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 1vm8-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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/1vm8-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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/1vm8-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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 1004 and 0 Target number of residues in the AU: 1004 Target solvent content: 0.5622 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-2.5-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: 4 Cell parameters: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.50 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: 105.560 2.500 Wilson plot Bfac: 39.13 42288 reflections ( 99.19 % complete ) and 0 restraints for refining 9409 atoms. Observations/parameters ratio is 1.12 ------------------------------------------------------ Starting model: R = 0.3407 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2566 (Rfree = 0.000) for 9409 atoms. Found 122 (170 requested) and removed 168 (85 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.57 2.47 NCS extension: 0 residues added, 9363 seeds are put forward Round 1: 526 peptides, 104 chains. Longest chain 12 peptides. Score 0.327 Round 2: 559 peptides, 97 chains. Longest chain 15 peptides. Score 0.410 Round 3: 577 peptides, 89 chains. Longest chain 19 peptides. Score 0.474 Round 4: 603 peptides, 85 chains. Longest chain 20 peptides. Score 0.524 Round 5: 626 peptides, 75 chains. Longest chain 26 peptides. Score 0.595 Taking the results from Round 5 Chains 82, Residues 551, Estimated correctness of the model 72.4 % 12 chains (117 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 16181 restraints for refining 8004 atoms. 13658 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2896 (Rfree = 0.000) for 8004 atoms. Found 145 (145 requested) and removed 86 (72 requested) atoms. Cycle 2: After refmac, R = 0.2624 (Rfree = 0.000) for 8015 atoms. Found 77 (146 requested) and removed 78 (73 requested) atoms. Cycle 3: After refmac, R = 0.2596 (Rfree = 0.000) for 7985 atoms. Found 72 (145 requested) and removed 78 (72 requested) atoms. Cycle 4: After refmac, R = 0.2563 (Rfree = 0.000) for 7967 atoms. Found 59 (144 requested) and removed 78 (72 requested) atoms. Cycle 5: After refmac, R = 0.2536 (Rfree = 0.000) for 7931 atoms. Found 72 (144 requested) and removed 72 (72 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.56 2.46 NCS extension: 66 residues added (6 deleted due to clashes), 8030 seeds are put forward Round 1: 609 peptides, 87 chains. Longest chain 25 peptides. Score 0.521 Round 2: 615 peptides, 76 chains. Longest chain 24 peptides. Score 0.579 Round 3: 615 peptides, 73 chains. Longest chain 31 peptides. Score 0.593 Round 4: 633 peptides, 73 chains. Longest chain 35 peptides. Score 0.610 Round 5: 612 peptides, 67 chains. Longest chain 44 peptides. Score 0.617 Taking the results from Round 5 Chains 71, Residues 545, Estimated correctness of the model 75.1 % 10 chains (184 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 15544 restraints for refining 8006 atoms. 12694 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2747 (Rfree = 0.000) for 8006 atoms. Found 101 (145 requested) and removed 90 (72 requested) atoms. Cycle 7: After refmac, R = 0.2642 (Rfree = 0.000) for 8000 atoms. Found 102 (145 requested) and removed 75 (72 requested) atoms. Cycle 8: After refmac, R = 0.2571 (Rfree = 0.000) for 8012 atoms. Found 86 (145 requested) and removed 72 (72 requested) atoms. Cycle 9: After refmac, R = 0.2533 (Rfree = 0.000) for 8012 atoms. Found 79 (145 requested) and removed 73 (72 requested) atoms. Cycle 10: After refmac, R = 0.2509 (Rfree = 0.000) for 8000 atoms. Found 83 (145 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.56 2.46 NCS extension: 