Mon 24 Dec 07:59:58 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 1vqr-3.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqr-3.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqr-3.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-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/1vqr-3.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-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 08:00:03 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/1vqr-3.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.0-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 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-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.0-parrot-noncs.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 10618 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3566 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3332 (Rfree = 0.000) for 10618 atoms. Found 66 (114 requested) and removed 201 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.70 2.74 Search for helices and strands: 0 residues in 0 chains, 10658 seeds are put forward NCS extension: 0 residues added, 10658 seeds are put forward Round 1: 308 peptides, 69 chains. Longest chain 7 peptides. Score 0.221 Round 2: 413 peptides, 84 chains. Longest chain 10 peptides. Score 0.285 Round 3: 406 peptides, 82 chains. Longest chain 9 peptides. Score 0.287 Round 4: 415 peptides, 81 chains. Longest chain 11 peptides. Score 0.306 Round 5: 432 peptides, 82 chains. Longest chain 11 peptides. Score 0.324 Taking the results from Round 5 Chains 82, Residues 350, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20468 restraints for refining 8721 atoms. 19129 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2939 (Rfree = 0.000) for 8721 atoms. Found 59 (94 requested) and removed 60 (47 requested) atoms. Cycle 2: After refmac, R = 0.2942 (Rfree = 0.000) for 8644 atoms. Found 86 (94 requested) and removed 55 (47 requested) atoms. Cycle 3: After refmac, R = 0.2709 (Rfree = 0.000) for 8639 atoms. Found 43 (93 requested) and removed 53 (46 requested) atoms. Cycle 4: After refmac, R = 0.2449 (Rfree = 0.000) for 8598 atoms. Found 22 (93 requested) and removed 49 (46 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2479 (Rfree = 0.000) for 8557 atoms. Found 43 (92 requested) and removed 51 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.67 2.71 Search for helices and strands: 0 residues in 0 chains, 8774 seeds are put forward NCS extension: 0 residues added, 8774 seeds are put forward Round 1: 399 peptides, 85 chains. Longest chain 9 peptides. Score 0.259 Round 2: 457 peptides, 88 chains. Longest chain 16 peptides. Score 0.324 Round 3: 459 peptides, 88 chains. Longest chain 12 peptides. Score 0.327 Round 4: 476 peptides, 90 chains. Longest chain 16 peptides. Score 0.338 Round 5: 488 peptides, 93 chains. Longest chain 12 peptides. Score 0.337 Taking the results from Round 4 Chains 91, Residues 386, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 18870 restraints for refining 8315 atoms. 17371 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2670 (Rfree = 0.000) for 8315 atoms. Found 50 (89 requested) and removed 61 (44 requested) atoms. Cycle 7: After refmac, R = 0.2533 (Rfree = 0.000) for 8272 atoms. Found 33 (89 requested) and removed 50 (44 requested) atoms. Cycle 8: After refmac, R = 0.2493 (Rfree = 0.000) for 8237 atoms. Found 35 (89 requested) and removed 49 (44 requested) atoms. Cycle 9: After refmac, R = 0.2490 (Rfree = 0.000) for 8214 atoms. Found 24 (88 requested) and removed 50 (44 requested) atoms. Cycle 10: After refmac, R = 0.2487 (Rfree = 0.000) for 8179 atoms. Found 30 (88 requested) and removed 50 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 8400 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 8412 seeds are put forward Round 1: 422 peptides, 85 chains. Longest chain 10 peptides. Score 0.292 Round 2: 498 peptides, 91 chains. Longest chain 15 peptides. Score 0.362 Round 3: 479 peptides, 87 chains. Longest chain 11 peptides. Score 0.360 Round 4: 473 peptides, 85 chains. Longest chain 13 peptides. Score 0.363 Round 5: 471 peptides, 81 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 5 Chains 81, Residues 390, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19174 restraints for refining 8387 atoms. 