Sun 23 Dec 22:22:59 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 1vr3-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.2-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/1vr3-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.2-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 22:23:08 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/1vr3-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.2-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 251 and 0 Target number of residues in the AU: 251 Target solvent content: 0.6198 Checking the provided sequence file Detected sequence length: 191 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 191 Adjusted target solvent content: 0.71 Input MTZ file: 1vr3-3.2-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: 79.137 79.137 114.115 90.000 90.000 90.000 Input sequence file: 1vr3-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1528 target number of atoms Had to go as low as 1.05 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: 65.030 3.201 Wilson plot Bfac: 61.20 6385 reflections ( 99.78 % complete ) and 0 restraints for refining 1686 atoms. Observations/parameters ratio is 0.95 ------------------------------------------------------ Starting model: R = 0.3349 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2755 (Rfree = 0.000) for 1686 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.29 Search for helices and strands: 0 residues in 0 chains, 1741 seeds are put forward Round 1: 136 peptides, 19 chains. Longest chain 21 peptides. Score 0.471 Round 2: 149 peptides, 14 chains. Longest chain 23 peptides. Score 0.610 Round 3: 157 peptides, 13 chains. Longest chain 41 peptides. Score 0.651 Round 4: 149 peptides, 11 chains. Longest chain 61 peptides. Score 0.657 Round 5: 160 peptides, 10 chains. Longest chain 55 peptides. Score 0.704 Taking the results from Round 5 Chains 11, Residues 150, Estimated correctness of the model 66.0 % 2 chains (77 residues) have been docked in sequence Building loops using Loopy2018 11 chains (150 residues) following loop building 2 chains (77 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 2501 restraints for refining 1612 atoms. 1553 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2860 (Rfree = 0.000) for 1612 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 2: After refmac, R = 0.2515 (Rfree = 0.000) for 1562 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 3: After refmac, R = 0.2604 (Rfree = 0.000) for 1547 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 4: After refmac, R = 0.2252 (Rfree = 0.000) for 1532 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 5: After refmac, R = 0.2423 (Rfree = 0.000) for 1527 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.32 Search for helices and strands: 0 residues in 0 chains, 1556 seeds are put forward Round 1: 150 peptides, 13 chains. Longest chain 41 peptides. Score 0.629 Round 2: 163 peptides, 10 chains. Longest chain 45 peptides. Score 0.712 Round 3: 154 peptides, 9 chains. Longest chain 43 peptides. Score 0.702 Round 4: 161 peptides, 9 chains. Longest chain 41 peptides. Score 0.721 Round 5: 150 peptides, 11 chains. Longest chain 33 peptides. Score 0.660 Taking the results from Round 4 Chains 13, Residues 152, Estimated correctness of the model 69.5 % 5 chains (109 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 146 A and 152 A 11 chains (154 residues) following loop building 4 chains (114 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 1944 restraints for refining 1517 atoms. 807 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2694 (Rfree = 0.000) for 1517 atoms. Found 12 (12 requested) and removed 35 (6 requested) atoms. Cycle 7: After refmac, R = 0.2430 (Rfree = 0.000) for 1481 atoms. Found 11 (11 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2313 (Rfree = 0.000) for 1470 atoms. Found 11 (11 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.2191 (Rfree = 0.000) for 1469 atoms. Found 11 (11 requested) and removed 14 (6 requested) atoms. Cycle 10: After refmac, R = 0.2162 (Rfree = 0.000) for 1457 atoms. Found 11 (11 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 2.27 Search for helices and strands: 0 residues in 0 chains, 1514 seeds are put forward Round 1: 150 peptides, 11 chains. Longest chain 48 peptides. Score 0.660 Round 2: 148 peptides, 11 chains. Longest chain 42 peptides. Score 0.654 Round 3: 147 peptides, 11 chains. Longest chain 50 peptides. Score 0.651 Round 4: 151 peptides, 11 chains. Longest chain 44 peptides. Score 0.663 Round 5: 146 peptides, 13 chains. Longest chain 32 peptides. Score 0.616 Taking the results from Round 4 Chains 13, Residues 140, Estimated correctness of the model 56.9 % 3 chains (64 residues) have been docked in sequence ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 2238 restraints for refining 1413 atoms. 