Mon 24 Dec 07:42:47 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqy-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqy-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:42:51 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-parrot-noncs/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 829 and 0 Target number of residues in the AU: 829 Target solvent content: 0.5420 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-3.2-parrot-noncs.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-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 7424 target number of atoms Had to go as low as 0.60 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 3.200 Wilson plot Bfac: 33.34 16523 reflections ( 98.25 % complete ) and 0 restraints for refining 8179 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3081 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2405 (Rfree = 0.000) for 8179 atoms. Found 57 (73 requested) and removed 79 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.72 2.76 Search for helices and strands: 0 residues in 0 chains, 8316 seeds are put forward NCS extension: 0 residues added, 8316 seeds are put forward Round 1: 442 peptides, 85 chains. Longest chain 16 peptides. Score 0.352 Round 2: 531 peptides, 88 chains. Longest chain 15 peptides. Score 0.472 Round 3: 573 peptides, 75 chains. Longest chain 25 peptides. Score 0.604 Round 4: 576 peptides, 75 chains. Longest chain 22 peptides. Score 0.607 Round 5: 602 peptides, 78 chains. Longest chain 21 peptides. Score 0.622 Taking the results from Round 5 Chains 81, Residues 524, Estimated correctness of the model 46.9 % 6 chains (66 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 13801 restraints for refining 6776 atoms. 11500 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2547 (Rfree = 0.000) for 6776 atoms. Found 55 (60 requested) and removed 52 (30 requested) atoms. Cycle 2: After refmac, R = 0.2393 (Rfree = 0.000) for 6710 atoms. Found 31 (60 requested) and removed 40 (30 requested) atoms. Cycle 3: After refmac, R = 0.2297 (Rfree = 0.000) for 6674 atoms. Found 16 (60 requested) and removed 40 (30 requested) atoms. Cycle 4: After refmac, R = 0.2214 (Rfree = 0.000) for 6637 atoms. Found 15 (59 requested) and removed 33 (29 requested) atoms. Cycle 5: After refmac, R = 0.2166 (Rfree = 0.000) for 6611 atoms. Found 12 (59 requested) and removed 37 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.70 2.74 Search for helices and strands: 0 residues in 0 chains, 6829 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 6843 seeds are put forward Round 1: 515 peptides, 70 chains. Longest chain 20 peptides. Score 0.559 Round 2: 573 peptides, 73 chains. Longest chain 22 peptides. Score 0.614 Round 3: 598 peptides, 75 chains. Longest chain 23 peptides. Score 0.633 Round 4: 588 peptides, 70 chains. Longest chain 22 peptides. Score 0.647 Round 5: 587 peptides, 74 chains. Longest chain 27 peptides. Score 0.625 Taking the results from Round 4 Chains 71, Residues 518, Estimated correctness of the model 53.1 % 6 chains (47 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 14138 restraints for refining 6777 atoms. 11935 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2460 (Rfree = 0.000) for 6777 atoms. Found 50 (60 requested) and removed 45 (30 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 6752 atoms. Found 15 (60 requested) and removed 38 (30 requested) atoms. Cycle 8: After refmac, R = 0.2250 (Rfree = 0.000) for 6706 atoms. Found 19 (60 requested) and removed 37 (30 requested) atoms. Cycle 9: After refmac, R = 0.2168 (Rfree = 0.000) for 6672 atoms. Found 20 (60 requested) and removed 35 (30 requested) atoms. Cycle 10: After refmac, R = 0.2124 (Rfree = 0.000) for 6649 atoms. Found 24 (59 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.71 2.75 Search for helices and strands: 0 residues in 0 chains, 6820 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 6831 seeds are put forward Round 1: 531 peptides, 78 chains. Longest chain 22 peptides. Score 0.533 Round 2: 604 peptides, 69 chains. Longest chain 31 peptides. Score 0.668 Round 3: 609 peptides, 73 chains. Longest chain 31 peptides. Score 0.655 Round 4: 597 peptides, 66 chains. Longest chain 26 peptides. Score 0.675 Round 5: 584 peptides, 62 chains. Longest chain 38 peptides. Score 0.681 Taking the results from Round 5 Chains 67, Residues 522, Estimated correctness of the model 61.0 % 7 chains (100 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 13822 restraints for refining 6776 atoms. 