17695 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2525 (Rfree = 0.000) for 8387 atoms. Found 49 (90 requested) and removed 59 (45 requested) atoms. Cycle 12: After refmac, R = 0.2366 (Rfree = 0.000) for 8358 atoms. Found 39 (90 requested) and removed 50 (45 requested) atoms. Cycle 13: After refmac, R = 0.2311 (Rfree = 0.000) for 8334 atoms. Found 35 (90 requested) and removed 53 (45 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2238 (Rfree = 0.000) for 8308 atoms. Found 29 (89 requested) and removed 48 (44 requested) atoms. Cycle 15: After refmac, R = 0.2123 (Rfree = 0.000) for 8285 atoms. Found 12 (89 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.67 2.71 Search for helices and strands: 0 residues in 0 chains, 8459 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 8478 seeds are put forward Round 1: 438 peptides, 89 chains. Longest chain 10 peptides. Score 0.291 Round 2: 515 peptides, 91 chains. Longest chain 12 peptides. Score 0.384 Round 3: 493 peptides, 89 chains. Longest chain 11 peptides. Score 0.367 Round 4: 512 peptides, 91 chains. Longest chain 14 peptides. Score 0.381 Round 5: 516 peptides, 86 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 5 Chains 86, Residues 430, Estimated correctness of the model 3.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 18954 restraints for refining 8503 atoms. 17281 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2438 (Rfree = 0.000) for 8503 atoms. Found 48 (91 requested) and removed 53 (45 requested) atoms. Cycle 17: After refmac, R = 0.2332 (Rfree = 0.000) for 8478 atoms. Found 24 (91 requested) and removed 53 (45 requested) atoms. Cycle 18: After refmac, R = 0.2289 (Rfree = 0.000) for 8445 atoms. Found 34 (91 requested) and removed 51 (45 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2235 (Rfree = 0.000) for 8424 atoms. Found 31 (90 requested) and removed 47 (45 requested) atoms. Cycle 20: After refmac, R = 0.2215 (Rfree = 0.000) for 8401 atoms. Found 24 (90 requested) and removed 48 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.72 2.76 Search for helices and strands: 0 residues in 0 chains, 8624 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 8635 seeds are put forward Round 1: 459 peptides, 86 chains. Longest chain 17 peptides. Score 0.338 Round 2: 502 peptides, 89 chains. Longest chain 13 peptides. Score 0.379 Round 3: 487 peptides, 82 chains. Longest chain 19 peptides. Score 0.399 Round 4: 514 peptides, 87 chains. Longest chain 14 peptides. Score 0.405 Round 5: 505 peptides, 85 chains. Longest chain 18 peptides. Score 0.405 Taking the results from Round 5 Chains 85, Residues 420, Estimated correctness of the model 0.5 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19792 restraints for refining 8700 atoms. 18177 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2362 (Rfree = 0.000) for 8700 atoms. Found 49 (93 requested) and removed 51 (46 requested) atoms. Cycle 22: After refmac, R = 0.2267 (Rfree = 0.000) for 8676 atoms. Found 31 (93 requested) and removed 52 (46 requested) atoms. Cycle 23: After refmac, R = 0.2278 (Rfree = 0.000) for 8650 atoms. Found 35 (93 requested) and removed 51 (46 requested) atoms. Cycle 24: After refmac, R = 0.2187 (Rfree = 0.000) for 8630 atoms. Found 23 (93 requested) and removed 48 (46 requested) atoms. Cycle 25: After refmac, R = 0.2239 (Rfree = 0.000) for 8594 atoms. Found 27 (92 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.71 2.75 Search for helices and strands: 0 residues in 0 chains, 8775 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 8794 seeds are put forward Round 1: 464 peptides, 99 chains. Longest chain 16 peptides. Score 0.269 Round 2: 524 peptides, 101 chains. Longest chain 17 peptides. Score 0.340 Round 3: 510 peptides, 95 chains. Longest chain 18 peptides. Score 0.355 Round 4: 506 peptides, 91 chains. Longest chain 12 peptides. Score 0.373 Round 5: 503 peptides, 87 chains. Longest chain 22 peptides. Score 0.391 Taking the results from Round 5 Chains 87, Residues 416, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19590 restraints for refining 8720 atoms. 17951 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2341 (Rfree = 0.000) for 8720 atoms. Found 63 (94 requested) and removed 53 (47 requested) atoms. Cycle 27: After refmac, R = 0.2297 (Rfree = 0.000) for 8716 atoms. Found 51 (94 requested) and removed 51 (47 requested) atoms. Cycle 28: After refmac, R = 0.2203 (Rfree = 0.000) for 8703 atoms. Found 23 (93 requested) and removed 47 (46 requested) atoms. Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 8667 atoms. Found 36 (93 requested) and removed 47 (46 requested) atoms. Cycle 30: After refmac, R = 0.2110 (Rfree = 0.000) for 8645 atoms. Found 34 (93 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.70 2.74 Search for helices and strands: 0 residues in 0 chains, 8826 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 8859 seeds are put forward Round 1: 423 peptides, 86 chains. Longest chain 9 peptides. Score 0.288 Round 2: 492 peptides, 94 chains. Longest chain 19 peptides. Score 0.337 Round 3: 504 peptides, 86 chains. Longest chain 17 peptides. Score 0.398 Round 4: 512 peptides, 90 chains. Longest chain 17 peptides. Score 0.386 Round 5: 488 peptides, 87 chains. Longest chain 14 peptides. Score 0.372 Taking the results from Round 3 Chains 86, Residues 418, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19672 restraints for refining 8722 atoms. 