Sun 23 Dec 22:23:08 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 1vqr-3.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-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/1vqr-3.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-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 22:23:18 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/1vqr-3.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-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 1001 and 0 Target number of residues in the AU: 1001 Target solvent content: 0.5680 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.0-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 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: 83.418 3.000 Wilson plot Bfac: 40.94 Failed to save intermediate PDB 21657 reflections ( 87.44 % complete ) and 0 restraints for refining 10554 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3545 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3120 (Rfree = 0.000) for 10554 atoms. Found 74 (113 requested) and removed 180 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.67 2.71 Search for helices and strands: 0 residues in 0 chains, 10614 seeds are put forward NCS extension: 0 residues added, 10614 seeds are put forward Round 1: 358 peptides, 79 chains. Longest chain 10 peptides. Score 0.234 Round 2: 423 peptides, 87 chains. Longest chain 11 peptides. Score 0.282 Round 3: 453 peptides, 90 chains. Longest chain 11 peptides. Score 0.306 Round 4: 468 peptides, 90 chains. Longest chain 10 peptides. Score 0.327 Round 5: 462 peptides, 87 chains. Longest chain 11 peptides. Score 0.337 Taking the results from Round 5 Chains 87, Residues 375, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20423 restraints for refining 8723 atoms. 19010 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2832 (Rfree = 0.000) for 8723 atoms. Found 52 (94 requested) and removed 54 (47 requested) atoms. Cycle 2: After refmac, R = 0.2874 (Rfree = 0.000) for 8686 atoms. Found 56 (94 requested) and removed 59 (47 requested) atoms. Cycle 3: After refmac, R = 0.2730 (Rfree = 0.000) for 8647 atoms. Found 54 (93 requested) and removed 54 (46 requested) atoms. Cycle 4: After refmac, R = 0.2557 (Rfree = 0.000) for 8629 atoms. Found 28 (93 requested) and removed 57 (46 requested) atoms. Cycle 5: After refmac, R = 0.2477 (Rfree = 0.000) for 8577 atoms. Found 19 (92 requested) and removed 52 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.61 2.65 Search for helices and strands: 0 residues in 0 chains, 8814 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8829 seeds are put forward Round 1: 466 peptides, 100 chains. Longest chain 10 peptides. Score 0.265 Round 2: 484 peptides, 93 chains. Longest chain 11 peptides. Score 0.332 Round 3: 486 peptides, 88 chains. Longest chain 10 peptides. Score 0.363 Round 4: 517 peptides, 92 chains. Longest chain 12 peptides. Score 0.381 Round 5: 530 peptides, 93 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Chains 93, Residues 437, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19814 restraints for refining 8669 atoms. 18104 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2576 (Rfree = 0.000) for 8669 atoms. Found 50 (93 requested) and removed 64 (46 requested) atoms. Cycle 7: After refmac, R = 0.2567 (Rfree = 0.000) for 8620 atoms. Found 41 (93 requested) and removed 54 (46 requested) atoms. Cycle 8: After refmac, R = 0.2637 (Rfree = 0.000) for 8591 atoms. Found 55 (92 requested) and removed 55 (46 requested) atoms. Cycle 9: After refmac, R = 0.2536 (Rfree = 0.000) for 8569 atoms. Found 31 (92 requested) and removed 59 (46 requested) atoms. Cycle 10: After refmac, R = 0.2385 (Rfree = 0.000) for 8530 atoms. Found 20 (92 requested) and removed 49 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.66 2.70 Search for helices and strands: 0 residues in 0 chains, 8726 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8739 seeds are put forward Round 1: 473 peptides, 97 chains. Longest chain 12 peptides. Score 0.293 Round 2: 491 peptides, 86 chains. Longest chain 15 peptides. Score 0.381 Round 3: 487 peptides, 87 chains. Longest chain 13 peptides. Score 0.370 Round 4: 502 peptides, 89 chains. Longest chain 15 peptides. Score 0.379 Round 5: 495 peptides, 85 chains. Longest chain 19 peptides. Score 0.392 Taking the results from Round 5 Chains 85, Residues 410, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20061 restraints for refining 8710 atoms. 