11377 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 6776 atoms. Found 45 (60 requested) and removed 60 (30 requested) atoms. Cycle 12: After refmac, R = 0.2320 (Rfree = 0.000) for 6753 atoms. Found 21 (60 requested) and removed 41 (30 requested) atoms. Cycle 13: After refmac, R = 0.2234 (Rfree = 0.000) for 6724 atoms. Found 12 (60 requested) and removed 40 (30 requested) atoms. Cycle 14: After refmac, R = 0.2174 (Rfree = 0.000) for 6694 atoms. Found 11 (60 requested) and removed 34 (30 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 6664 atoms. Found 12 (59 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.71 2.75 Search for helices and strands: 0 residues in 0 chains, 6845 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6868 seeds are put forward Round 1: 536 peptides, 72 chains. Longest chain 19 peptides. Score 0.575 Round 2: 572 peptides, 69 chains. Longest chain 24 peptides. Score 0.634 Round 3: 590 peptides, 69 chains. Longest chain 24 peptides. Score 0.654 Round 4: 575 peptides, 68 chains. Longest chain 24 peptides. Score 0.642 Round 5: 570 peptides, 67 chains. Longest chain 20 peptides. Score 0.642 Taking the results from Round 3 Chains 75, Residues 521, Estimated correctness of the model 54.8 % 7 chains (83 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 13824 restraints for refining 6777 atoms. 11466 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2467 (Rfree = 0.000) for 6777 atoms. Found 38 (60 requested) and removed 44 (30 requested) atoms. Cycle 17: After refmac, R = 0.2368 (Rfree = 0.000) for 6744 atoms. Found 22 (60 requested) and removed 42 (30 requested) atoms. Cycle 18: After refmac, R = 0.2302 (Rfree = 0.000) for 6715 atoms. Found 17 (60 requested) and removed 36 (30 requested) atoms. Cycle 19: After refmac, R = 0.2275 (Rfree = 0.000) for 6694 atoms. Found 10 (60 requested) and removed 31 (30 requested) atoms. Cycle 20: After refmac, R = 0.2253 (Rfree = 0.000) for 6671 atoms. Found 8 (59 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.68 2.72 Search for helices and strands: 0 residues in 0 chains, 6820 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 6834 seeds are put forward Round 1: 514 peptides, 73 chains. Longest chain 20 peptides. Score 0.540 Round 2: 559 peptides, 64 chains. Longest chain 31 peptides. Score 0.645 Round 3: 566 peptides, 63 chains. Longest chain 26 peptides. Score 0.658 Round 4: 542 peptides, 65 chains. Longest chain 28 peptides. Score 0.620 Round 5: 553 peptides, 68 chains. Longest chain 29 peptides. Score 0.617 Taking the results from Round 3 Chains 66, Residues 503, Estimated correctness of the model 55.7 % 5 chains (78 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 14069 restraints for refining 6777 atoms. 11801 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2452 (Rfree = 0.000) for 6777 atoms. Found 40 (60 requested) and removed 52 (30 requested) atoms. Cycle 22: After refmac, R = 0.2296 (Rfree = 0.000) for 6748 atoms. Found 22 (60 requested) and removed 35 (30 requested) atoms. Cycle 23: After refmac, R = 0.2280 (Rfree = 0.000) for 6724 atoms. Found 16 (60 requested) and removed 34 (30 requested) atoms. Cycle 24: After refmac, R = 0.2228 (Rfree = 0.000) for 6698 atoms. Found 14 (60 requested) and removed 31 (30 requested) atoms. Cycle 25: After refmac, R = 0.2226 (Rfree = 0.000) for 6675 atoms. Found 16 (59 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 6842 seeds are put forward NCS extension: 15 residues added (13 deleted due to clashes), 6857 seeds are put forward Round 1: 512 peptides, 69 chains. Longest chain 18 peptides. Score 0.561 Round 2: 555 peptides, 63 chains. Longest chain 29 peptides. Score 0.646 Round 3: 572 peptides, 65 chains. Longest chain 29 peptides. Score 0.654 Round 4: 567 peptides, 64 chains. Longest chain 29 peptides. Score 0.654 Round 5: 550 peptides, 67 chains. Longest chain 30 peptides. Score 0.619 Taking the results from Round 4 Chains 69, Residues 503, Estimated correctness of the model 54.8 % 6 chains (87 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 13626 restraints for refining 6777 atoms. 11299 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2467 (Rfree = 0.000) for 6777 atoms. Found 33 (60 requested) and removed 48 (30 requested) atoms. Cycle 27: After refmac, R = 0.2347 (Rfree = 0.000) for 6744 atoms. Found 19 (60 requested) and removed 31 (30 requested) atoms. Cycle 28: After refmac, R = 0.2268 (Rfree = 0.000) for 6725 atoms. Found 14 (60 requested) and removed 33 (30 requested) atoms. Cycle 29: After refmac, R = 0.2227 (Rfree = 0.000) for 6701 atoms. Found 11 (60 requested) and removed 31 (30 requested) atoms. Cycle 30: After refmac, R = 0.2175 (Rfree = 0.000) for 6673 atoms. Found 13 (59 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.65 2.69 Search for helices and strands: 0 residues in 0 chains, 6817 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 6834 seeds are put forward Round 1: 508 peptides, 74 chains. Longest chain 20 peptides. Score 0.526 Round 2: 543 peptides, 73 chains. Longest chain 23 peptides. Score 0.578 Round 3: 533 peptides, 70 chains. Longest chain 29 peptides. Score 0.582 Round 4: 523 peptides, 64 chains. Longest chain 29 peptides. Score 0.603 Round 5: 548 peptides, 70 chains. Longest chain 24 peptides. Score 0.601 Taking the results from Round 4 Chains 67, Residues 459, Estimated correctness of the model 41.9 % 6 chains (94 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 13964 restraints for refining 6777 atoms. 