and removed 57 (64 requested) atoms. Cycle 49: After refmac, R = 0.1508 (Rfree = 0.000) for 17046 atoms. TimeTaking 169.48