1363 conditional restraints added. Observations/parameters ratio is 1.13 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2591 (Rfree = 0.000) for 1413 atoms. Found 10 (10 requested) and removed 20 (6 requested) atoms. Cycle 12: After refmac, R = 0.2426 (Rfree = 0.000) for 1399 atoms. Found 10 (10 requested) and removed 15 (6 requested) atoms. Cycle 13: After refmac, R = 0.2368 (Rfree = 0.000) for 1392 atoms. Found 10 (10 requested) and removed 11 (6 requested) atoms. Cycle 14: After refmac, R = 0.2355 (Rfree = 0.000) for 1391 atoms. Found 10 (10 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.2395 (Rfree = 0.000) for 1388 atoms. Found 10 (10 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 2.26 Search for helices and strands: 0 residues in 0 chains, 1440 seeds are put forward Round 1: 146 peptides, 10 chains. Longest chain 29 peptides. Score 0.664 Round 2: 143 peptides, 11 chains. Longest chain 32 peptides. Score 0.638 Round 3: 158 peptides, 8 chains. Longest chain 57 peptides. Score 0.727 Round 4: 153 peptides, 12 chains. Longest chain 39 peptides. Score 0.654 Round 5: 153 peptides, 7 chains. Longest chain 63 peptides. Score 0.727 Taking the results from Round 5 Chains 8, Residues 146, Estimated correctness of the model 70.7 % 4 chains (109 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 90 A Built loop between residues 151 A and 156 A Built loop between residues 172 A and 177 A 5 chains (161 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 1930 restraints for refining 1589 atoms. 693 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2859 (Rfree = 0.000) for 1589 atoms. Found 11 (11 requested) and removed 28 (7 requested) atoms. Cycle 17: After refmac, R = 0.2541 (Rfree = 0.000) for 1553 atoms. Found 11 (11 requested) and removed 24 (7 requested) atoms. Cycle 18: After refmac, R = 0.2331 (Rfree = 0.000) for 1531 atoms. Found 10 (10 requested) and removed 14 (6 requested) atoms. Cycle 19: After refmac, R = 0.2252 (Rfree = 0.000) for 1526 atoms. Found 10 (10 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.2269 (Rfree = 0.000) for 1522 atoms. Found 9 (9 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 2.27 Search for helices and strands: 0 residues in 0 chains, 1569 seeds are put forward Round 1: 151 peptides, 11 chains. Longest chain 50 peptides. Score 0.663 Round 2: 146 peptides, 10 chains. Longest chain 60 peptides. Score 0.664 Round 3: 152 peptides, 11 chains. Longest chain 34 peptides. Score 0.666 Round 4: 163 peptides, 10 chains. Longest chain 61 peptides. Score 0.712 Round 5: 162 peptides, 9 chains. Longest chain 48 peptides. Score 0.723 Taking the results from Round 5 Chains 12, Residues 153, Estimated correctness of the model 69.9 % 4 chains (116 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 91 A Built loop between residues 121 A and 125 A 8 chains (161 residues) following loop building 2 chains (127 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 1997 restraints for refining 1563 atoms. 753 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2481 (Rfree = 0.000) for 1563 atoms. Found 10 (10 requested) and removed 25 (7 requested) atoms. Cycle 22: After refmac, R = 0.2109 (Rfree = 0.000) for 1536 atoms. Found 9 (9 requested) and removed 17 (6 requested) atoms. Cycle 23: After refmac, R = 0.2030 (Rfree = 0.000) for 1524 atoms. Found 9 (9 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.1926 (Rfree = 0.000) for 1519 atoms. Found 8 (8 requested) and removed 11 (6 requested) atoms. Cycle 25: After refmac, R = 0.2047 (Rfree = 0.000) for 1514 atoms. Found 8 (8 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 2.32 Search for helices and strands: 0 residues in 0 chains, 1546 seeds are put forward Round 1: 147 peptides, 10 chains. Longest chain 36 peptides. Score 0.667 Round 2: 160 peptides, 6 chains. Longest chain 63 peptides. Score 0.758 Round 3: 164 peptides, 9 chains. Longest chain 71 peptides. Score 0.728 Round 4: 164 peptides, 9 chains. Longest chain 64 peptides. Score 0.728 Round 5: 159 peptides, 9 chains. Longest chain 58 peptides. Score 0.715 Taking the results from Round 2 Chains 9, Residues 154, Estimated correctness of the model 76.5 % 5 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 34 A Built loop between residues 95 A and 102 A Built loop between residues 118 A and 125 A 5 chains (171 residues) following loop building 2 chains (149 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 1749 restraints for refining 1592 atoms. 397 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2950 (Rfree = 0.000) for 1592 atoms. Found 8 (8 requested) and removed 31 (7 requested) atoms. Cycle 27: After refmac, R = 0.2471 (Rfree = 0.000) for 1561 atoms. Found 8 (8 requested) and removed 16 (7 requested) atoms. Cycle 28: After refmac, R = 0.2309 (Rfree = 0.000) for 1550 atoms. Found 7 (7 requested) and removed 16 (6 requested) atoms. Cycle 29: After refmac, R = 0.2176 (Rfree = 0.000) for 1537 atoms. Found 7 (7 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2128 (Rfree = 0.000) for 1533 atoms. Found 7 (7 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.33 Search for helices and strands: 0 residues in 0 chains, 1581 seeds are put forward Round 1: 155 peptides, 11 chains. Longest chain 28 peptides. Score 0.675 Round 2: 154 peptides, 8 chains. Longest chain 44 peptides. Score 0.716 Round 3: 154 peptides, 9 chains. Longest chain 48 peptides. Score 0.702 Round 4: 150 peptides, 9 chains. Longest chain 57 peptides. Score 0.691 Round 5: 151 peptides, 9 chains. Longest chain 30 peptides. Score 0.693 Taking the results from Round 2 Chains 8, Residues 146, Estimated correctness of the model 68.5 % 5 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 29 A Built loop between residues 119 A and 125 A Built loop between residues 151 A and 154 A 5 chains (158 residues) following loop building 2 chains (132 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 2084 restraints for refining 1608 atoms. 