Sun 23 Dec 22:22:43 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 2gm6-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.2-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/2gm6-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.2-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 ============================================================ Sun 23 Dec 22:22:53 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/2gm6-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.2-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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6325 Checking the provided sequence file Detected sequence length: 208 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 208 Adjusted target solvent content: 0.68 Input MTZ file: 2gm6-3.2-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: 92 Cell parameters: 57.001 57.001 216.648 90.000 90.000 90.000 Input sequence file: 2gm6-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1664 target number of atoms Had to go as low as 1.00 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: 55.125 3.200 Wilson plot Bfac: 67.21 6453 reflections ( 99.80 % complete ) and 0 restraints for refining 1866 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Starting model: R = 0.3565 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 1866 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 2.54 Search for helices and strands: 0 residues in 0 chains, 1913 seeds are put forward Round 1: 135 peptides, 17 chains. Longest chain 28 peptides. Score 0.508 Round 2: 154 peptides, 15 chains. Longest chain 23 peptides. Score 0.614 Round 3: 151 peptides, 11 chains. Longest chain 51 peptides. Score 0.668 Round 4: 152 peptides, 11 chains. Longest chain 56 peptides. Score 0.671 Round 5: 145 peptides, 12 chains. Longest chain 34 peptides. Score 0.633 Taking the results from Round 4 Chains 12, Residues 141, Estimated correctness of the model 58.8 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2868 restraints for refining 1518 atoms. 2228 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2960 (Rfree = 0.000) for 1518 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2815 (Rfree = 0.000) for 1483 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2705 (Rfree = 0.000) for 1464 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2639 (Rfree = 0.000) for 1461 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.2577 (Rfree = 0.000) for 1451 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.49 Search for helices and strands: 0 residues in 0 chains, 1488 seeds are put forward Round 1: 146 peptides, 13 chains. Longest chain 39 peptides. Score 0.620 Round 2: 145 peptides, 13 chains. Longest chain 36 peptides. Score 0.617 Round 3: 153 peptides, 12 chains. Longest chain 42 peptides. Score 0.659 Round 4: 157 peptides, 12 chains. Longest chain 48 peptides. Score 0.671 Round 5: 164 peptides, 8 chains. Longest chain 54 peptides. Score 0.746 Taking the results from Round 5 Chains 8, Residues 156, Estimated correctness of the model 74.3 % 1 chains (53 residues) have been docked in sequence ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2557 restraints for refining 1519 atoms. 1736 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2795 (Rfree = 0.000) for 1519 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 7: After refmac, R = 0.2799 (Rfree = 0.000) for 1495 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2631 (Rfree = 0.000) for 1484 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2521 (Rfree = 0.000) for 1476 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.2505 (Rfree = 0.000) for 1472 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.49 Search for helices and strands: 0 residues in 0 chains, 1514 seeds are put forward Round 1: 137 peptides, 16 chains. Longest chain 23 peptides. Score 0.535 Round 2: 153 peptides, 12 chains. Longest chain 47 peptides. Score 0.659 Round 3: 158 peptides, 14 chains. Longest chain 32 peptides. Score 0.643 Round 4: 150 peptides, 15 chains. Longest chain 33 peptides. Score 0.601 Round 5: 151 peptides, 14 chains. Longest chain 33 peptides. Score 0.620 Taking the results from Round 2 Chains 13, Residues 141, Estimated correctness of the model 56.0 % 2 chains (59 residues) have been docked in sequence ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2657 restraints for refining 1519 atoms. 