Mon 24 Dec 08:01:21 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 2pbl-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.4-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/2pbl-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.4-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 08:01:25 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/2pbl-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.4-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 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-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.4-parrot-noncs.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 9249 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3513 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4129 (Rfree = 0.000) for 9249 atoms. Found 69 (69 requested) and removed 102 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 9423 seeds are put forward NCS extension: 0 residues added, 9423 seeds are put forward Round 1: 366 peptides, 78 chains. Longest chain 8 peptides. Score 0.268 Round 2: 457 peptides, 85 chains. Longest chain 12 peptides. Score 0.372 Round 3: 471 peptides, 82 chains. Longest chain 13 peptides. Score 0.414 Round 4: 476 peptides, 83 chains. Longest chain 12 peptides. Score 0.415 Round 5: 501 peptides, 84 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 86, Residues 417, Estimated correctness of the model 0.0 % 10 chains (79 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16790 restraints for refining 7622 atoms. 14975 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3485 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 81 (28 requested) atoms. Cycle 2: After refmac, R = 0.3314 (Rfree = 0.000) for 7435 atoms. Found 57 (57 requested) and removed 45 (28 requested) atoms. Cycle 3: After refmac, R = 0.3206 (Rfree = 0.000) for 7376 atoms. Found 56 (56 requested) and removed 41 (28 requested) atoms. Cycle 4: After refmac, R = 0.3142 (Rfree = 0.000) for 7358 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Cycle 5: After refmac, R = 0.3055 (Rfree = 0.000) for 7333 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 7684 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7699 seeds are put forward Round 1: 440 peptides, 86 chains. Longest chain 10 peptides. Score 0.337 Round 2: 516 peptides, 85 chains. Longest chain 15 peptides. Score 0.462 Round 3: 559 peptides, 88 chains. Longest chain 15 peptides. Score 0.505 Round 4: 541 peptides, 84 chains. Longest chain 13 peptides. Score 0.504 Round 5: 543 peptides, 77 chains. Longest chain 16 peptides. Score 0.547 Taking the results from Round 5 Chains 78, Residues 466, Estimated correctness of the model 10.4 % 12 chains (89 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16421 restraints for refining 7616 atoms. 14340 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3108 (Rfree = 0.000) for 7616 atoms. Found 57 (57 requested) and removed 93 (28 requested) atoms. Cycle 7: After refmac, R = 0.2911 (Rfree = 0.000) for 7492 atoms. Found 57 (57 requested) and removed 55 (28 requested) atoms. Cycle 8: After refmac, R = 0.2811 (Rfree = 0.000) for 7445 atoms. Found 56 (56 requested) and removed 43 (28 requested) atoms. Cycle 9: After refmac, R = 0.2737 (Rfree = 0.000) for 7422 atoms. Found 56 (56 requested) and removed 45 (28 requested) atoms. Cycle 10: After refmac, R = 0.2682 (Rfree = 0.000) for 7413 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 7703 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7723 seeds are put forward Round 1: 489 peptides, 85 chains. Longest chain 16 peptides. Score 0.422 Round 2: 555 peptides, 86 chains. Longest chain 18 peptides. Score 0.511 Round 3: 529 peptides, 81 chains. Longest chain 19 peptides. Score 0.505 Round 4: 541 peptides, 82 chains. Longest chain 21 peptides. Score 0.516 Round 5: 547 peptides, 77 chains. Longest chain 22 peptides. Score 0.552 Taking the results from Round 5 Chains 82, Residues 470, Estimated correctness of the model 12.2 % 12 chains (95 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16484 restraints for refining 7623 atoms. 