18506 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2585 (Rfree = 0.000) for 8710 atoms. Found 56 (93 requested) and removed 60 (46 requested) atoms. Cycle 12: After refmac, R = 0.2532 (Rfree = 0.000) for 8685 atoms. Found 40 (93 requested) and removed 54 (46 requested) atoms. Cycle 13: After refmac, R = 0.2545 (Rfree = 0.000) for 8655 atoms. Found 50 (93 requested) and removed 64 (46 requested) atoms. Cycle 14: After refmac, R = 0.2478 (Rfree = 0.000) for 8630 atoms. Found 30 (93 requested) and removed 56 (46 requested) atoms. Cycle 15: After refmac, R = 0.2448 (Rfree = 0.000) for 8587 atoms. Found 36 (92 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.65 2.69 Search for helices and strands: 0 residues in 0 chains, 8836 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 8868 seeds are put forward Round 1: 472 peptides, 94 chains. Longest chain 13 peptides. Score 0.309 Round 2: 510 peptides, 92 chains. Longest chain 12 peptides. Score 0.372 Round 3: 536 peptides, 95 chains. Longest chain 13 peptides. Score 0.389 Round 4: 482 peptides, 84 chains. Longest chain 14 peptides. Score 0.381 Round 5: 512 peptides, 89 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 89, Residues 423, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 21657 reflections ( 87.44 % complete ) and 19747 restraints for refining 8723 atoms. 18144 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2488 (Rfree = 0.000) for 8723 atoms. Found 66 (94 requested) and removed 58 (47 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 8709 atoms. Found 49 (94 requested) and removed 54 (47 requested) atoms. Cycle 18: After refmac, R = 0.2360 (Rfree = 0.000) for 8695 atoms. Found 38 (93 requested) and removed 53 (46 requested) atoms. Cycle 19: After refmac, R = 0.2390 (Rfree = 0.000) for 8670 atoms. Found 50 (93 requested) and removed 53 (46 requested) atoms. Cycle 20: After refmac, R = 0.2327 (Rfree = 0.000) for 8660 atoms. Found 35 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.64 2.68 Search for helices and strands: 0 residues in 0 chains, 8878 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 8889 seeds are put forward Round 1: 415 peptides, 89 chains. Longest chain 9 peptides. Score 0.258 Round 2: 471 peptides, 84 chains. Longest chain 13 peptides. Score 0.366 Round 3: 493 peptides, 85 chains. Longest chain 14 peptides. Score 0.389 Round 4: 499 peptides, 92 chains. Longest chain 12 peptides. Score 0.358 Round 5: 509 peptides, 87 chains. Longest chain 16 peptides. Score 0.399 Taking the results from Round 5 Chains 88, Residues 422, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19511 restraints for refining 8723 atoms. 17879 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2549 (Rfree = 0.000) for 8723 atoms. Found 58 (94 requested) and removed 64 (47 requested) atoms. Cycle 22: After refmac, R = 0.2366 (Rfree = 0.000) for 8704 atoms. Found 38 (94 requested) and removed 50 (47 requested) atoms. Cycle 23: After refmac, R = 0.2336 (Rfree = 0.000) for 8678 atoms. Found 24 (93 requested) and removed 48 (46 requested) atoms. Cycle 24: After refmac, R = 0.2311 (Rfree = 0.000) for 8643 atoms. Found 31 (93 requested) and removed 48 (46 requested) atoms. Cycle 25: After refmac, R = 0.2304 (Rfree = 0.000) for 8616 atoms. Found 28 (93 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.64 2.68 Search for helices and strands: 0 residues in 0 chains, 8829 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 8853 seeds are put forward Round 1: 415 peptides, 88 chains. Longest chain 10 peptides. Score 0.264 Round 2: 464 peptides, 88 chains. Longest chain 11 peptides. Score 0.333 Round 3: 469 peptides, 87 chains. Longest chain 11 peptides. Score 0.346 Round 4: 448 peptides, 85 chains. Longest chain 15 peptides. Score 0.329 Round 5: 460 peptides, 78 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 5 Chains 78, Residues 382, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19836 restraints for refining 8722 atoms. 18386 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2367 (Rfree = 0.000) for 8722 atoms. Found 55 (94 requested) and removed 48 (47 requested) atoms. Cycle 27: After refmac, R = 0.2261 (Rfree = 0.000) for 8713 atoms. Found 39 (94 requested) and removed 48 (47 requested) atoms. Cycle 28: After refmac, R = 0.2178 (Rfree = 0.000) for 8699 atoms. Found 23 (93 requested) and removed 50 (46 requested) atoms. Cycle 29: After refmac, R = 0.2159 (Rfree = 0.000) for 8663 atoms. Found 22 (93 requested) and removed 49 (46 requested) atoms. Cycle 30: After refmac, R = 0.2032 (Rfree = 0.000) for 8633 atoms. Found 9 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.68 2.72 Search for helices and strands: 0 residues in 0 chains, 8811 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8827 seeds are put forward Round 1: 427 peptides, 89 chains. Longest chain 10 peptides. Score 0.275 Round 2: 481 peptides, 91 chains. Longest chain 11 peptides. Score 0.339 Round 3: 467 peptides, 90 chains. Longest chain 11 peptides. Score 0.326 Round 4: 477 peptides, 88 chains. Longest chain 13 peptides. Score 0.351 Round 5: 472 peptides, 87 chains. Longest chain 14 peptides. Score 0.350 Taking the results from Round 4 Chains 88, Residues 389, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19725 restraints for refining 8722 atoms. 