836 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2448 (Rfree = 0.000) for 1608 atoms. Found 7 (7 requested) and removed 30 (7 requested) atoms. Cycle 32: After refmac, R = 0.2238 (Rfree = 0.000) for 1577 atoms. Found 7 (7 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.2085 (Rfree = 0.000) for 1562 atoms. Found 7 (7 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.1958 (Rfree = 0.000) for 1549 atoms. Found 6 (6 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.1899 (Rfree = 0.000) for 1544 atoms. Found 6 (6 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 2.27 Search for helices and strands: 0 residues in 0 chains, 1581 seeds are put forward Round 1: 155 peptides, 12 chains. Longest chain 27 peptides. Score 0.660 Round 2: 156 peptides, 7 chains. Longest chain 69 peptides. Score 0.735 Round 3: 154 peptides, 11 chains. Longest chain 32 peptides. Score 0.672 Round 4: 157 peptides, 6 chains. Longest chain 83 peptides. Score 0.751 Round 5: 150 peptides, 13 chains. Longest chain 28 peptides. Score 0.629 Taking the results from Round 4 Chains 8, Residues 151, Estimated correctness of the model 75.2 % 2 chains (107 residues) have been docked in sequence Building loops using Loopy2018 8 chains (151 residues) following loop building 2 chains (107 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 2136 restraints for refining 1533 atoms. 1032 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2501 (Rfree = 0.000) for 1533 atoms. Found 6 (6 requested) and removed 34 (6 requested) atoms. Cycle 37: After refmac, R = 0.2226 (Rfree = 0.000) for 1502 atoms. Found 6 (6 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.2313 (Rfree = 0.000) for 1485 atoms. Found 6 (6 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.2230 (Rfree = 0.000) for 1473 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 40: After refmac, R = 0.2307 (Rfree = 0.000) for 1466 atoms. Found 6 (6 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.31 Search for helices and strands: 0 residues in 0 chains, 1514 seeds are put forward Round 1: 151 peptides, 10 chains. Longest chain 27 peptides. Score 0.679 Round 2: 151 peptides, 8 chains. Longest chain 60 peptides. Score 0.708 Round 3: 153 peptides, 11 chains. Longest chain 50 peptides. Score 0.669 Round 4: 155 peptides, 13 chains. Longest chain 35 peptides. Score 0.645 Round 5: 143 peptides, 12 chains. Longest chain 49 peptides. Score 0.622 Taking the results from Round 2 Chains 9, Residues 143, Estimated correctness of the model 66.8 % 5 chains (121 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 65 A Built loop between residues 87 A and 92 A Built loop between residues 150 A and 160 A 4 chains (159 residues) following loop building 2 chains (141 residues) in sequence following loop building ------------------------------------------------------ 6385 reflections ( 99.78 % complete ) and 1846 restraints for refining 1568 atoms. 538 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2491 (Rfree = 0.000) for 1568 atoms. Found 7 (7 requested) and removed 19 (7 requested) atoms. Cycle 42: After refmac, R = 0.2363 (Rfree = 0.000) for 1545 atoms. Found 6 (6 requested) and removed 17 (6 requested) atoms. Cycle 43: After refmac, R = 0.2204 (Rfree = 0.000) for 1529 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.2180 (Rfree = 0.000) for 1521 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 45: After refmac, R = 0.2158 (Rfree = 0.000) for 1511 atoms. Found 6 (6 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.31 Search for helices and strands: 0 residues in 0 chains, 1569 seeds are put forward Round 1: 157 peptides, 8 chains. Longest chain 38 peptides. Score 0.724 Round 2: 154 peptides, 8 chains. Longest chain 76 peptides. Score 0.716 Round 3: 161 peptides, 7 chains. Longest chain 46 peptides. Score 0.747 Round 4: 148 peptides, 10 chains. Longest chain 43 peptides. Score 0.670 Round 5: 151 peptides, 11 chains. Longest chain 51 peptides. Score 0.663 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 154, Estimated correctness of the model 74.5 % 4 chains (105 residues) have been docked in sequence Sequence coverage is 67 % Consider running further cycles of model building using 1vr3-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 64 A and 68 A Built loop between residues 82 A and 90 A 7 chains (163 residues) following loop building 2 chains (115 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6385 reflections ( 99.78 % complete ) and 1933 restraints for refining 1510 atoms. 725 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2497 (Rfree = 0.000) for 1510 atoms. Found 0 (6 requested) and removed 4 (6 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 1501 atoms. Found 0 (6 requested) and removed 5 (6 requested) atoms. Cycle 48: After refmac, R = 0.2195 (Rfree = 0.000) for 1491 atoms. Found 0 (6 requested) and removed 0 (6 requested) atoms. Cycle 49: After refmac, R = 0.2179 (Rfree = 0.000) for 1488 atoms. TimeTaking 44.53