75 residues added (20 deleted due to clashes), 8112 seeds are put forward Round 1: 594 peptides, 84 chains. Longest chain 40 peptides. Score 0.519 Round 2: 641 peptides, 74 chains. Longest chain 59 peptides. Score 0.613 Round 3: 657 peptides, 66 chains. Longest chain 68 peptides. Score 0.661 Round 4: 635 peptides, 70 chains. Longest chain 66 peptides. Score 0.625 Round 5: 614 peptides, 67 chains. Longest chain 33 peptides. Score 0.618 Taking the results from Round 3 Chains 76, Residues 591, Estimated correctness of the model 80.1 % 12 chains (198 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 14745 restraints for refining 8005 atoms. 11648 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2616 (Rfree = 0.000) for 8005 atoms. Found 119 (145 requested) and removed 99 (72 requested) atoms. Cycle 12: After refmac, R = 0.2455 (Rfree = 0.000) for 8010 atoms. Found 74 (145 requested) and removed 76 (72 requested) atoms. Cycle 13: After refmac, R = 0.2409 (Rfree = 0.000) for 7999 atoms. Found 82 (145 requested) and removed 74 (72 requested) atoms. Cycle 14: After refmac, R = 0.2348 (Rfree = 0.000) for 7989 atoms. Found 90 (145 requested) and removed 74 (72 requested) atoms. Cycle 15: After refmac, R = 0.2323 (Rfree = 0.000) for 7992 atoms. Found 85 (145 requested) and removed 72 (72 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.56 2.46 NCS extension: 148 residues added (14 deleted due to clashes), 8180 seeds are put forward Round 1: 600 peptides, 71 chains. Longest chain 37 peptides. Score 0.587 Round 2: 651 peptides, 62 chains. Longest chain 43 peptides. Score 0.672 Round 3: 659 peptides, 66 chains. Longest chain 51 peptides. Score 0.663 Round 4: 671 peptides, 66 chains. Longest chain 36 peptides. Score 0.673 Round 5: 673 peptides, 69 chains. Longest chain 42 peptides. Score 0.663 Taking the results from Round 4 Chains 73, Residues 605, Estimated correctness of the model 81.3 % 10 chains (175 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 14905 restraints for refining 8006 atoms. 11868 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2463 (Rfree = 0.000) for 8006 atoms. Found 105 (145 requested) and removed 79 (72 requested) atoms. Cycle 17: After refmac, R = 0.2385 (Rfree = 0.000) for 8012 atoms. Found 83 (145 requested) and removed 72 (72 requested) atoms. Cycle 18: After refmac, R = 0.2317 (Rfree = 0.000) for 8013 atoms. Found 75 (145 requested) and removed 76 (72 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 8002 atoms. Found 82 (145 requested) and removed 72 (72 requested) atoms. Cycle 20: After refmac, R = 0.2270 (Rfree = 0.000) for 8000 atoms. Found 54 (145 requested) and removed 72 (72 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.56 2.46 NCS extension: 32 residues added (20 deleted due to clashes), 8054 seeds are put forward Round 1: 635 peptides, 72 chains. Longest chain 43 peptides. Score 0.616 Round 2: 687 peptides, 69 chains. Longest chain 60 peptides. Score 0.674 Round 3: 679 peptides, 63 chains. Longest chain 62 peptides. Score 0.691 Round 4: 674 peptides, 66 chains. Longest chain 56 peptides. Score 0.675 Round 5: 677 peptides, 64 chains. Longest chain 62 peptides. Score 0.685 Taking the results from Round 3 Chains 71, Residues 616, Estimated correctness of the model 83.2 % 11 chains (223 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 14297 restraints for refining 8006 atoms. 