Tue 25 Dec 19:27:55 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 1vqy-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-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/1vqy-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-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 ============================================================ Tue 25 Dec 19:28:05 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/1vqy-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-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 795 and 0 Target number of residues in the AU: 795 Target solvent content: 0.5608 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 7424 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 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: 29.074 3.400 Wilson plot Bfac: 38.67 13838 reflections ( 98.37 % complete ) and 0 restraints for refining 8177 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.2771 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2530 (Rfree = 0.000) for 8177 atoms. Found 56 (61 requested) and removed 56 (30 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.85 2.89 Search for helices and strands: 0 residues in 0 chains, 8350 seeds are put forward NCS extension: 0 residues added, 8350 seeds are put forward Round 1: 437 peptides, 80 chains. Longest chain 17 peptides. Score 0.379 Round 2: 574 peptides, 81 chains. Longest chain 19 peptides. Score 0.572 Round 3: 584 peptides, 77 chains. Longest chain 37 peptides. Score 0.606 Round 4: 623 peptides, 68 chains. Longest chain 29 peptides. Score 0.692 Round 5: 626 peptides, 64 chains. Longest chain 37 peptides. Score 0.712 Taking the results from Round 5 Chains 72, Residues 562, Estimated correctness of the model 60.9 % 7 chains (99 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 61 A Built loop between residues 72 B and 83 B 68 chains (566 residues) following loop building 5 chains (117 residues) in sequence following loop building ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 13122 restraints for refining 6747 atoms. 10616 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2546 (Rfree = 0.000) for 6747 atoms. Found 43 (50 requested) and removed 57 (25 requested) atoms. Cycle 2: After refmac, R = 0.2307 (Rfree = 0.000) for 6634 atoms. Found 27 (49 requested) and removed 47 (25 requested) atoms. Cycle 3: After refmac, R = 0.2300 (Rfree = 0.000) for 6557 atoms. Found 23 (47 requested) and removed 38 (24 requested) atoms. Cycle 4: After refmac, R = 0.2216 (Rfree = 0.000) for 6523 atoms. Found 22 (46 requested) and removed 38 (24 requested) atoms. Cycle 5: After refmac, R = 0.2155 (Rfree = 0.000) for 6490 atoms. Found 16 (45 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.83 2.87 Search for helices and strands: 0 residues in 0 chains, 6736 seeds are put forward NCS extension: 11 residues added (13 deleted due to clashes), 6747 seeds are put forward Round 1: 546 peptides, 80 chains. Longest chain 19 peptides. Score 0.542 Round 2: 617 peptides, 80 chains. Longest chain 23 peptides. Score 0.629 Round 3: 617 peptides, 73 chains. Longest chain 22 peptides. Score 0.663 Round 4: 635 peptides, 75 chains. Longest chain 28 peptides. Score 0.672 Round 5: 616 peptides, 72 chains. Longest chain 26 peptides. Score 0.667 Taking the results from Round 4 Chains 76, Residues 560, Estimated correctness of the model 50.4 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14145 restraints for refining 6750 atoms. 11783 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2622 (Rfree = 0.000) for 6750 atoms. Found 33 (45 requested) and removed 54 (25 requested) atoms. Cycle 7: After refmac, R = 0.2316 (Rfree = 0.000) for 6691 atoms. Found 28 (45 requested) and removed 40 (25 requested) atoms. Cycle 8: After refmac, R = 0.2260 (Rfree = 0.000) for 6664 atoms. Found 27 (45 requested) and removed 37 (25 requested) atoms. Cycle 9: After refmac, R = 0.2034 (Rfree = 0.000) for 6638 atoms. Found 6 (45 requested) and removed 33 (25 requested) atoms. Cycle 10: After refmac, R = 0.1995 (Rfree = 0.000) for 6606 atoms. Found 10 (44 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6789 seeds are put forward NCS extension: 22 residues added (12 deleted due to clashes), 6811 seeds are put forward Round 1: 539 peptides, 76 chains. Longest chain 24 peptides. Score 0.556 Round 2: 603 peptides, 71 chains. Longest chain 30 peptides. Score 0.658 Round 3: 575 peptides, 69 chains. Longest chain 32 peptides. Score 0.637 Round 4: 595 peptides, 70 chains. Longest chain 30 peptides. Score 0.654 Round 5: 591 peptides, 69 chains. Longest chain 35 peptides. Score 0.655 Taking the results from Round 2 Chains 72, Residues 532, Estimated correctness of the model 46.5 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13838 reflections ( 98.37 % complete ) and 14262 restraints for refining 6750 atoms. 