11811 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2505 (Rfree = 0.000) for 6777 atoms. Found 50 (60 requested) and removed 42 (30 requested) atoms. Cycle 32: After refmac, R = 0.2232 (Rfree = 0.000) for 6762 atoms. Found 26 (60 requested) and removed 35 (30 requested) atoms. Cycle 33: After refmac, R = 0.2188 (Rfree = 0.000) for 6739 atoms. Found 23 (60 requested) and removed 32 (30 requested) atoms. Cycle 34: After refmac, R = 0.2127 (Rfree = 0.000) for 6721 atoms. Found 18 (60 requested) and removed 33 (30 requested) atoms. Cycle 35: After refmac, R = 0.2099 (Rfree = 0.000) for 6702 atoms. Found 12 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.66 2.70 Search for helices and strands: 0 residues in 0 chains, 6853 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 6875 seeds are put forward Round 1: 461 peptides, 71 chains. Longest chain 16 peptides. Score 0.477 Round 2: 490 peptides, 67 chains. Longest chain 22 peptides. Score 0.544 Round 3: 518 peptides, 73 chains. Longest chain 21 peptides. Score 0.545 Round 4: 522 peptides, 66 chains. Longest chain 31 peptides. Score 0.591 Round 5: 545 peptides, 73 chains. Longest chain 31 peptides. Score 0.580 Taking the results from Round 4 Chains 66, Residues 456, Estimated correctness of the model 38.6 % 2 chains (47 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 14551 restraints for refining 6777 atoms. 12598 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2349 (Rfree = 0.000) for 6777 atoms. Found 40 (60 requested) and removed 40 (30 requested) atoms. Cycle 37: After refmac, R = 0.2184 (Rfree = 0.000) for 6761 atoms. Found 21 (60 requested) and removed 34 (30 requested) atoms. Cycle 38: After refmac, R = 0.2141 (Rfree = 0.000) for 6736 atoms. Found 17 (60 requested) and removed 34 (30 requested) atoms. Cycle 39: After refmac, R = 0.2154 (Rfree = 0.000) for 6715 atoms. Found 23 (60 requested) and removed 35 (30 requested) atoms. Cycle 40: After refmac, R = 0.2090 (Rfree = 0.000) for 6700 atoms. Found 16 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.68 2.72 Search for helices and strands: 0 residues in 0 chains, 6827 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6853 seeds are put forward Round 1: 422 peptides, 67 chains. Longest chain 18 peptides. Score 0.445 Round 2: 462 peptides, 62 chains. Longest chain 31 peptides. Score 0.536 Round 3: 493 peptides, 66 chains. Longest chain 25 peptides. Score 0.554 Round 4: 474 peptides, 57 chains. Longest chain 32 peptides. Score 0.582 Round 5: 472 peptides, 61 chains. Longest chain 25 peptides. Score 0.555 Taking the results from Round 4 Chains 60, Residues 417, Estimated correctness of the model 36.1 % 4 chains (65 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 14182 restraints for refining 6777 atoms. 12290 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2280 (Rfree = 0.000) for 6777 atoms. Found 30 (60 requested) and removed 44 (30 requested) atoms. Cycle 42: After refmac, R = 0.2175 (Rfree = 0.000) for 6754 atoms. Found 18 (60 requested) and removed 34 (30 requested) atoms. Cycle 43: After refmac, R = 0.2189 (Rfree = 0.000) for 6733 atoms. Found 15 (60 requested) and removed 33 (30 requested) atoms. Cycle 44: After refmac, R = 0.2158 (Rfree = 0.000) for 6707 atoms. Found 8 (60 requested) and removed 34 (30 requested) atoms. Cycle 45: After refmac, R = 0.2184 (Rfree = 0.000) for 6680 atoms. Found 12 (59 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.71 2.75 Search for helices and strands: 0 residues in 0 chains, 6835 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 6859 seeds are put forward Round 1: 403 peptides, 63 chains. Longest chain 18 peptides. Score 0.442 Round 2: 433 peptides, 57 chains. Longest chain 32 peptides. Score 0.527 Round 3: 448 peptides, 61 chains. Longest chain 32 peptides. Score 0.523 Round 4: 443 peptides, 61 chains. Longest chain 32 peptides. Score 0.516 Round 5: 470 peptides, 62 chains. Longest chain 26 peptides. Score 0.547 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 408, Estimated correctness of the model 26.0 % 2 chains (27 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vqy-3_warpNtrace.pdb as input Building loops using Loopy2018 65 chains (408 residues) following loop building 2 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16523 reflections ( 98.25 % complete ) and 14795 restraints for refining 6777 atoms. 13111 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2256 (Rfree = 0.000) for 6777 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.2189 (Rfree = 0.000) for 6736 atoms. Found 0 (60 requested) and removed 28 (30 requested) atoms. Cycle 48: After refmac, R = 0.2126 (Rfree = 0.000) for 6702 atoms. Found 0 (60 requested) and removed 7 (30 requested) atoms. Cycle 49: After refmac, R = 0.2116 (Rfree = 0.000) for 6694 atoms. TimeTaking 75.75