10998 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2427 (Rfree = 0.000) for 8006 atoms. Found 100 (145 requested) and removed 77 (72 requested) atoms. Cycle 22: After refmac, R = 0.2331 (Rfree = 0.000) for 8016 atoms. Found 87 (145 requested) and removed 74 (72 requested) atoms. Cycle 23: After refmac, R = 0.2277 (Rfree = 0.000) for 8013 atoms. Found 82 (145 requested) and removed 73 (72 requested) atoms. Cycle 24: After refmac, R = 0.2279 (Rfree = 0.000) for 8012 atoms. Found 74 (145 requested) and removed 72 (72 requested) atoms. Cycle 25: After refmac, R = 0.2251 (Rfree = 0.000) for 8003 atoms. Found 74 (145 requested) and removed 72 (72 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.54 2.44 NCS extension: 64 residues added (55 deleted due to clashes), 8100 seeds are put forward Round 1: 632 peptides, 71 chains. Longest chain 61 peptides. Score 0.618 Round 2: 664 peptides, 60 chains. Longest chain 94 peptides. Score 0.690 Round 3: 661 peptides, 61 chains. Longest chain 67 peptides. Score 0.684 Round 4: 658 peptides, 63 chains. Longest chain 54 peptides. Score 0.674 Round 5: 666 peptides, 64 chains. Longest chain 58 peptides. Score 0.677 Taking the results from Round 2 Chains 66, Residues 604, Estimated correctness of the model 83.1 % 11 chains (269 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13727 restraints for refining 8006 atoms. 10301 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2392 (Rfree = 0.000) for 8006 atoms. Found 114 (145 requested) and removed 86 (72 requested) atoms. Cycle 27: After refmac, R = 0.2244 (Rfree = 0.000) for 8017 atoms. Found 72 (145 requested) and removed 74 (72 requested) atoms. Cycle 28: After refmac, R = 0.2203 (Rfree = 0.000) for 8001 atoms. Found 65 (145 requested) and removed 73 (72 requested) atoms. Cycle 29: After refmac, R = 0.2165 (Rfree = 0.000) for 7980 atoms. Found 87 (144 requested) and removed 74 (72 requested) atoms. Cycle 30: After refmac, R = 0.2169 (Rfree = 0.000) for 7985 atoms. Found 76 (144 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.56 2.46 NCS extension: 126 residues added (137 deleted due to clashes), 8125 seeds are put forward Round 1: 650 peptides, 71 chains. Longest chain 88 peptides. Score 0.635 Round 2: 672 peptides, 59 chains. Longest chain 51 peptides. Score 0.700 Round 3: 682 peptides, 59 chains. Longest chain 70 peptides. Score 0.708 Round 4: 672 peptides, 59 chains. Longest chain 77 peptides. Score 0.700 Round 5: 678 peptides, 58 chains. Longest chain 72 peptides. Score 0.709 Taking the results from Round 5 Chains 67, Residues 620, Estimated correctness of the model 84.9 % 16 chains (281 residues) have been docked in sequence Building loops using Loopy2018 67 chains (620 residues) following loop building 15 chains (281 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13507 restraints for refining 8006 atoms. 9883 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2481 (Rfree = 0.000) for 8006 atoms. Found 118 (145 requested) and removed 101 (72 requested) atoms. Cycle 32: After refmac, R = 0.2309 (Rfree = 0.000) for 8011 atoms. Found 67 (142 requested) and removed 78 (72 requested) atoms. Cycle 33: After refmac, R = 0.2276 (Rfree = 0.000) for 7994 atoms. Found 68 (139 requested) and removed 73 (72 requested) atoms. Cycle 34: After refmac, R = 0.2273 (Rfree = 0.000) for 7979 atoms. Found 89 (135 requested) and removed 74 (72 requested) atoms. Cycle 35: After refmac, R = 0.2234 (Rfree = 0.000) for 7980 atoms. Found 70 (132 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.56 2.46 NCS extension: 21 residues added (42 deleted due to clashes), 8031 seeds are put forward Round 1: 638 peptides, 66 chains. Longest chain 35 peptides. Score 0.645 Round 2: 655 peptides, 60 chains. Longest chain 73 peptides. Score 0.683 Round 3: 676 peptides, 60 chains. Longest chain 66 peptides. Score 0.700 Round 4: 670 peptides, 61 chains. Longest chain 72 peptides. Score 0.691 Round 5: 664 peptides, 64 chains. Longest chain 55 peptides. Score 0.675 Taking the results from Round 3 Chains 63, Residues 616, Estimated correctness of the model 84.0 % 13 chains (284 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13807 restraints for refining 8006 atoms. 