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 2pbl-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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/2pbl-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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/2pbl-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.6136 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.70 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: 87.858 3.400 Wilson plot Bfac: 58.38 13810 reflections ( 99.18 % complete ) and 0 restraints for refining 9344 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3443 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4066 (Rfree = 0.000) for 9344 atoms. Found 70 (70 requested) and removed 102 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 3.33 Search for helices and strands: 0 residues in 0 chains, 9520 seeds are put forward NCS extension: 0 residues added, 9520 seeds are put forward Round 1: 349 peptides, 73 chains. Longest chain 13 peptides. Score 0.274 Round 2: 461 peptides, 83 chains. Longest chain 22 peptides. Score 0.392 Round 3: 521 peptides, 78 chains. Longest chain 24 peptides. Score 0.512 Round 4: 559 peptides, 81 chains. Longest chain 22 peptides. Score 0.545 Round 5: 582 peptides, 82 chains. Longest chain 24 peptides. Score 0.569 Taking the results from Round 5 Chains 90, Residues 500, Estimated correctness of the model 18.2 % 17 chains (148 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 15474 restraints for refining 7621 atoms. 13035 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3341 (Rfree = 0.000) for 7621 atoms. Found 57 (57 requested) and removed 116 (28 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.3063 (Rfree = 0.000) for 7398 atoms. Found 57 (57 requested) and removed 50 (28 requested) atoms. Cycle 3: After refmac, R = 0.2882 (Rfree = 0.000) for 7342 atoms. Found 55 (55 requested) and removed 33 (27 requested) atoms. Cycle 4: After refmac, R = 0.2731 (Rfree = 0.000) for 7321 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 5: After refmac, R = 0.2609 (Rfree = 0.000) for 7304 atoms. Found 55 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 7662 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7677 seeds are put forward Round 1: 526 peptides, 95 chains. Longest chain 16 peptides. Score 0.414 Round 2: 586 peptides, 84 chains. Longest chain 18 peptides. Score 0.563 Round 3: 618 peptides, 81 chains. Longest chain 23 peptides. Score 0.616 Round 4: 615 peptides, 90 chains. Longest chain 14 peptides. Score 0.566 Round 5: 621 peptides, 83 chains. Longest chain 22 peptides. Score 0.610 Taking the results from Round 3 Chains 84, Residues 537, Estimated correctness of the model 33.8 % 10 chains (83 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16184 restraints for refining 7623 atoms. 13864 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2820 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 88 (28 requested) atoms. Cycle 7: After refmac, R = 0.2545 (Rfree = 0.000) for 7528 atoms. Found 57 (57 requested) and removed 47 (28 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2427 (Rfree = 0.000) for 7512 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. Cycle 9: After refmac, R = 0.2380 (Rfree = 0.000) for 7505 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. Cycle 10: After refmac, R = 0.2357 (Rfree = 0.000) for 7510 atoms. Found 56 (56 requested) and removed 38 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 7833 seeds are put forward NCS extension: 26 residues added (14 deleted due to clashes), 7859 seeds are put forward Round 1: 551 peptides, 97 chains. Longest chain 21 peptides. Score 0.439 Round 2: 610 peptides, 94 chains. Longest chain 24 peptides. Score 0.538 Round 3: 630 peptides, 91 chains. Longest chain 20 peptides. Score 0.579 Round 4: 634 peptides, 90 chains. Longest chain 26 peptides. Score 0.589 Round 5: 636 peptides, 87 chains. Longest chain 23 peptides. Score 0.606 Taking the results from Round 5 Chains 89, Residues 549, Estimated correctness of the model 30.6 % 9 chains (65 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13810 reflections ( 99.18 % complete ) and 16404 restraints for refining 7622 atoms. 