Sun 23 Dec 22:22:52 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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 22:23:02 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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 975 and 0 Target number of residues in the AU: 975 Target solvent content: 0.6410 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.90 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 3.600 Wilson plot Bfac: 72.53 17421 reflections ( 99.85 % complete ) and 0 restraints for refining 8273 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3346 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2891 (Rfree = 0.000) for 8273 atoms. Found 53 (53 requested) and removed 63 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.81 Search for helices and strands: 0 residues in 0 chains, 8457 seeds are put forward NCS extension: 0 residues added, 8457 seeds are put forward Round 1: 455 peptides, 72 chains. Longest chain 15 peptides. Score 0.388 Round 2: 541 peptides, 69 chains. Longest chain 24 peptides. Score 0.495 Round 3: 545 peptides, 54 chains. Longest chain 33 peptides. Score 0.565 Round 4: 541 peptides, 52 chains. Longest chain 28 peptides. Score 0.571 Round 5: 550 peptides, 58 chains. Longest chain 32 peptides. Score 0.553 Taking the results from Round 4 Chains 55, Residues 489, Estimated correctness of the model 3.0 % 5 chains (81 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14755 restraints for refining 6783 atoms. 12575 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2547 (Rfree = 0.000) for 6783 atoms. Found 43 (43 requested) and removed 61 (21 requested) atoms. Cycle 2: After refmac, R = 0.2410 (Rfree = 0.000) for 6654 atoms. Found 39 (43 requested) and removed 38 (21 requested) atoms. Cycle 3: After refmac, R = 0.2323 (Rfree = 0.000) for 6608 atoms. Found 32 (42 requested) and removed 33 (21 requested) atoms. Cycle 4: After refmac, R = 0.2297 (Rfree = 0.000) for 6570 atoms. Found 23 (42 requested) and removed 33 (21 requested) atoms. Cycle 5: After refmac, R = 0.2258 (Rfree = 0.000) for 6539 atoms. Found 16 (42 requested) and removed 37 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 2.77 Search for helices and strands: 0 residues in 0 chains, 6793 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 6804 seeds are put forward Round 1: 518 peptides, 69 chains. Longest chain 23 peptides. Score 0.471 Round 2: 557 peptides, 62 chains. Longest chain 31 peptides. Score 0.542 Round 3: 553 peptides, 58 chains. Longest chain 31 peptides. Score 0.555 Round 4: 562 peptides, 59 chains. Longest chain 34 peptides. Score 0.559 Round 5: 568 peptides, 54 chains. Longest chain 38 peptides. Score 0.586 Taking the results from Round 5 Chains 60, Residues 514, Estimated correctness of the model 9.1 % 9 chains (125 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 13705 restraints for refining 6787 atoms. 11263 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2564 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 68 (21 requested) atoms. Cycle 7: After refmac, R = 0.2373 (Rfree = 0.000) for 6703 atoms. Found 35 (43 requested) and removed 41 (21 requested) atoms. Cycle 8: After refmac, R = 0.2288 (Rfree = 0.000) for 6669 atoms. Found 25 (42 requested) and removed 37 (21 requested) atoms. Cycle 9: After refmac, R = 0.2263 (Rfree = 0.000) for 6637 atoms. Found 14 (42 requested) and removed 30 (21 requested) atoms. Cycle 10: After refmac, R = 0.2215 (Rfree = 0.000) for 6605 atoms. Found 11 (42 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.77 Search for helices and strands: 0 residues in 0 chains, 6808 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 6845 seeds are put forward Round 1: 526 peptides, 68 chains. Longest chain 22 peptides. Score 0.484 Round 2: 545 peptides, 55 chains. Longest chain 34 peptides. Score 0.561 Round 3: 552 peptides, 63 chains. Longest chain 24 peptides. Score 0.532 Round 4: 559 peptides, 55 chains. Longest chain 24 peptides. Score 0.574 Round 5: 556 peptides, 59 chains. Longest chain 28 peptides. Score 0.554 Taking the results from Round 4 Chains 64, Residues 504, Estimated correctness of the model 4.2 % 8 chains (89 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14134 restraints for refining 6787 atoms. 