null Tue 25 Dec 19:27:57 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 1vlu-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-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/1vlu-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-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 ============================================================ Tue 25 Dec 19:28:07 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/1vlu-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-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 1033 and 0 Target number of residues in the AU: 1033 Target solvent content: 0.6196 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.85 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: 44.569 3.200 Wilson plot Bfac: 61.18 24672 reflections ( 99.89 % complete ) and 0 restraints for refining 8308 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.3416 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2930 (Rfree = 0.000) for 8308 atoms. Found 74 (74 requested) and removed 74 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 2.53 Search for helices and strands: 0 residues in 0 chains, 8491 seeds are put forward NCS extension: 0 residues added, 8491 seeds are put forward Round 1: 512 peptides, 72 chains. Longest chain 23 peptides. Score 0.451 Round 2: 568 peptides, 61 chains. Longest chain 26 peptides. Score 0.556 Round 3: 581 peptides, 58 chains. Longest chain 42 peptides. Score 0.580 Round 4: 585 peptides, 52 chains. Longest chain 39 peptides. Score 0.609 Round 5: 596 peptides, 58 chains. Longest chain 30 peptides. Score 0.593 Taking the results from Round 4 Chains 56, Residues 533, Estimated correctness of the model 43.5 % 10 chains (183 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13133 restraints for refining 6829 atoms. 10377 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2825 (Rfree = 0.000) for 6829 atoms. Found 61 (61 requested) and removed 74 (30 requested) atoms. Cycle 2: After refmac, R = 0.2701 (Rfree = 0.000) for 6697 atoms. Found 61 (61 requested) and removed 47 (30 requested) atoms. Cycle 3: After refmac, R = 0.2660 (Rfree = 0.000) for 6652 atoms. Found 44 (60 requested) and removed 50 (30 requested) atoms. Cycle 4: After refmac, R = 0.2565 (Rfree = 0.000) for 6607 atoms. Found 36 (59 requested) and removed 39 (29 requested) atoms. Cycle 5: After refmac, R = 0.2496 (Rfree = 0.000) for 6587 atoms. Found 25 (59 requested) and removed 39 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.55 Search for helices and strands: 0 residues in 0 chains, 6834 seeds are put forward NCS extension: 29 residues added (16 deleted due to clashes), 6863 seeds are put forward Round 1: 557 peptides, 62 chains. Longest chain 23 peptides. Score 0.542 Round 2: 589 peptides, 53 chains. Longest chain 51 peptides. Score 0.608 Round 3: 599 peptides, 60 chains. Longest chain 31 peptides. Score 0.588 Round 4: 603 peptides, 58 chains. Longest chain 33 peptides. Score 0.599 Round 5: 601 peptides, 50 chains. Longest chain 51 peptides. Score 0.630 Taking the results from Round 5 Chains 57, Residues 551, Estimated correctness of the model 48.9 % 13 chains (275 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12020 restraints for refining 6835 atoms. 8806 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2824 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 105 (30 requested) atoms. Cycle 7: After refmac, R = 0.2526 (Rfree = 0.000) for 6714 atoms. Found 43 (60 requested) and removed 51 (30 requested) atoms. Cycle 8: After refmac, R = 0.2424 (Rfree = 0.000) for 6672 atoms. Found 29 (60 requested) and removed 41 (30 requested) atoms. Cycle 9: After refmac, R = 0.2359 (Rfree = 0.000) for 6643 atoms. Found 23 (59 requested) and removed 36 (29 requested) atoms. Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 6609 atoms. Found 16 (59 requested) and removed 37 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6820 seeds are put forward NCS extension: 82 residues added (8 deleted due to clashes), 6902 seeds are put forward Round 1: 585 peptides, 62 chains. Longest chain 27 peptides. Score 0.567 Round 2: 613 peptides, 61 chains. Longest chain 29 peptides. Score 0.596 Round 3: 613 peptides, 58 chains. Longest chain 42 peptides. Score 0.608 Round 4: 611 peptides, 59 chains. Longest chain 46 peptides. Score 0.602 Round 5: 613 peptides, 62 chains. Longest chain 33 peptides. Score 0.592 Taking the results from Round 3 Chains 64, Residues 555, Estimated correctness of the model 43.2 % 10 chains (167 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13155 restraints for refining 6835 atoms. 10391 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2671 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 82 (30 requested) atoms. Cycle 12: After refmac, R = 0.2526 (Rfree = 0.000) for 6782 atoms. Found 37 (61 requested) and removed 49 (30 requested) atoms. Cycle 13: After refmac, R = 0.2465 (Rfree = 0.000) for 6747 atoms. Found 27 (60 requested) and removed 41 (30 requested) atoms. Cycle 14: After refmac, R = 0.2383 (Rfree = 0.000) for 6717 atoms. Found 16 (60 requested) and removed 34 (30 requested) atoms. Cycle 15: After refmac, R = 0.2364 (Rfree = 0.000) for 6686 atoms. Found 20 (60 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6883 seeds are put forward NCS extension: 23 residues added (21 deleted due to clashes), 6906 seeds are put forward Round 1: 579 peptides, 65 chains. Longest chain 23 peptides. Score 0.549 Round 2: 625 peptides, 51 chains. Longest chain 37 peptides. Score 0.644 Round 3: 598 peptides, 55 chains. Longest chain 44 peptides. Score 0.607 Round 4: 603 peptides, 52 chains. Longest chain 57 peptides. Score 0.623 Round 5: 581 peptides, 60 chains. Longest chain 38 peptides. Score 0.572 Taking the results from Round 2 Chains 58, Residues 574, Estimated correctness of the model 52.4 % 14 chains (252 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 11929 restraints for refining 6836 atoms. 8749 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2616 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 67 (30 requested) atoms. Cycle 17: After refmac, R = 0.2423 (Rfree = 0.000) for 6795 atoms. Found 29 (61 requested) and removed 35 (30 requested) atoms. Cycle 18: After refmac, R = 0.2354 (Rfree = 0.000) for 6766 atoms. Found 37 (60 requested) and removed 33 (30 requested) atoms. Cycle 19: After refmac, R = 0.2281 (Rfree = 0.000) for 6758 atoms. Found 24 (60 requested) and removed 32 (30 requested) atoms. Cycle 20: After refmac, R = 0.2191 (Rfree = 0.000) for 6739 atoms. Found 14 (60 requested) and removed 35 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.53 Search for helices and strands: 0 residues in 0 chains, 6951 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6976 seeds are put forward Round 1: 572 peptides, 68 chains. Longest chain 37 peptides. Score 0.529 Round 2: 599 peptides, 56 chains. Longest chain 38 peptides. Score 0.604 Round 3: 595 peptides, 52 chains. Longest chain 50 peptides. Score 0.617 Round 4: 599 peptides, 60 chains. Longest chain 29 peptides. Score 0.588 Round 5: 580 peptides, 53 chains. Longest chain 41 peptides. Score 0.600 Taking the results from Round 3 Chains 59, Residues 543, Estimated correctness of the model 45.6 % 10 chains (191 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12596 restraints for refining 6836 atoms. 