14091 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2893 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 82 (28 requested) atoms. Cycle 12: After refmac, R = 0.2633 (Rfree = 0.000) for 7550 atoms. Found 57 (57 requested) and removed 45 (28 requested) atoms. Cycle 13: After refmac, R = 0.2424 (Rfree = 0.000) for 7527 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2331 (Rfree = 0.000) for 7530 atoms. Found 56 (56 requested) and removed 37 (28 requested) atoms. Cycle 15: After refmac, R = 0.2290 (Rfree = 0.000) for 7529 atoms. Found 56 (56 requested) and removed 37 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 7809 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 7830 seeds are put forward Round 1: 547 peptides, 99 chains. Longest chain 14 peptides. Score 0.420 Round 2: 590 peptides, 88 chains. Longest chain 16 peptides. Score 0.546 Round 3: 587 peptides, 90 chains. Longest chain 27 peptides. Score 0.530 Round 4: 607 peptides, 87 chains. Longest chain 17 peptides. Score 0.572 Round 5: 605 peptides, 86 chains. Longest chain 21 peptides. Score 0.575 Taking the results from Round 5 Chains 87, Residues 519, Estimated correctness of the model 20.3 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17125 restraints for refining 7622 atoms. 15069 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2807 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 64 (28 requested) atoms. Cycle 17: After refmac, R = 0.2691 (Rfree = 0.000) for 7567 atoms. Found 57 (57 requested) and removed 40 (28 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2597 (Rfree = 0.000) for 7546 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2518 (Rfree = 0.000) for 7541 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2417 (Rfree = 0.000) for 7549 atoms. Found 57 (57 requested) and removed 41 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.37 Search for helices and strands: 0 residues in 0 chains, 7833 seeds are put forward NCS extension: 10 residues added (9 deleted due to clashes), 7843 seeds are put forward Round 1: 493 peptides, 92 chains. Longest chain 13 peptides. Score 0.382 Round 2: 574 peptides, 88 chains. Longest chain 21 peptides. Score 0.525 Round 3: 561 peptides, 82 chains. Longest chain 19 peptides. Score 0.542 Round 4: 571 peptides, 78 chains. Longest chain 18 peptides. Score 0.577 Round 5: 552 peptides, 80 chains. Longest chain 23 peptides. Score 0.542 Taking the results from Round 4 Chains 82, Residues 493, Estimated correctness of the model 21.0 % 11 chains (76 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16639 restraints for refining 7620 atoms. 14464 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2757 (Rfree = 0.000) for 7620 atoms. Found 57 (57 requested) and removed 65 (28 requested) atoms. Cycle 22: After refmac, R = 0.2554 (Rfree = 0.000) for 7560 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2395 (Rfree = 0.000) for 7563 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. Cycle 24: After refmac, R = 0.2293 (Rfree = 0.000) for 7572 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 25: After refmac, R = 0.2225 (Rfree = 0.000) for 7586 atoms. Found 57 (57 requested) and removed 41 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.34 Search for helices and strands: 0 residues in 0 chains, 7883 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7896 seeds are put forward Round 1: 500 peptides, 95 chains. Longest chain 13 peptides. Score 0.373 Round 2: 543 peptides, 86 chains. Longest chain 22 peptides. Score 0.495 Round 3: 542 peptides, 81 chains. Longest chain 16 peptides. Score 0.523 Round 4: 553 peptides, 83 chains. Longest chain 16 peptides. Score 0.526 Round 5: 547 peptides, 81 chains. Longest chain 16 peptides. Score 0.529 Taking the results from Round 5 Chains 82, Residues 466, Estimated correctness of the model 3.8 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17298 restraints for refining 7623 atoms. 15460 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2791 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 50 (28 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2568 (Rfree = 0.000) for 7589 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. Cycle 28: After refmac, R = 0.2477 (Rfree = 0.000) for 7587 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. Cycle 29: After refmac, R = 0.2425 (Rfree = 0.000) for 7589 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. Cycle 30: After refmac, R = 0.2399 (Rfree = 0.000) for 7604 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 7903 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7919 seeds are put forward Round 1: 469 peptides, 88 chains. Longest chain 12 peptides. Score 0.371 Round 2: 502 peptides, 86 chains. Longest chain 19 peptides. Score 0.435 Round 3: 523 peptides, 83 chains. Longest chain 19 peptides. Score 0.485 Round 4: 520 peptides, 80 chains. Longest chain 18 peptides. Score 0.499 Round 5: 508 peptides, 75 chains. Longest chain 16 peptides. Score 0.512 Taking the results from Round 5 Chains 75, Residues 433, Estimated correctness of the model 0.0 % 6 chains (24 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17464 restraints for refining 7623 atoms. 