1873 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2850 (Rfree = 0.000) for 1519 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2485 (Rfree = 0.000) for 1511 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2393 (Rfree = 0.000) for 1504 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2322 (Rfree = 0.000) for 1506 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2232 (Rfree = 0.000) for 1503 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 2.52 Search for helices and strands: 0 residues in 0 chains, 1548 seeds are put forward Round 1: 157 peptides, 14 chains. Longest chain 46 peptides. Score 0.640 Round 2: 159 peptides, 12 chains. Longest chain 24 peptides. Score 0.677 Round 3: 153 peptides, 14 chains. Longest chain 30 peptides. Score 0.627 Round 4: 165 peptides, 12 chains. Longest chain 30 peptides. Score 0.694 Round 5: 156 peptides, 13 chains. Longest chain 31 peptides. Score 0.653 Taking the results from Round 4 Chains 13, Residues 153, Estimated correctness of the model 63.9 % 3 chains (64 residues) have been docked in sequence ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2495 restraints for refining 1519 atoms. 1625 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3031 (Rfree = 0.000) for 1519 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.2780 (Rfree = 0.000) for 1495 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2718 (Rfree = 0.000) for 1484 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.2703 (Rfree = 0.000) for 1478 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2582 (Rfree = 0.000) for 1479 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 2.50 Search for helices and strands: 0 residues in 0 chains, 1530 seeds are put forward Round 1: 148 peptides, 13 chains. Longest chain 33 peptides. Score 0.627 Round 2: 159 peptides, 9 chains. Longest chain 49 peptides. Score 0.720 Round 3: 164 peptides, 11 chains. Longest chain 33 peptides. Score 0.706 Round 4: 167 peptides, 10 chains. Longest chain 66 peptides. Score 0.727 Round 5: 160 peptides, 14 chains. Longest chain 34 peptides. Score 0.650 Taking the results from Round 4 Chains 10, Residues 157, Estimated correctness of the model 70.7 % 3 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 90 A 9 chains (158 residues) following loop building 2 chains (107 residues) in sequence following loop building ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2172 restraints for refining 1519 atoms. 1136 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3010 (Rfree = 0.000) for 1519 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2612 (Rfree = 0.000) for 1499 atoms. Found 11 (11 requested) and removed 19 (6 requested) atoms. Cycle 23: After refmac, R = 0.2420 (Rfree = 0.000) for 1482 atoms. Found 11 (11 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2227 (Rfree = 0.000) for 1480 atoms. Found 8 (11 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2189 (Rfree = 0.000) for 1478 atoms. Found 8 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.50 Search for helices and strands: 0 residues in 0 chains, 1524 seeds are put forward Round 1: 160 peptides, 14 chains. Longest chain 29 peptides. Score 0.650 Round 2: 158 peptides, 11 chains. Longest chain 44 peptides. Score 0.689 Round 3: 168 peptides, 10 chains. Longest chain 37 peptides. Score 0.730 Round 4: 165 peptides, 11 chains. Longest chain 48 peptides. Score 0.708 Round 5: 165 peptides, 10 chains. Longest chain 42 peptides. Score 0.722 Taking the results from Round 3 Chains 12, Residues 158, Estimated correctness of the model 71.3 % 4 chains (83 residues) have been docked in sequence Building loops using Loopy2018 12 chains (158 residues) following loop building 4 chains (83 residues) in sequence following loop building ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2296 restraints for refining 1517 atoms. 1319 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2751 (Rfree = 0.000) for 1517 atoms. Found 10 (10 requested) and removed 12 (6 requested) atoms. Cycle 27: After refmac, R = 0.2627 (Rfree = 0.000) for 1506 atoms. Found 10 (10 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2670 (Rfree = 0.000) for 1495 atoms. Found 10 (10 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2315 (Rfree = 0.000) for 1486 atoms. Found 10 (10 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2191 (Rfree = 0.000) for 1484 atoms. Found 8 (9 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.47 Search for helices and strands: 0 residues in 0 chains, 1530 seeds are put forward Round 1: 163 peptides, 11 chains. Longest chain 35 peptides. Score 0.703 Round 2: 163 peptides, 11 chains. Longest chain 43 peptides. Score 0.703 Round 3: 161 peptides, 11 chains. Longest chain 45 peptides. Score 0.697 Round 4: 161 peptides, 10 chains. Longest chain 33 peptides. Score 0.711 Round 5: 164 peptides, 10 chains. Longest chain 43 peptides. Score 0.719 Taking the results from Round 5 Chains 12, Residues 154, Estimated correctness of the model 69.1 % 4 chains (111 residues) have been docked in sequence Building loops using Loopy2018 12 chains (154 residues) following loop building 4 chains (111 residues) in sequence following loop building ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2257 restraints for refining 1553 atoms. 