11942 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2232 (Rfree = 0.000) for 6750 atoms. Found 31 (45 requested) and removed 52 (25 requested) atoms. Cycle 12: After refmac, R = 0.2146 (Rfree = 0.000) for 6713 atoms. Found 19 (45 requested) and removed 44 (25 requested) atoms. Cycle 13: After refmac, R = 0.2110 (Rfree = 0.000) for 6678 atoms. Found 26 (45 requested) and removed 44 (25 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2078 (Rfree = 0.000) for 6647 atoms. Found 24 (45 requested) and removed 39 (25 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2038 (Rfree = 0.000) for 6625 atoms. Found 25 (45 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.84 2.88 Search for helices and strands: 0 residues in 0 chains, 6821 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 6834 seeds are put forward Round 1: 526 peptides, 77 chains. Longest chain 24 peptides. Score 0.532 Round 2: 579 peptides, 67 chains. Longest chain 26 peptides. Score 0.652 Round 3: 568 peptides, 70 chains. Longest chain 26 peptides. Score 0.624 Round 4: 574 peptides, 67 chains. Longest chain 25 peptides. Score 0.646 Round 5: 569 peptides, 63 chains. Longest chain 25 peptides. Score 0.661 Taking the results from Round 5 Chains 68, Residues 506, Estimated correctness of the model 47.3 % 5 chains (78 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13838 reflections ( 98.37 % complete ) and 13997 restraints for refining 6749 atoms. 11728 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2498 (Rfree = 0.000) for 6749 atoms. Found 38 (45 requested) and removed 45 (25 requested) atoms. Cycle 17: After refmac, R = 0.2261 (Rfree = 0.000) for 6699 atoms. Found 27 (45 requested) and removed 45 (25 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2230 (Rfree = 0.000) for 6667 atoms. Found 20 (45 requested) and removed 42 (25 requested) atoms. Cycle 19: After refmac, R = 0.2168 (Rfree = 0.000) for 6618 atoms. Found 20 (45 requested) and removed 38 (25 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 6586 atoms. Found 32 (44 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.85 2.89 Search for helices and strands: 0 residues in 0 chains, 6750 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6777 seeds are put forward Round 1: 494 peptides, 74 chains. Longest chain 20 peptides. Score 0.506 Round 2: 562 peptides, 72 chains. Longest chain 25 peptides. Score 0.607 Round 3: 576 peptides, 69 chains. Longest chain 23 peptides. Score 0.638 Round 4: 552 peptides, 71 chains. Longest chain 21 peptides. Score 0.600 Round 5: 548 peptides, 70 chains. Longest chain 22 peptides. Score 0.601 Taking the results from Round 3 Chains 74, Residues 507, Estimated correctness of the model 40.6 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13838 reflections ( 98.37 % complete ) and 14212 restraints for refining 6749 atoms. 12069 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2594 (Rfree = 0.000) for 6749 atoms. Found 45 (45 requested) and removed 66 (25 requested) atoms. Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 6700 atoms. Found 24 (45 requested) and removed 47 (25 requested) atoms. Cycle 23: After refmac, R = 0.2112 (Rfree = 0.000) for 6655 atoms. Found 30 (45 requested) and removed 30 (25 requested) atoms. Cycle 24: After refmac, R = 0.2044 (Rfree = 0.000) for 6648 atoms. Found 13 (45 requested) and removed 28 (25 requested) atoms. Cycle 25: After refmac, R = 0.2018 (Rfree = 0.000) for 6628 atoms. Found 21 (45 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 2.94 Search for helices and strands: 0 residues in 0 chains, 6812 seeds are put forward NCS extension: 15 residues added (10 deleted due to clashes), 6827 seeds are put forward Round 1: 507 peptides, 76 chains. Longest chain 20 peptides. Score 0.512 Round 2: 544 peptides, 72 chains. Longest chain 20 peptides. Score 0.585 Round 3: 529 peptides, 73 chains. Longest chain 18 peptides. Score 0.560 Round 4: 534 peptides, 75 chains. Longest chain 24 peptides. Score 0.555 Round 5: 539 peptides, 73 chains. Longest chain 23 peptides. Score 0.573 Taking the results from Round 2 Chains 74, Residues 472, Estimated correctness of the model 23.7 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13838 reflections ( 98.37 % complete ) and 15008 restraints for refining 6750 atoms. 13151 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2722 (Rfree = 0.000) for 6750 atoms. Found 45 (45 requested) and removed 82 (25 requested) atoms. Cycle 27: After refmac, R = 0.2428 (Rfree = 0.000) for 6700 atoms. Found 38 (45 requested) and removed 53 (25 requested) atoms. Cycle 28: After refmac, R = 0.2290 (Rfree = 0.000) for 6676 atoms. Found 34 (45 requested) and removed 37 (25 requested) atoms. Cycle 29: After refmac, R = 0.2264 (Rfree = 0.000) for 6668 atoms. Found 23 (45 requested) and removed 42 (25 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2061 (Rfree = 0.000) for 6647 atoms. Found 13 (45 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6780 seeds are put forward NCS extension: 25 residues added (8 deleted due to clashes), 6805 seeds are put forward Round 1: 466 peptides, 71 chains. Longest chain 24 peptides. Score 0.485 Round 2: 502 peptides, 70 chains. Longest chain 21 peptides. Score 0.542 Round 3: 486 peptides, 67 chains. Longest chain 20 peptides. Score 0.538 Round 4: 483 peptides, 69 chains. Longest chain 21 peptides. Score 0.522 Round 5: 495 peptides, 72 chains. Longest chain 24 peptides. Score 0.520 Taking the results from Round 2 Chains 71, Residues 432, Estimated correctness of the model 8.6 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 15074 restraints for refining 6750 atoms. 