14363 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2965 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 88 (28 requested) atoms. Cycle 12: After refmac, R = 0.2690 (Rfree = 0.000) for 7505 atoms. Found 57 (57 requested) and removed 49 (28 requested) atoms. Cycle 13: After refmac, R = 0.2532 (Rfree = 0.000) for 7477 atoms. Found 56 (56 requested) and removed 39 (28 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2391 (Rfree = 0.000) for 7477 atoms. Found 56 (56 requested) and removed 39 (28 requested) atoms. Cycle 15: After refmac, R = 0.2372 (Rfree = 0.000) for 7481 atoms. Found 56 (56 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.34 Search for helices and strands: 0 residues in 0 chains, 7812 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 7829 seeds are put forward Round 1: 497 peptides, 87 chains. Longest chain 14 peptides. Score 0.421 Round 2: 525 peptides, 79 chains. Longest chain 18 peptides. Score 0.512 Round 3: 527 peptides, 76 chains. Longest chain 19 peptides. Score 0.532 Round 4: 542 peptides, 79 chains. Longest chain 27 peptides. Score 0.534 Round 5: 524 peptides, 78 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 4 Chains 84, Residues 463, Estimated correctness of the model 5.7 % 11 chains (75 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16716 restraints for refining 7623 atoms. 14682 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2745 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 71 (28 requested) atoms. Cycle 17: After refmac, R = 0.2613 (Rfree = 0.000) for 7549 atoms. Found 57 (57 requested) and removed 45 (28 requested) atoms. Cycle 18: After refmac, R = 0.2421 (Rfree = 0.000) for 7524 atoms. Found 57 (57 requested) and removed 43 (28 requested) atoms. Cycle 19: After refmac, R = 0.2381 (Rfree = 0.000) for 7519 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. Cycle 20: After refmac, R = 0.2289 (Rfree = 0.000) for 7526 atoms. Found 56 (56 requested) and removed 41 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 7819 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7832 seeds are put forward Round 1: 440 peptides, 77 chains. Longest chain 16 peptides. Score 0.399 Round 2: 492 peptides, 77 chains. Longest chain 16 peptides. Score 0.478 Round 3: 518 peptides, 77 chains. Longest chain 17 peptides. Score 0.514 Round 4: 506 peptides, 77 chains. Longest chain 22 peptides. Score 0.497 Round 5: 512 peptides, 78 chains. Longest chain 18 peptides. Score 0.500 Taking the results from Round 3 Chains 79, Residues 441, Estimated correctness of the model 0.0 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16825 restraints for refining 7622 atoms. 14917 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2681 (Rfree = 0.000) for 7622 atoms. Found 57 (57 requested) and removed 63 (28 requested) atoms. Cycle 22: After refmac, R = 0.2613 (Rfree = 0.000) for 7563 atoms. Found 57 (57 requested) and removed 39 (28 requested) atoms. Cycle 23: After refmac, R = 0.2465 (Rfree = 0.000) for 7552 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. Cycle 24: After refmac, R = 0.2458 (Rfree = 0.000) for 7553 atoms. Found 57 (57 requested) and removed 33 (28 requested) atoms. Cycle 25: After refmac, R = 0.2332 (Rfree = 0.000) for 7555 atoms. Found 57 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 7814 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7829 seeds are put forward Round 1: 444 peptides, 83 chains. Longest chain 11 peptides. Score 0.365 Round 2: 507 peptides, 79 chains. Longest chain 15 peptides. Score 0.487 Round 3: 500 peptides, 77 chains. Longest chain 15 peptides. Score 0.489 Round 4: 489 peptides, 78 chains. Longest chain 17 peptides. Score 0.467 Round 5: 509 peptides, 74 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 5 Chains 75, Residues 435, Estimated correctness of the model 0.4 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17172 restraints for refining 7623 atoms. 15391 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2806 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 58 (28 requested) atoms. Cycle 27: After refmac, R = 0.2663 (Rfree = 0.000) for 7580 atoms. Found 57 (57 requested) and removed 39 (28 requested) atoms. Cycle 28: After refmac, R = 0.2528 (Rfree = 0.000) for 7582 atoms. Found 57 (57 requested) and removed 39 (28 requested) atoms. Cycle 29: After refmac, R = 0.2517 (Rfree = 0.000) for 7583 atoms. Found 57 (57 requested) and removed 39 (28 requested) atoms. Cycle 30: After refmac, R = 0.2421 (Rfree = 0.000) for 7588 atoms. Found 57 (57 requested) and removed 39 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 7871 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7886 seeds are put forward Round 1: 425 peptides, 79 chains. Longest chain 16 peptides. Score 0.361 Round 2: 461 peptides, 72 chains. Longest chain 15 peptides. Score 0.464 Round 3: 500 peptides, 77 chains. Longest chain 24 peptides. Score 0.489 Round 4: 475 peptides, 70 chains. Longest chain 26 peptides. Score 0.497 Round 5: 485 peptides, 72 chains. Longest chain 18 peptides. Score 0.499 Taking the results from Round 5 Chains 73, Residues 413, Estimated correctness of the model 0.0 % 7 chains (33 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17386 restraints for refining 7623 atoms. 