9794 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2561 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 67 (30 requested) atoms. Cycle 22: After refmac, R = 0.2348 (Rfree = 0.000) for 6800 atoms. Found 38 (61 requested) and removed 42 (30 requested) atoms. Cycle 23: After refmac, R = 0.2278 (Rfree = 0.000) for 6780 atoms. Found 18 (60 requested) and removed 34 (30 requested) atoms. Cycle 24: After refmac, R = 0.2255 (Rfree = 0.000) for 6751 atoms. Found 22 (60 requested) and removed 31 (30 requested) atoms. Cycle 25: After refmac, R = 0.2220 (Rfree = 0.000) for 6729 atoms. Found 15 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.53 Search for helices and strands: 0 residues in 0 chains, 6929 seeds are put forward NCS extension: 30 residues added (13 deleted due to clashes), 6959 seeds are put forward Round 1: 557 peptides, 67 chains. Longest chain 28 peptides. Score 0.519 Round 2: 589 peptides, 61 chains. Longest chain 32 peptides. Score 0.575 Round 3: 592 peptides, 61 chains. Longest chain 45 peptides. Score 0.578 Round 4: 600 peptides, 63 chains. Longest chain 32 peptides. Score 0.576 Round 5: 605 peptides, 61 chains. Longest chain 34 peptides. Score 0.589 Taking the results from Round 5 Chains 65, Residues 544, Estimated correctness of the model 38.1 % 10 chains (164 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12994 restraints for refining 6836 atoms. 10267 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2619 (Rfree = 0.000) for 6836 atoms. Found 61 (61 requested) and removed 58 (30 requested) atoms. Cycle 27: After refmac, R = 0.2503 (Rfree = 0.000) for 6793 atoms. Found 36 (61 requested) and removed 45 (30 requested) atoms. Cycle 28: After refmac, R = 0.2429 (Rfree = 0.000) for 6776 atoms. Found 29 (60 requested) and removed 37 (30 requested) atoms. Cycle 29: After refmac, R = 0.2369 (Rfree = 0.000) for 6755 atoms. Found 18 (60 requested) and removed 34 (30 requested) atoms. Cycle 30: After refmac, R = 0.2327 (Rfree = 0.000) for 6729 atoms. Found 20 (60 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 2.50 Search for helices and strands: 0 residues in 0 chains, 6945 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 6964 seeds are put forward Round 1: 561 peptides, 61 chains. Longest chain 36 peptides. Score 0.550 Round 2: 606 peptides, 60 chains. Longest chain 44 peptides. Score 0.594 Round 3: 602 peptides, 60 chains. Longest chain 36 peptides. Score 0.590 Round 4: 611 peptides, 58 chains. Longest chain 40 peptides. Score 0.606 Round 5: 595 peptides, 60 chains. Longest chain 28 peptides. Score 0.584 Taking the results from Round 4 Chains 63, Residues 553, Estimated correctness of the model 42.7 % 12 chains (192 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 12647 restraints for refining 6835 atoms. 9789 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2620 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 66 (30 requested) atoms. Cycle 32: After refmac, R = 0.2426 (Rfree = 0.000) for 6802 atoms. Found 38 (61 requested) and removed 36 (30 requested) atoms. Cycle 33: After refmac, R = 0.2346 (Rfree = 0.000) for 6783 atoms. Found 19 (61 requested) and removed 37 (30 requested) atoms. Cycle 34: After refmac, R = 0.2271 (Rfree = 0.000) for 6747 atoms. Found 24 (60 requested) and removed 35 (30 requested) atoms. Cycle 35: After refmac, R = 0.2413 (Rfree = 0.000) for 6729 atoms. Found 38 (60 requested) and removed 33 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 2.49 Search for helices and strands: 0 residues in 0 chains, 6964 seeds are put forward NCS extension: 24 residues added (16 deleted due to clashes), 6988 seeds are put forward Round 1: 525 peptides, 65 chains. Longest chain 31 peptides. Score 0.497 Round 2: 563 peptides, 61 chains. Longest chain 26 peptides. Score 0.551 Round 3: 598 peptides, 65 chains. Longest chain 24 peptides. Score 0.566 Round 4: 595 peptides, 62 chains. Longest chain 49 peptides. Score 0.576 Round 5: 592 peptides, 62 chains. Longest chain 38 peptides. Score 0.573 Taking the results from Round 4 Chains 65, Residues 533, Estimated correctness of the model 34.4 % 10 chains (148 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13271 restraints for refining 6835 atoms. 