10277 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2402 (Rfree = 0.000) for 8006 atoms. Found 109 (130 requested) and removed 84 (72 requested) atoms. Cycle 37: After refmac, R = 0.2283 (Rfree = 0.000) for 8018 atoms. Found 72 (130 requested) and removed 74 (72 requested) atoms. Cycle 38: After refmac, R = 0.2245 (Rfree = 0.000) for 8008 atoms. Found 63 (130 requested) and removed 76 (72 requested) atoms. Cycle 39: After refmac, R = 0.2232 (Rfree = 0.000) for 7989 atoms. Found 97 (130 requested) and removed 74 (72 requested) atoms. Cycle 40: After refmac, R = 0.2216 (Rfree = 0.000) for 8001 atoms. Found 79 (130 requested) and removed 79 (72 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.55 2.45 NCS extension: 41 residues added (32 deleted due to clashes), 8060 seeds are put forward Round 1: 625 peptides, 62 chains. Longest chain 44 peptides. Score 0.650 Round 2: 654 peptides, 56 chains. Longest chain 46 peptides. Score 0.698 Round 3: 647 peptides, 57 chains. Longest chain 41 peptides. Score 0.688 Round 4: 653 peptides, 53 chains. Longest chain 76 peptides. Score 0.708 Round 5: 660 peptides, 55 chains. Longest chain 49 peptides. Score 0.706 Taking the results from Round 4 Chains 58, Residues 600, Estimated correctness of the model 84.8 % 11 chains (283 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 331 A and 342 A Built loop between residues 422 A and 433 A 54 chains (614 residues) following loop building 9 chains (303 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13362 restraints for refining 8006 atoms. 9710 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2409 (Rfree = 0.000) for 8006 atoms. Found 102 (130 requested) and removed 87 (72 requested) atoms. Cycle 42: After refmac, R = 0.2294 (Rfree = 0.000) for 8013 atoms. Found 98 (128 requested) and removed 74 (72 requested) atoms. Cycle 43: After refmac, R = 0.2271 (Rfree = 0.000) for 8022 atoms. Found 81 (125 requested) and removed 73 (72 requested) atoms. Cycle 44: After refmac, R = 0.2121 (Rfree = 0.000) for 8016 atoms. Found 53 (122 requested) and removed 74 (72 requested) atoms. Cycle 45: After refmac, R = 0.2147 (Rfree = 0.000) for 7985 atoms. Found 53 (119 requested) and removed 73 (72 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.55 2.45 NCS extension: 212 residues added (147 deleted due to clashes), 8203 seeds are put forward Round 1: 634 peptides, 57 chains. Longest chain 46 peptides. Score 0.678 Round 2: 663 peptides, 54 chains. Longest chain 96 peptides. Score 0.712 Round 3: 666 peptides, 51 chains. Longest chain 88 peptides. Score 0.725 Round 4: 676 peptides, 56 chains. Longest chain 63 peptides. Score 0.715 Round 5: 667 peptides, 55 chains. Longest chain 59 peptides. Score 0.712 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 615, Estimated correctness of the model 86.4 % 12 chains (328 residues) have been docked in sequence Sequence coverage is 53 % Consider running further cycles of model building using 1vm8-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 322 A and 334 A Built loop between residues 421 A and 430 A Built loop between residues 308 B and 311 B 49 chains (628 residues) following loop building 9 chains (349 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 42288 reflections ( 99.19 % complete ) and 12607 restraints for refining 8006 atoms. 8673 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2380 (Rfree = 0.000) for 8006 atoms. Found 0 (116 requested) and removed 37 (72 requested) atoms. Cycle 47: After refmac, R = 0.2376 (Rfree = 0.000) for 7947 atoms. Found 0 (112 requested) and removed 22 (72 requested) atoms. Cycle 48: After refmac, R = 0.2370 (Rfree = 0.000) for 7914 atoms. Found 0 (109 requested) and removed 37 (71 requested) atoms. Cycle 49: After refmac, R = 0.2316 (Rfree = 0.000) for 7868 atoms. Found 0 (105 requested) and removed 28 (71 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:25:04 GMT 2018 Job finished. TimeTaking 117.11 Used memory is bytes: 23876440