15718 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2903 (Rfree = 0.000) for 7623 atoms. Found 57 (57 requested) and removed 49 (28 requested) atoms. Cycle 32: After refmac, R = 0.2782 (Rfree = 0.000) for 7580 atoms. Found 57 (57 requested) and removed 39 (28 requested) atoms. Cycle 33: After refmac, R = 0.2843 (Rfree = 0.000) for 7569 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. Cycle 34: After refmac, R = 0.2715 (Rfree = 0.000) for 7578 atoms. Found 57 (57 requested) and removed 32 (28 requested) atoms. Cycle 35: After refmac, R = 0.2710 (Rfree = 0.000) for 7588 atoms. Found 57 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 7906 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 7920 seeds are put forward Round 1: 405 peptides, 78 chains. Longest chain 14 peptides. Score 0.335 Round 2: 431 peptides, 70 chains. Longest chain 17 peptides. Score 0.432 Round 3: 426 peptides, 66 chains. Longest chain 20 peptides. Score 0.451 Round 4: 436 peptides, 74 chains. Longest chain 16 peptides. Score 0.413 Round 5: 424 peptides, 73 chains. Longest chain 16 peptides. Score 0.401 Taking the results from Round 3 Chains 66, Residues 360, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 17274 restraints for refining 7527 atoms. 15815 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2762 (Rfree = 0.000) for 7527 atoms. Found 56 (56 requested) and removed 47 (28 requested) atoms. Cycle 37: After refmac, R = 0.2796 (Rfree = 0.000) for 7511 atoms. Found 56 (56 requested) and removed 48 (28 requested) atoms. Cycle 38: After refmac, R = 0.2771 (Rfree = 0.000) for 7495 atoms. Found 56 (56 requested) and removed 37 (28 requested) atoms. Cycle 39: After refmac, R = 0.2607 (Rfree = 0.000) for 7501 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. Cycle 40: After refmac, R = 0.2669 (Rfree = 0.000) for 7507 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 7808 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 7823 seeds are put forward Round 1: 344 peptides, 69 chains. Longest chain 9 peptides. Score 0.295 Round 2: 394 peptides, 73 chains. Longest chain 11 peptides. Score 0.352 Round 3: 402 peptides, 64 chains. Longest chain 20 peptides. Score 0.428 Round 4: 412 peptides, 67 chains. Longest chain 14 peptides. Score 0.423 Round 5: 408 peptides, 67 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 3 Chains 65, Residues 338, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 13810 reflections ( 99.18 % complete ) and 16854 restraints for refining 7382 atoms. 15459 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2756 (Rfree = 0.000) for 7382 atoms. Found 55 (55 requested) and removed 63 (27 requested) atoms. Cycle 42: After refmac, R = 0.2628 (Rfree = 0.000) for 7347 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Cycle 43: After refmac, R = 0.2501 (Rfree = 0.000) for 7333 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. Cycle 44: After refmac, R = 0.2531 (Rfree = 0.000) for 7334 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. Cycle 45: After refmac, R = 0.2448 (Rfree = 0.000) for 7342 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 7583 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 7601 seeds are put forward Round 1: 329 peptides, 68 chains. Longest chain 11 peptides. Score 0.276 Round 2: 362 peptides, 66 chains. Longest chain 15 peptides. Score 0.349 Round 3: 347 peptides, 61 chains. Longest chain 13 peptides. Score 0.360 Round 4: 360 peptides, 62 chains. Longest chain 15 peptides. Score 0.375 Round 5: 348 peptides, 59 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 289, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (289 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13810 reflections ( 99.18 % complete ) and 17330 restraints for refining 7386 atoms. 16214 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2805 (Rfree = 0.000) for 7386 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2752 (Rfree = 0.000) for 7347 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2693 (Rfree = 0.000) for 7308 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2797 (Rfree = 0.000) for 7270 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. TimeTaking 72.22