Mon 24 Dec 07:42:18 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqr-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqr-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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 07:42:22 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.2-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 967 and 0 Target number of residues in the AU: 967 Target solvent content: 0.5827 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-3.2-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-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.75 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 3.200 Wilson plot Bfac: 45.87 18027 reflections ( 88.16 % complete ) and 0 restraints for refining 10530 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3589 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3255 (Rfree = 0.000) for 10530 atoms. Found 86 (94 requested) and removed 183 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 3.04 Search for helices and strands: 0 residues in 0 chains, 10561 seeds are put forward NCS extension: 0 residues added, 10561 seeds are put forward Round 1: 322 peptides, 72 chains. Longest chain 9 peptides. Score 0.223 Round 2: 421 peptides, 82 chains. Longest chain 11 peptides. Score 0.309 Round 3: 462 peptides, 89 chains. Longest chain 12 peptides. Score 0.325 Round 4: 454 peptides, 86 chains. Longest chain 13 peptides. Score 0.331 Round 5: 455 peptides, 83 chains. Longest chain 16 peptides. Score 0.350 Taking the results from Round 5 Chains 83, Residues 372, Estimated correctness of the model 0.0 % 6 chains (19 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20498 restraints for refining 8676 atoms. 19045 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2712 (Rfree = 0.000) for 8676 atoms. Found 45 (77 requested) and removed 51 (38 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 8603 atoms. Found 36 (77 requested) and removed 46 (38 requested) atoms. Cycle 3: After refmac, R = 0.2494 (Rfree = 0.000) for 8565 atoms. Found 40 (77 requested) and removed 47 (38 requested) atoms. Cycle 4: After refmac, R = 0.2404 (Rfree = 0.000) for 8533 atoms. Found 39 (76 requested) and removed 44 (38 requested) atoms. Cycle 5: After refmac, R = 0.2332 (Rfree = 0.000) for 8504 atoms. Found 30 (76 requested) and removed 46 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 2.95 Search for helices and strands: 0 residues in 0 chains, 8722 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 8738 seeds are put forward Round 1: 462 peptides, 95 chains. Longest chain 11 peptides. Score 0.289 Round 2: 478 peptides, 90 chains. Longest chain 14 peptides. Score 0.341 Round 3: 495 peptides, 91 chains. Longest chain 14 peptides. Score 0.358 Round 4: 513 peptides, 90 chains. Longest chain 15 peptides. Score 0.387 Round 5: 519 peptides, 95 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 4 Chains 90, Residues 423, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 19978 restraints for refining 8578 atoms. 18344 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2435 (Rfree = 0.000) for 8578 atoms. Found 48 (76 requested) and removed 62 (38 requested) atoms. Cycle 7: After refmac, R = 0.2326 (Rfree = 0.000) for 8513 atoms. Found 38 (76 requested) and removed 50 (38 requested) atoms. Cycle 8: After refmac, R = 0.2287 (Rfree = 0.000) for 8472 atoms. Found 25 (76 requested) and removed 53 (38 requested) atoms. Cycle 9: After refmac, R = 0.2255 (Rfree = 0.000) for 8429 atoms. Found 24 (75 requested) and removed 45 (37 requested) atoms. Cycle 10: After refmac, R = 0.2255 (Rfree = 0.000) for 8394 atoms. Found 36 (75 requested) and removed 52 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 2.93 Search for helices and strands: 0 residues in 0 chains, 8573 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8591 seeds are put forward Round 1: 477 peptides, 99 chains. Longest chain 11 peptides. Score 0.287 Round 2: 527 peptides, 97 chains. Longest chain 15 peptides. Score 0.367 Round 3: 499 peptides, 91 chains. Longest chain 11 peptides. Score 0.363 Round 4: 517 peptides, 94 chains. Longest chain 14 peptides. Score 0.370 Round 5: 519 peptides, 92 chains. Longest chain 17 peptides. Score 0.384 Taking the results from Round 5 Chains 93, Residues 427, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 19806 restraints for refining 8674 atoms. 