15739 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2725 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 47 (28 requested) atoms. Cycle 32: After refmac, R = 0.2632 (Rfree = 0.000) for 7602 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Cycle 33: After refmac, R = 0.2608 (Rfree = 0.000) for 7604 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Cycle 34: After refmac, R = 0.2471 (Rfree = 0.000) for 7612 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2522 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 7889 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 7904 seeds are put forward Round 1: 418 peptides, 76 chains. Longest chain 11 peptides. Score 0.371 Round 2: 469 peptides, 77 chains. Longest chain 15 peptides. Score 0.444 Round 3: 489 peptides, 73 chains. Longest chain 15 peptides. Score 0.498 Round 4: 491 peptides, 75 chains. Longest chain 15 peptides. Score 0.489 Round 5: 512 peptides, 78 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 5 Chains 80, Residues 434, Estimated correctness of the model 0.0 % 6 chains (28 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17406 restraints for refining 7623 atoms. 15688 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2706 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 47 (28 requested) atoms. Cycle 37: After refmac, R = 0.2664 (Rfree = 0.000) for 7612 atoms. Found 57 (57 requested) and removed 45 (28 requested) atoms. Cycle 38: After refmac, R = 0.2696 (Rfree = 0.000) for 7602 atoms. Found 57 (57 requested) and removed 38 (28 requested) atoms. Cycle 39: After refmac, R = 0.2700 (Rfree = 0.000) for 7608 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2728 (Rfree = 0.000) for 7617 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 7940 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7955 seeds are put forward Round 1: 374 peptides, 67 chains. Longest chain 11 peptides. Score 0.362 Round 2: 419 peptides, 68 chains. Longest chain 13 peptides. Score 0.427 Round 3: 425 peptides, 66 chains. Longest chain 17 peptides. Score 0.450 Round 4: 424 peptides, 66 chains. Longest chain 17 peptides. Score 0.448 Round 5: 453 peptides, 65 chains. Longest chain 15 peptides. Score 0.497 Taking the results from Round 5 Chains 65, Residues 388, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17351 restraints for refining 7522 atoms. 15805 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2784 (Rfree = 0.000) for 7522 atoms. Found 56 (56 requested) and removed 57 (28 requested) atoms. Cycle 42: After refmac, R = 0.2712 (Rfree = 0.000) for 7502 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. Cycle 43: After refmac, R = 0.2706 (Rfree = 0.000) for 7498 atoms. Found 56 (56 requested) and removed 40 (28 requested) atoms. Cycle 44: After refmac, R = 0.2700 (Rfree = 0.000) for 7503 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. Cycle 45: After refmac, R = 0.2789 (Rfree = 0.000) for 7510 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 3.34 Search for helices and strands: 0 residues in 0 chains, 7782 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7800 seeds are put forward Round 1: 310 peptides, 60 chains. Longest chain 9 peptides. Score 0.303 Round 2: 342 peptides, 59 chains. Longest chain 12 peptides. Score 0.366 Round 3: 356 peptides, 57 chains. Longest chain 15 peptides. Score 0.404 Round 4: 364 peptides, 57 chains. Longest chain 16 peptides. Score 0.417 Round 5: 346 peptides, 55 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 307, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (307 residues) following loop building 4 chains (15 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 13810 reflections ( 99.18 % complete ) and 17153 restraints for refining 7397 atoms. 15950 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2951 (Rfree = 0.000) for 7397 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.3004 (Rfree = 0.000) for 7343 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2946 (Rfree = 0.000) for 7299 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2773 (Rfree = 0.000) for 7266 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:14:09 GMT 2018 Job finished. TimeTaking 106.24