11864 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2565 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 65 (21 requested) atoms. Cycle 12: After refmac, R = 0.2341 (Rfree = 0.000) for 6711 atoms. Found 18 (43 requested) and removed 41 (21 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2330 (Rfree = 0.000) for 6635 atoms. Found 20 (42 requested) and removed 37 (21 requested) atoms. Cycle 14: After refmac, R = 0.2268 (Rfree = 0.000) for 6596 atoms. Found 25 (42 requested) and removed 40 (21 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2209 (Rfree = 0.000) for 6568 atoms. Found 16 (42 requested) and removed 43 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 2.77 Search for helices and strands: 0 residues in 0 chains, 6785 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 6796 seeds are put forward Round 1: 524 peptides, 68 chains. Longest chain 36 peptides. Score 0.482 Round 2: 563 peptides, 63 chains. Longest chain 30 peptides. Score 0.543 Round 3: 550 peptides, 55 chains. Longest chain 39 peptides. Score 0.566 Round 4: 566 peptides, 60 chains. Longest chain 55 peptides. Score 0.559 Failed to save intermediate PDB Round 5: 542 peptides, 56 chains. Longest chain 46 peptides. Score 0.554 Taking the results from Round 3 Chains 64, Residues 495, Estimated correctness of the model 0.9 % 9 chains (130 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 13712 restraints for refining 6787 atoms. 11325 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2529 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 69 (21 requested) atoms. Cycle 17: After refmac, R = 0.2354 (Rfree = 0.000) for 6718 atoms. Found 26 (43 requested) and removed 42 (21 requested) atoms. Cycle 18: After refmac, R = 0.2288 (Rfree = 0.000) for 6679 atoms. Found 21 (42 requested) and removed 41 (21 requested) atoms. Cycle 19: After refmac, R = 0.2263 (Rfree = 0.000) for 6645 atoms. Found 21 (42 requested) and removed 34 (21 requested) atoms. Cycle 20: After refmac, R = 0.2187 (Rfree = 0.000) for 6617 atoms. Found 13 (42 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.77 Search for helices and strands: 0 residues in 0 chains, 6844 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 6866 seeds are put forward Round 1: 527 peptides, 67 chains. Longest chain 26 peptides. Score 0.490 Round 2: 532 peptides, 62 chains. Longest chain 33 peptides. Score 0.518 Round 3: 534 peptides, 60 chains. Longest chain 20 peptides. Score 0.529 Round 4: 538 peptides, 61 chains. Longest chain 33 peptides. Score 0.528 Round 5: 537 peptides, 65 chains. Longest chain 22 peptides. Score 0.509 Taking the results from Round 3 Chains 67, Residues 474, Estimated correctness of the model 0.0 % 10 chains (119 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 13890 restraints for refining 6788 atoms. 11644 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2476 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 52 (21 requested) atoms. Cycle 22: After refmac, R = 0.2296 (Rfree = 0.000) for 6729 atoms. Found 20 (43 requested) and removed 42 (21 requested) atoms. Cycle 23: After refmac, R = 0.2236 (Rfree = 0.000) for 6675 atoms. Found 17 (43 requested) and removed 41 (21 requested) atoms. Cycle 24: After refmac, R = 0.2212 (Rfree = 0.000) for 6627 atoms. Found 20 (42 requested) and removed 28 (21 requested) atoms. Cycle 25: After refmac, R = 0.2162 (Rfree = 0.000) for 6602 atoms. Found 17 (42 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 2.81 Search for helices and strands: 0 residues in 0 chains, 6845 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 6859 seeds are put forward Round 1: 491 peptides, 70 chains. Longest chain 18 peptides. Score 0.438 Round 2: 525 peptides, 59 chains. Longest chain 28 peptides. Score 0.525 Round 3: 518 peptides, 62 chains. Longest chain 23 peptides. Score 0.504 Round 4: 499 peptides, 62 chains. Longest chain 24 peptides. Score 0.485 Round 5: 516 peptides, 60 chains. Longest chain 33 peptides. Score 0.511 Taking the results from Round 2 Chains 64, Residues 466, Estimated correctness of the model 0.0 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14541 restraints for refining 6788 atoms. 12544 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2366 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 42 (21 requested) atoms. Cycle 27: After refmac, R = 0.2245 (Rfree = 0.000) for 6746 atoms. Found 26 (43 requested) and removed 35 (21 requested) atoms. Cycle 28: After refmac, R = 0.2188 (Rfree = 0.000) for 6708 atoms. Found 30 (43 requested) and removed 28 (21 requested) atoms. Cycle 29: After refmac, R = 0.2168 (Rfree = 0.000) for 6684 atoms. Found 28 (43 requested) and removed 30 (21 requested) atoms. Cycle 30: After refmac, R = 0.2140 (Rfree = 0.000) for 6663 atoms. Found 26 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.78 Search for helices and strands: 0 residues in 0 chains, 6900 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6912 seeds are put forward Round 1: 478 peptides, 72 chains. Longest chain 20 peptides. Score 0.414 Round 2: 530 peptides, 66 chains. Longest chain 18 peptides. Score 0.497 Round 3: 543 peptides, 63 chains. Longest chain 25 peptides. Score 0.524 Round 4: 537 peptides, 63 chains. Longest chain 23 peptides. Score 0.518 Round 5: 546 peptides, 67 chains. Longest chain 37 peptides. Score 0.509 Taking the results from Round 3 Chains 68, Residues 480, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14824 restraints for refining 6788 atoms. 