18075 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2389 (Rfree = 0.000) for 8674 atoms. Found 41 (77 requested) and removed 57 (38 requested) atoms. Cycle 12: After refmac, R = 0.2378 (Rfree = 0.000) for 8619 atoms. Found 50 (77 requested) and removed 43 (38 requested) atoms. Cycle 13: After refmac, R = 0.2353 (Rfree = 0.000) for 8604 atoms. Found 42 (77 requested) and removed 51 (38 requested) atoms. Cycle 14: After refmac, R = 0.2320 (Rfree = 0.000) for 8580 atoms. Found 47 (77 requested) and removed 44 (38 requested) atoms. Cycle 15: After refmac, R = 0.2144 (Rfree = 0.000) for 8572 atoms. Found 10 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.91 2.95 Search for helices and strands: 0 residues in 0 chains, 8757 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8772 seeds are put forward Round 1: 481 peptides, 101 chains. Longest chain 10 peptides. Score 0.281 Round 2: 485 peptides, 89 chains. Longest chain 16 peptides. Score 0.356 Round 3: 506 peptides, 84 chains. Longest chain 16 peptides. Score 0.412 Round 4: 514 peptides, 88 chains. Longest chain 18 peptides. Score 0.400 Round 5: 513 peptides, 88 chains. Longest chain 16 peptides. Score 0.399 Taking the results from Round 3 Chains 84, Residues 422, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20111 restraints for refining 8676 atoms. 18470 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2353 (Rfree = 0.000) for 8676 atoms. Found 40 (77 requested) and removed 52 (38 requested) atoms. Cycle 17: After refmac, R = 0.2334 (Rfree = 0.000) for 8641 atoms. Found 34 (77 requested) and removed 39 (38 requested) atoms. Cycle 18: After refmac, R = 0.2353 (Rfree = 0.000) for 8620 atoms. Found 51 (77 requested) and removed 46 (38 requested) atoms. Cycle 19: After refmac, R = 0.2349 (Rfree = 0.000) for 8613 atoms. Found 49 (77 requested) and removed 43 (38 requested) atoms. Cycle 20: After refmac, R = 0.2161 (Rfree = 0.000) for 8610 atoms. Found 16 (77 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.94 2.98 Search for helices and strands: 0 residues in 0 chains, 8783 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8805 seeds are put forward Round 1: 410 peptides, 85 chains. Longest chain 9 peptides. Score 0.275 Round 2: 458 peptides, 81 chains. Longest chain 17 peptides. Score 0.366 Round 3: 481 peptides, 84 chains. Longest chain 16 peptides. Score 0.379 Round 4: 469 peptides, 79 chains. Longest chain 15 peptides. Score 0.392 Round 5: 484 peptides, 77 chains. Longest chain 19 peptides. Score 0.423 Taking the results from Round 5 Chains 77, Residues 407, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20189 restraints for refining 8675 atoms. 18638 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2387 (Rfree = 0.000) for 8675 atoms. Found 46 (77 requested) and removed 49 (38 requested) atoms. Cycle 22: After refmac, R = 0.2401 (Rfree = 0.000) for 8654 atoms. Found 45 (77 requested) and removed 50 (38 requested) atoms. Cycle 23: After refmac, R = 0.2304 (Rfree = 0.000) for 8637 atoms. Found 38 (77 requested) and removed 47 (38 requested) atoms. Cycle 24: After refmac, R = 0.2278 (Rfree = 0.000) for 8614 atoms. Found 31 (77 requested) and removed 44 (38 requested) atoms. Cycle 25: After refmac, R = 0.2139 (Rfree = 0.000) for 8592 atoms. Found 12 (77 requested) and removed 42 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.00 3.04 Search for helices and strands: 0 residues in 0 chains, 8754 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 8776 seeds are put forward Round 1: 435 peptides, 91 chains. Longest chain 9 peptides. Score 0.275 Round 2: 469 peptides, 90 chains. Longest chain 9 peptides. Score 0.329 Round 3: 463 peptides, 84 chains. Longest chain 13 peptides. Score 0.355 Round 4: 480 peptides, 87 chains. Longest chain 13 peptides. Score 0.361 Round 5: 473 peptides, 85 chains. Longest chain 14 peptides. Score 0.363 Taking the results from Round 5 Chains 85, Residues 388, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20389 restraints for refining 8676 atoms. 18922 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2292 (Rfree = 0.000) for 8676 atoms. Found 52 (77 requested) and removed 42 (38 requested) atoms. Cycle 27: After refmac, R = 0.2236 (Rfree = 0.000) for 8673 atoms. Found 21 (77 requested) and removed 42 (38 requested) atoms. Cycle 28: After refmac, R = 0.2199 (Rfree = 0.000) for 8648 atoms. Found 10 (77 requested) and removed 40 (38 requested) atoms. Cycle 29: After refmac, R = 0.2148 (Rfree = 0.000) for 8612 atoms. Found 11 (77 requested) and removed 38 (38 requested) atoms. Cycle 30: After refmac, R = 0.2118 (Rfree = 0.000) for 8581 atoms. Found 15 (77 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.92 2.96 Search for helices and strands: 0 residues in 0 chains, 8768 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 8786 seeds are put forward Round 1: 441 peptides, 92 chains. Longest chain 9 peptides. Score 0.277 Round 2: 442 peptides, 76 chains. Longest chain 16 peptides. Score 0.374 Round 3: 428 peptides, 75 chains. Longest chain 11 peptides. Score 0.361 Round 4: 433 peptides, 78 chains. Longest chain 10 peptides. Score 0.350 Round 5: 443 peptides, 79 chains. Longest chain 13 peptides. Score 0.357 Taking the results from Round 2 Chains 76, Residues 366, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20302 restraints for refining 8667 atoms. 