18086 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2242 (Rfree = 0.000) for 8722 atoms. Found 54 (94 requested) and removed 50 (47 requested) atoms. Cycle 32: After refmac, R = 0.2174 (Rfree = 0.000) for 8713 atoms. Found 36 (94 requested) and removed 54 (47 requested) atoms. Cycle 33: After refmac, R = 0.2159 (Rfree = 0.000) for 8692 atoms. Found 33 (93 requested) and removed 51 (46 requested) atoms. Cycle 34: After refmac, R = 0.2181 (Rfree = 0.000) for 8667 atoms. Found 37 (93 requested) and removed 49 (46 requested) atoms. Cycle 35: After refmac, R = 0.2150 (Rfree = 0.000) for 8651 atoms. Found 23 (93 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.73 2.77 Search for helices and strands: 0 residues in 0 chains, 8828 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 8855 seeds are put forward Round 1: 400 peptides, 81 chains. Longest chain 11 peptides. Score 0.285 Round 2: 466 peptides, 82 chains. Longest chain 15 peptides. Score 0.371 Round 3: 485 peptides, 82 chains. Longest chain 12 peptides. Score 0.396 Round 4: 454 peptides, 79 chains. Longest chain 17 peptides. Score 0.372 Round 5: 451 peptides, 72 chains. Longest chain 21 peptides. Score 0.409 Taking the results from Round 5 Chains 72, Residues 379, Estimated correctness of the model 1.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 20078 restraints for refining 8723 atoms. 18634 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2240 (Rfree = 0.000) for 8723 atoms. Found 69 (94 requested) and removed 48 (47 requested) atoms. Cycle 37: After refmac, R = 0.2165 (Rfree = 0.000) for 8742 atoms. Found 25 (94 requested) and removed 50 (47 requested) atoms. Cycle 38: After refmac, R = 0.2160 (Rfree = 0.000) for 8711 atoms. Found 32 (94 requested) and removed 47 (47 requested) atoms. Cycle 39: After refmac, R = 0.2133 (Rfree = 0.000) for 8694 atoms. Found 27 (93 requested) and removed 46 (46 requested) atoms. Cycle 40: After refmac, R = 0.1994 (Rfree = 0.000) for 8668 atoms. Found 24 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.73 2.77 Search for helices and strands: 0 residues in 0 chains, 8851 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8865 seeds are put forward Round 1: 450 peptides, 90 chains. Longest chain 14 peptides. Score 0.302 Round 2: 477 peptides, 84 chains. Longest chain 18 peptides. Score 0.374 Round 3: 455 peptides, 76 chains. Longest chain 18 peptides. Score 0.391 Round 4: 484 peptides, 83 chains. Longest chain 20 peptides. Score 0.389 Round 5: 469 peptides, 77 chains. Longest chain 16 peptides. Score 0.403 Taking the results from Round 5 Chains 79, Residues 392, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 21657 reflections ( 87.44 % complete ) and 19577 restraints for refining 8723 atoms. 18020 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2114 (Rfree = 0.000) for 8723 atoms. Found 52 (94 requested) and removed 47 (47 requested) atoms. Cycle 42: After refmac, R = 0.2061 (Rfree = 0.000) for 8717 atoms. Found 34 (94 requested) and removed 47 (47 requested) atoms. Cycle 43: After refmac, R = 0.2009 (Rfree = 0.000) for 8697 atoms. Found 25 (93 requested) and removed 46 (46 requested) atoms. Cycle 44: After refmac, R = 0.1992 (Rfree = 0.000) for 8672 atoms. Found 22 (93 requested) and removed 46 (46 requested) atoms. Cycle 45: After refmac, R = 0.1954 (Rfree = 0.000) for 8647 atoms. Found 22 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.73 2.77 Search for helices and strands: 0 residues in 0 chains, 8826 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8843 seeds are put forward Round 1: 396 peptides, 84 chains. Longest chain 9 peptides. Score 0.260 Round 2: 435 peptides, 80 chains. Longest chain 11 peptides. Score 0.341 Round 3: 438 peptides, 79 chains. Longest chain 14 peptides. Score 0.351 Round 4: 433 peptides, 74 chains. Longest chain 13 peptides. Score 0.373 Round 5: 437 peptides, 79 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 359, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 2 % 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 19872 restraints for refining 8723 atoms. 18485 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2048 (Rfree = 0.000) for 8723 atoms. Found 0 (94 requested) and removed 37 (47 requested) atoms. Cycle 47: After refmac, R = 0.2017 (Rfree = 0.000) for 8681 atoms. Found 0 (93 requested) and removed 16 (46 requested) atoms. Cycle 48: After refmac, R = 0.2046 (Rfree = 0.000) for 8663 atoms. Found 0 (93 requested) and removed 18 (46 requested) atoms. Cycle 49: After refmac, R = 0.1993 (Rfree = 0.000) for 8643 atoms. Found 0 (93 requested) and removed 22 (46 requested) atoms. Writing output files ... TimeTaking 89.22