13342 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2391 (Rfree = 0.000) for 6750 atoms. Found 35 (45 requested) and removed 49 (25 requested) atoms. Cycle 32: After refmac, R = 0.2198 (Rfree = 0.000) for 6721 atoms. Found 30 (45 requested) and removed 36 (25 requested) atoms. Cycle 33: After refmac, R = 0.2121 (Rfree = 0.000) for 6712 atoms. Found 26 (45 requested) and removed 28 (25 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 34: After refmac, R = 0.2057 (Rfree = 0.000) for 6702 atoms. Found 24 (45 requested) and removed 32 (25 requested) atoms. Cycle 35: After refmac, R = 0.2043 (Rfree = 0.000) for 6691 atoms. Found 23 (45 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.89 2.93 Search for helices and strands: 0 residues in 0 chains, 6837 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 6851 seeds are put forward Round 1: 431 peptides, 68 chains. Longest chain 21 peptides. Score 0.452 Round 2: 472 peptides, 75 chains. Longest chain 17 peptides. Score 0.468 Round 3: 462 peptides, 64 chains. Longest chain 19 peptides. Score 0.523 Round 4: 461 peptides, 65 chains. Longest chain 19 peptides. Score 0.516 Round 5: 473 peptides, 65 chains. Longest chain 19 peptides. Score 0.533 Taking the results from Round 5 Chains 65, Residues 408, Estimated correctness of the model 5.3 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13838 reflections ( 98.37 % complete ) and 15391 restraints for refining 6750 atoms. 13768 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2229 (Rfree = 0.000) for 6750 atoms. Found 33 (45 requested) and removed 44 (25 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2144 (Rfree = 0.000) for 6729 atoms. Found 31 (45 requested) and removed 31 (25 requested) atoms. Cycle 38: After refmac, R = 0.2042 (Rfree = 0.000) for 6722 atoms. Found 13 (45 requested) and removed 36 (25 requested) atoms. Cycle 39: After refmac, R = 0.2079 (Rfree = 0.000) for 6690 atoms. Found 36 (45 requested) and removed 28 (25 requested) atoms. Cycle 40: After refmac, R = 0.2040 (Rfree = 0.000) for 6696 atoms. Found 20 (45 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.87 2.91 Search for helices and strands: 0 residues in 0 chains, 6840 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 6857 seeds are put forward Round 1: 399 peptides, 68 chains. Longest chain 13 peptides. Score 0.401 Round 2: 438 peptides, 66 chains. Longest chain 19 peptides. Score 0.476 Round 3: 474 peptides, 71 chains. Longest chain 15 peptides. Score 0.496 Round 4: 473 peptides, 70 chains. Longest chain 19 peptides. Score 0.501 Round 5: 464 peptides, 69 chains. Longest chain 19 peptides. Score 0.495 Taking the results from Round 4 Chains 71, Residues 403, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 13838 reflections ( 98.37 % complete ) and 14867 restraints for refining 6749 atoms. 13177 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2198 (Rfree = 0.000) for 6749 atoms. Found 37 (45 requested) and removed 36 (25 requested) atoms. Cycle 42: After refmac, R = 0.2078 (Rfree = 0.000) for 6729 atoms. Found 30 (45 requested) and removed 38 (25 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2036 (Rfree = 0.000) for 6706 atoms. Found 27 (45 requested) and removed 29 (25 requested) atoms. Cycle 44: After refmac, R = 0.2020 (Rfree = 0.000) for 6702 atoms. Found 25 (45 requested) and removed 33 (25 requested) atoms. Cycle 45: After refmac, R = 0.1952 (Rfree = 0.000) for 6693 atoms. Found 24 (45 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.88 2.92 Search for helices and strands: 0 residues in 0 chains, 6845 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 6874 seeds are put forward Round 1: 370 peptides, 65 chains. Longest chain 15 peptides. Score 0.374 Round 2: 401 peptides, 58 chains. Longest chain 18 peptides. Score 0.474 Round 3: 422 peptides, 64 chains. Longest chain 18 peptides. Score 0.465 Round 4: 419 peptides, 61 chains. Longest chain 21 peptides. Score 0.480 Round 5: 427 peptides, 63 chains. Longest chain 20 peptides. Score 0.479 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 358, 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 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13838 reflections ( 98.37 % complete ) and 15441 restraints for refining 6750 atoms. 14070 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2101 (Rfree = 0.000) for 6750 atoms. Found 0 (45 requested) and removed 25 (25 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2083 (Rfree = 0.000) for 6709 atoms. Found 0 (45 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2069 (Rfree = 0.000) for 6678 atoms. Found 0 (45 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2030 (Rfree = 0.000) for 6646 atoms. Found 0 (45 requested) and removed 25 (25 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:06:13 GMT 2018 Job finished. TimeTaking 98.3