18914 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2193 (Rfree = 0.000) for 8667 atoms. Found 43 (77 requested) and removed 40 (38 requested) atoms. Cycle 32: After refmac, R = 0.2121 (Rfree = 0.000) for 8661 atoms. Found 21 (77 requested) and removed 39 (38 requested) atoms. Cycle 33: After refmac, R = 0.2078 (Rfree = 0.000) for 8635 atoms. Found 9 (77 requested) and removed 41 (38 requested) atoms. Cycle 34: After refmac, R = 0.2055 (Rfree = 0.000) for 8601 atoms. Found 10 (77 requested) and removed 38 (38 requested) atoms. Cycle 35: After refmac, R = 0.2067 (Rfree = 0.000) for 8569 atoms. Found 15 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.89 2.93 Search for helices and strands: 0 residues in 0 chains, 8725 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8750 seeds are put forward Round 1: 388 peptides, 82 chains. Longest chain 9 peptides. Score 0.261 Round 2: 430 peptides, 80 chains. Longest chain 12 peptides. Score 0.334 Round 3: 447 peptides, 84 chains. Longest chain 11 peptides. Score 0.333 Round 4: 455 peptides, 79 chains. Longest chain 13 peptides. Score 0.374 Round 5: 445 peptides, 80 chains. Longest chain 12 peptides. Score 0.354 Taking the results from Round 4 Chains 79, Residues 376, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20190 restraints for refining 8676 atoms. 18715 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2163 (Rfree = 0.000) for 8676 atoms. Found 32 (77 requested) and removed 45 (38 requested) atoms. Cycle 37: After refmac, R = 0.2091 (Rfree = 0.000) for 8649 atoms. Found 17 (77 requested) and removed 41 (38 requested) atoms. Cycle 38: After refmac, R = 0.2038 (Rfree = 0.000) for 8616 atoms. Found 15 (77 requested) and removed 38 (38 requested) atoms. Cycle 39: After refmac, R = 0.2013 (Rfree = 0.000) for 8587 atoms. Found 10 (77 requested) and removed 38 (38 requested) atoms. Cycle 40: After refmac, R = 0.1992 (Rfree = 0.000) for 8556 atoms. Found 12 (76 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.89 2.93 Search for helices and strands: 0 residues in 0 chains, 8714 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8728 seeds are put forward Round 1: 381 peptides, 80 chains. Longest chain 9 peptides. Score 0.263 Round 2: 416 peptides, 78 chains. Longest chain 11 peptides. Score 0.326 Round 3: 421 peptides, 74 chains. Longest chain 13 peptides. Score 0.357 Round 4: 395 peptides, 73 chains. Longest chain 12 peptides. Score 0.327 Round 5: 424 peptides, 80 chains. Longest chain 13 peptides. Score 0.325 Taking the results from Round 3 Chains 74, Residues 347, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18027 reflections ( 88.16 % complete ) and 20388 restraints for refining 8675 atoms. 19074 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2022 (Rfree = 0.000) for 8675 atoms. Found 39 (77 requested) and removed 41 (38 requested) atoms. Cycle 42: After refmac, R = 0.1971 (Rfree = 0.000) for 8661 atoms. Found 21 (77 requested) and removed 39 (38 requested) atoms. Cycle 43: After refmac, R = 0.1877 (Rfree = 0.000) for 8639 atoms. Found 12 (77 requested) and removed 38 (38 requested) atoms. Cycle 44: After refmac, R = 0.1847 (Rfree = 0.000) for 8609 atoms. Found 13 (77 requested) and removed 38 (38 requested) atoms. Cycle 45: After refmac, R = 0.1849 (Rfree = 0.000) for 8579 atoms. Found 7 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.93 2.97 Search for helices and strands: 0 residues in 0 chains, 8711 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8729 seeds are put forward Round 1: 355 peptides, 74 chains. Longest chain 10 peptides. Score 0.262 Round 2: 389 peptides, 72 chains. Longest chain 10 peptides. Score 0.324 Round 3: 403 peptides, 72 chains. Longest chain 12 peptides. Score 0.344 Round 4: 419 peptides, 75 chains. Longest chain 12 peptides. Score 0.348 Round 5: 381 peptides, 67 chains. Longest chain 12 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 344, 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. 18027 reflections ( 88.16 % complete ) and 20511 restraints for refining 8676 atoms. 19210 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2132 (Rfree = 0.000) for 8676 atoms. Found 0 (77 requested) and removed 36 (38 requested) atoms. Cycle 47: After refmac, R = 0.2060 (Rfree = 0.000) for 8634 atoms. Found 0 (77 requested) and removed 8 (38 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2079 (Rfree = 0.000) for 8625 atoms. Found 0 (77 requested) and removed 3 (38 requested) atoms. Cycle 49: After refmac, R = 0.2074 (Rfree = 0.000) for 8621 atoms. TimeTaking 99.35