1189 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2725 (Rfree = 0.000) for 1553 atoms. Found 9 (9 requested) and removed 18 (6 requested) atoms. Cycle 32: After refmac, R = 0.2624 (Rfree = 0.000) for 1524 atoms. Found 9 (9 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2585 (Rfree = 0.000) for 1507 atoms. Found 9 (9 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2473 (Rfree = 0.000) for 1506 atoms. Found 8 (8 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2149 (Rfree = 0.000) for 1503 atoms. Found 8 (8 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 2.46 Search for helices and strands: 0 residues in 0 chains, 1519 seeds are put forward Round 1: 154 peptides, 13 chains. Longest chain 31 peptides. Score 0.646 Round 2: 172 peptides, 12 chains. Longest chain 31 peptides. Score 0.714 Round 3: 169 peptides, 10 chains. Longest chain 30 peptides. Score 0.732 Round 4: 165 peptides, 12 chains. Longest chain 32 peptides. Score 0.694 Round 5: 161 peptides, 10 chains. Longest chain 51 peptides. Score 0.711 Taking the results from Round 3 Chains 15, Residues 159, Estimated correctness of the model 71.7 % 6 chains (117 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 115 A and 122 A Built loop between residues 143 A and 148 A 11 chains (164 residues) following loop building 4 chains (127 residues) in sequence following loop building ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2084 restraints for refining 1543 atoms. 923 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2776 (Rfree = 0.000) for 1543 atoms. Found 8 (8 requested) and removed 19 (6 requested) atoms. Cycle 37: After refmac, R = 0.2628 (Rfree = 0.000) for 1522 atoms. Found 8 (8 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.2513 (Rfree = 0.000) for 1513 atoms. Found 7 (7 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2492 (Rfree = 0.000) for 1508 atoms. Found 7 (7 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.2381 (Rfree = 0.000) for 1503 atoms. Found 7 (7 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.47 Search for helices and strands: 0 residues in 0 chains, 1549 seeds are put forward Round 1: 159 peptides, 12 chains. Longest chain 38 peptides. Score 0.677 Round 2: 170 peptides, 10 chains. Longest chain 57 peptides. Score 0.735 Round 3: 153 peptides, 9 chains. Longest chain 33 peptides. Score 0.704 Round 4: 165 peptides, 13 chains. Longest chain 42 peptides. Score 0.680 Round 5: 163 peptides, 10 chains. Longest chain 30 peptides. Score 0.717 Taking the results from Round 2 Chains 11, Residues 160, Estimated correctness of the model 72.3 % 3 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 86 A 9 chains (165 residues) following loop building 2 chains (120 residues) in sequence following loop building ------------------------------------------------------ 6453 reflections ( 99.80 % complete ) and 2051 restraints for refining 1530 atoms. 900 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2626 (Rfree = 0.000) for 1530 atoms. Found 6 (6 requested) and removed 22 (6 requested) atoms. Cycle 42: After refmac, R = 0.2534 (Rfree = 0.000) for 1505 atoms. Found 6 (6 requested) and removed 15 (6 requested) atoms. Cycle 43: After refmac, R = 0.2496 (Rfree = 0.000) for 1491 atoms. Found 6 (6 requested) and removed 18 (6 requested) atoms. Cycle 44: After refmac, R = 0.2384 (Rfree = 0.000) for 1477 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.2412 (Rfree = 0.000) for 1473 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 2.47 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward Round 1: 156 peptides, 12 chains. Longest chain 54 peptides. Score 0.668 Round 2: 159 peptides, 11 chains. Longest chain 44 peptides. Score 0.692 Round 3: 162 peptides, 11 chains. Longest chain 39 peptides. Score 0.700 Round 4: 173 peptides, 9 chains. Longest chain 55 peptides. Score 0.755 Round 5: 168 peptides, 10 chains. Longest chain 40 peptides. Score 0.730 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 164, Estimated correctness of the model 76.0 % 7 chains (148 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 129 A and 132 A Built loop between residues 141 A and 146 A Built loop between residues 168 A and 172 A Built loop between residues 188 A and 192 A 5 chains (175 residues) following loop building 3 chains (160 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 6453 reflections ( 99.80 % complete ) and 1356 restraints for refining 1321 atoms. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3321 (Rfree = 0.000) for 1321 atoms. Found 5 (5 requested) and removed 0 (5 requested) atoms. Cycle 47: After refmac, R = 0.3038 (Rfree = 0.000) for 1321 atoms. Found 5 (5 requested) and removed 1 (5 requested) atoms. Cycle 48: After refmac, R = 0.2947 (Rfree = 0.000) for 1321 atoms. Found 5 (5 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2841 (Rfree = 0.000) for 1321 atoms. TimeTaking 43.77