18257 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2277 (Rfree = 0.000) for 8722 atoms. Found 45 (94 requested) and removed 50 (47 requested) atoms. Cycle 32: After refmac, R = 0.2143 (Rfree = 0.000) for 8707 atoms. Found 25 (93 requested) and removed 48 (46 requested) atoms. Cycle 33: After refmac, R = 0.2141 (Rfree = 0.000) for 8681 atoms. Found 22 (93 requested) and removed 46 (46 requested) atoms. Cycle 34: After refmac, R = 0.2105 (Rfree = 0.000) for 8651 atoms. Found 34 (93 requested) and removed 46 (46 requested) atoms. Cycle 35: After refmac, R = 0.2072 (Rfree = 0.000) for 8634 atoms. Found 21 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 8821 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8840 seeds are put forward Round 1: 383 peptides, 82 chains. Longest chain 11 peptides. Score 0.253 Round 2: 432 peptides, 82 chains. Longest chain 13 peptides. Score 0.324 Round 3: 446 peptides, 81 chains. Longest chain 14 peptides. Score 0.350 Round 4: 461 peptides, 86 chains. Longest chain 12 peptides. Score 0.341 Round 5: 448 peptides, 80 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 5 Chains 80, Residues 368, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 21657 reflections ( 87.44 % complete ) and 19657 restraints for refining 8723 atoms. 18226 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2253 (Rfree = 0.000) for 8723 atoms. Found 38 (94 requested) and removed 48 (47 requested) atoms. Cycle 37: After refmac, R = 0.2205 (Rfree = 0.000) for 8704 atoms. Found 35 (93 requested) and removed 47 (46 requested) atoms. Cycle 38: After refmac, R = 0.2212 (Rfree = 0.000) for 8684 atoms. Found 30 (93 requested) and removed 47 (46 requested) atoms. Cycle 39: After refmac, R = 0.2137 (Rfree = 0.000) for 8659 atoms. Found 32 (93 requested) and removed 47 (46 requested) atoms. Cycle 40: After refmac, R = 0.2109 (Rfree = 0.000) for 8636 atoms. Found 21 (93 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 8813 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8832 seeds are put forward Round 1: 378 peptides, 80 chains. Longest chain 10 peptides. Score 0.258 Round 2: 426 peptides, 77 chains. Longest chain 12 peptides. Score 0.346 Round 3: 416 peptides, 73 chains. Longest chain 14 peptides. Score 0.356 Round 4: 434 peptides, 79 chains. Longest chain 12 peptides. Score 0.345 Round 5: 443 peptides, 75 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 75, Residues 368, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19473 restraints for refining 8720 atoms. 18038 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2129 (Rfree = 0.000) for 8720 atoms. Found 32 (94 requested) and removed 48 (47 requested) atoms. Cycle 42: After refmac, R = 0.2072 (Rfree = 0.000) for 8690 atoms. Found 22 (93 requested) and removed 48 (46 requested) atoms. Cycle 43: After refmac, R = 0.2051 (Rfree = 0.000) for 8659 atoms. Found 15 (93 requested) and removed 46 (46 requested) atoms. Cycle 44: After refmac, R = 0.2019 (Rfree = 0.000) for 8624 atoms. Found 17 (93 requested) and removed 46 (46 requested) atoms. Cycle 45: After refmac, R = 0.2004 (Rfree = 0.000) for 8589 atoms. Found 11 (92 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 8732 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8747 seeds are put forward Round 1: 337 peptides, 71 chains. Longest chain 11 peptides. Score 0.253 Round 2: 392 peptides, 71 chains. Longest chain 13 peptides. Score 0.335 Round 3: 392 peptides, 75 chains. Longest chain 9 peptides. Score 0.310 Round 4: 425 peptides, 76 chains. Longest chain 15 peptides. Score 0.351 Round 5: 433 peptides, 75 chains. Longest chain 14 peptides. Score 0.367 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 358, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21657 reflections ( 87.44 % complete ) and 19625 restraints for refining 8696 atoms. 18268 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2149 (Rfree = 0.000) for 8696 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 47: After refmac, R = 0.2087 (Rfree = 0.000) for 8644 atoms. Found 0 (93 requested) and removed 36 (46 requested) atoms. Cycle 48: After refmac, R = 0.2074 (Rfree = 0.000) for 8601 atoms. Found 0 (92 requested) and removed 27 (46 requested) atoms. Cycle 49: After refmac, R = 0.2081 (Rfree = 0.000) for 8569 atoms. TimeTaking 106.02