12883 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2296 (Rfree = 0.000) for 6788 atoms. Found 31 (43 requested) and removed 34 (21 requested) atoms. Cycle 32: After refmac, R = 0.2113 (Rfree = 0.000) for 6731 atoms. Found 18 (43 requested) and removed 33 (21 requested) atoms. Cycle 33: After refmac, R = 0.2069 (Rfree = 0.000) for 6702 atoms. Found 11 (43 requested) and removed 31 (21 requested) atoms. Cycle 34: After refmac, R = 0.2050 (Rfree = 0.000) for 6673 atoms. Found 17 (42 requested) and removed 33 (21 requested) atoms. Cycle 35: After refmac, R = 0.2018 (Rfree = 0.000) for 6642 atoms. Found 13 (42 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 2.78 Search for helices and strands: 0 residues in 0 chains, 6924 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6948 seeds are put forward Round 1: 483 peptides, 76 chains. Longest chain 14 peptides. Score 0.399 Round 2: 523 peptides, 68 chains. Longest chain 20 peptides. Score 0.481 Round 3: 525 peptides, 64 chains. Longest chain 32 peptides. Score 0.502 Round 4: 529 peptides, 61 chains. Longest chain 24 peptides. Score 0.519 Round 5: 530 peptides, 61 chains. Longest chain 23 peptides. Score 0.520 Taking the results from Round 5 Chains 66, Residues 469, Estimated correctness of the model 0.0 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14738 restraints for refining 6787 atoms. 12740 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2435 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 47 (21 requested) atoms. Cycle 37: After refmac, R = 0.2273 (Rfree = 0.000) for 6747 atoms. Found 27 (43 requested) and removed 36 (21 requested) atoms. Cycle 38: After refmac, R = 0.2288 (Rfree = 0.000) for 6729 atoms. Found 27 (43 requested) and removed 34 (21 requested) atoms. Cycle 39: After refmac, R = 0.2229 (Rfree = 0.000) for 6709 atoms. Found 26 (43 requested) and removed 34 (21 requested) atoms. Cycle 40: After refmac, R = 0.2249 (Rfree = 0.000) for 6689 atoms. Found 26 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 2.77 Search for helices and strands: 0 residues in 0 chains, 6969 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6987 seeds are put forward Round 1: 480 peptides, 71 chains. Longest chain 22 peptides. Score 0.421 Round 2: 516 peptides, 61 chains. Longest chain 22 peptides. Score 0.507 Round 3: 523 peptides, 59 chains. Longest chain 47 peptides. Score 0.523 Round 4: 540 peptides, 57 chains. Longest chain 47 peptides. Score 0.548 Round 5: 546 peptides, 61 chains. Longest chain 28 peptides. Score 0.536 Taking the results from Round 4 Chains 65, Residues 483, Estimated correctness of the model 0.0 % 7 chains (122 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 13802 restraints for refining 6788 atoms. 11503 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2494 (Rfree = 0.000) for 6788 atoms. Found 39 (43 requested) and removed 60 (21 requested) atoms. Cycle 42: After refmac, R = 0.2336 (Rfree = 0.000) for 6735 atoms. Found 28 (43 requested) and removed 31 (21 requested) atoms. Cycle 43: After refmac, R = 0.2288 (Rfree = 0.000) for 6705 atoms. Found 21 (43 requested) and removed 33 (21 requested) atoms. Cycle 44: After refmac, R = 0.2235 (Rfree = 0.000) for 6675 atoms. Found 19 (42 requested) and removed 32 (21 requested) atoms. Cycle 45: After refmac, R = 0.2215 (Rfree = 0.000) for 6644 atoms. Found 21 (42 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 2.76 Search for helices and strands: 0 residues in 0 chains, 6884 seeds are put forward NCS extension: 43 residues added (0 deleted due to clashes), 6927 seeds are put forward Round 1: 458 peptides, 67 chains. Longest chain 21 peptides. Score 0.416 Round 2: 477 peptides, 61 chains. Longest chain 26 peptides. Score 0.467 Round 3: 483 peptides, 58 chains. Longest chain 29 peptides. Score 0.488 Round 4: 484 peptides, 60 chains. Longest chain 28 peptides. Score 0.479 Round 5: 491 peptides, 56 chains. Longest chain 25 peptides. Score 0.505 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 435, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (435 residues) following loop building 4 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17421 reflections ( 99.85 % complete ) and 14899 restraints for refining 6787 atoms. 13080 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2343 (Rfree = 0.000) for 6787 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2243 (Rfree = 0.000) for 6734 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2208 (Rfree = 0.000) for 6691 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2156 (Rfree = 0.000) for 6652 atoms. TimeTaking 92.45