10681 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2478 (Rfree = 0.000) for 6835 atoms. Found 56 (61 requested) and removed 55 (30 requested) atoms. Cycle 37: After refmac, R = 0.2456 (Rfree = 0.000) for 6812 atoms. Found 21 (61 requested) and removed 50 (30 requested) atoms. Cycle 38: After refmac, R = 0.2311 (Rfree = 0.000) for 6768 atoms. Found 33 (60 requested) and removed 45 (30 requested) atoms. Cycle 39: After refmac, R = 0.2231 (Rfree = 0.000) for 6748 atoms. Found 8 (60 requested) and removed 40 (30 requested) atoms. Cycle 40: After refmac, R = 0.2215 (Rfree = 0.000) for 6706 atoms. Found 30 (60 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 2.51 Search for helices and strands: 0 residues in 0 chains, 6940 seeds are put forward NCS extension: 19 residues added (26 deleted due to clashes), 6959 seeds are put forward Round 1: 535 peptides, 66 chains. Longest chain 32 peptides. Score 0.502 Round 2: 570 peptides, 67 chains. Longest chain 28 peptides. Score 0.532 Round 3: 573 peptides, 64 chains. Longest chain 26 peptides. Score 0.548 Round 4: 565 peptides, 64 chains. Longest chain 30 peptides. Score 0.540 Round 5: 562 peptides, 64 chains. Longest chain 22 peptides. Score 0.537 Taking the results from Round 3 Chains 71, Residues 509, Estimated correctness of the model 26.3 % 9 chains (120 residues) have been docked in sequence ------------------------------------------------------ 24672 reflections ( 99.89 % complete ) and 13610 restraints for refining 6835 atoms. 11184 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2478 (Rfree = 0.000) for 6835 atoms. Found 61 (61 requested) and removed 49 (30 requested) atoms. Cycle 42: After refmac, R = 0.2321 (Rfree = 0.000) for 6828 atoms. Found 22 (61 requested) and removed 36 (30 requested) atoms. Cycle 43: After refmac, R = 0.2308 (Rfree = 0.000) for 6799 atoms. Found 35 (61 requested) and removed 33 (30 requested) atoms. Cycle 44: After refmac, R = 0.2272 (Rfree = 0.000) for 6796 atoms. Found 20 (61 requested) and removed 35 (30 requested) atoms. Cycle 45: After refmac, R = 0.2242 (Rfree = 0.000) for 6774 atoms. Found 24 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.55 Search for helices and strands: 0 residues in 0 chains, 6985 seeds are put forward NCS extension: 21 residues added (9 deleted due to clashes), 7006 seeds are put forward Round 1: 522 peptides, 64 chains. Longest chain 22 peptides. Score 0.499 Round 2: 570 peptides, 61 chains. Longest chain 33 peptides. Score 0.558 Round 3: 570 peptides, 65 chains. Longest chain 31 peptides. Score 0.541 Round 4: 577 peptides, 60 chains. Longest chain 34 peptides. Score 0.568 Round 5: 572 peptides, 65 chains. Longest chain 30 peptides. Score 0.542 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 517, Estimated correctness of the model 32.1 % 9 chains (142 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 134 A and 141 A 68 chains (520 residues) following loop building 8 chains (148 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24672 reflections ( 99.89 % complete ) and 13511 restraints for refining 6836 atoms. 10968 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2574 (Rfree = 0.000) for 6836 atoms. Found 0 (61 requested) and removed 15 (30 requested) atoms. Cycle 47: After refmac, R = 0.2464 (Rfree = 0.000) for 6798 atoms. Found 0 (61 requested) and removed 4 (30 requested) atoms. Cycle 48: After refmac, R = 0.2452 (Rfree = 0.000) for 6785 atoms. Found 0 (60 requested) and removed 7 (30 requested) atoms. Cycle 49: After refmac, R = 0.2424 (Rfree = 0.000) for 6776 atoms. Found 0 (60 requested) and removed 2 (30 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:23:46 GMT 2018 Job finished. TimeTaking 115.82 Used memory is bytes: 19482584