null Mon 24 Dec 08:03:59 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 1vl4-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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/1vl4-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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 08:04:04 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/1vl4-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.6-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 719 and 0 Target number of residues in the AU: 719 Target solvent content: 0.6219 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.6-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.65 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: 79.862 3.600 Wilson plot Bfac: 62.30 12391 reflections ( 99.37 % complete ) and 0 restraints for refining 7877 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3116 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3248 (Rfree = 0.000) for 7877 atoms. Found 50 (50 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7998 seeds are put forward NCS extension: 0 residues added, 7998 seeds are put forward Round 1: 363 peptides, 69 chains. Longest chain 13 peptides. Score 0.326 Round 2: 495 peptides, 74 chains. Longest chain 20 peptides. Score 0.496 Round 3: 523 peptides, 73 chains. Longest chain 22 peptides. Score 0.539 Round 4: 539 peptides, 69 chains. Longest chain 23 peptides. Score 0.581 Round 5: 549 peptides, 68 chains. Longest chain 22 peptides. Score 0.599 Taking the results from Round 5 Chains 74, Residues 481, Estimated correctness of the model 14.3 % 6 chains (48 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14158 restraints for refining 6479 atoms. 12143 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2747 (Rfree = 0.000) for 6479 atoms. Found 24 (41 requested) and removed 67 (20 requested) atoms. Cycle 2: After refmac, R = 0.2512 (Rfree = 0.000) for 6326 atoms. Found 26 (41 requested) and removed 28 (20 requested) atoms. Cycle 3: After refmac, R = 0.2438 (Rfree = 0.000) for 6265 atoms. Found 25 (40 requested) and removed 39 (20 requested) atoms. Cycle 4: After refmac, R = 0.2399 (Rfree = 0.000) for 6209 atoms. Found 25 (40 requested) and removed 29 (20 requested) atoms. Cycle 5: After refmac, R = 0.2232 (Rfree = 0.000) for 6179 atoms. Found 13 (39 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.21 Search for helices and strands: 0 residues in 0 chains, 6324 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 6364 seeds are put forward Round 1: 496 peptides, 82 chains. Longest chain 18 peptides. Score 0.448 Round 2: 516 peptides, 73 chains. Longest chain 30 peptides. Score 0.530 Round 3: 545 peptides, 76 chains. Longest chain 23 peptides. Score 0.550 Round 4: 554 peptides, 70 chains. Longest chain 26 peptides. Score 0.594 Round 5: 559 peptides, 74 chains. Longest chain 25 peptides. Score 0.579 Taking the results from Round 4 Chains 74, Residues 484, Estimated correctness of the model 12.3 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13694 restraints for refining 6413 atoms. 11649 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2648 (Rfree = 0.000) for 6413 atoms. Found 36 (41 requested) and removed 75 (20 requested) atoms. Cycle 7: After refmac, R = 0.2390 (Rfree = 0.000) for 6296 atoms. Found 30 (40 requested) and removed 45 (20 requested) atoms. Cycle 8: After refmac, R = 0.2347 (Rfree = 0.000) for 6243 atoms. Found 19 (40 requested) and removed 31 (20 requested) atoms. Cycle 9: After refmac, R = 0.2189 (Rfree = 0.000) for 6216 atoms. Found 6 (39 requested) and removed 20 (19 requested) atoms. Cycle 10: After refmac, R = 0.2262 (Rfree = 0.000) for 6187 atoms. Found 23 (39 requested) and removed 35 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6350 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 6366 seeds are put forward Round 1: 486 peptides, 78 chains. Longest chain 17 peptides. Score 0.459 Round 2: 520 peptides, 70 chains. Longest chain 20 peptides. Score 0.552 Round 3: 530 peptides, 71 chains. Longest chain 22 peptides. Score 0.559 Round 4: 512 peptides, 66 chains. Longest chain 26 peptides. Score 0.565 Round 5: 504 peptides, 63 chains. Longest chain 26 peptides. Score 0.572 Taking the results from Round 5 Chains 69, Residues 441, Estimated correctness of the model 3.4 % 9 chains (111 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 13609 restraints for refining 6483 atoms. 11495 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2650 (Rfree = 0.000) for 6483 atoms. Found 41 (41 requested) and removed 62 (20 requested) atoms. Cycle 12: After refmac, R = 0.2458 (Rfree = 0.000) for 6411 atoms. Found 38 (41 requested) and removed 45 (20 requested) atoms. Cycle 13: After refmac, R = 0.2345 (Rfree = 0.000) for 6367 atoms. Found 26 (41 requested) and removed 50 (20 requested) atoms. Cycle 14: After refmac, R = 0.2370 (Rfree = 0.000) for 6326 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 15: After refmac, R = 0.2419 (Rfree = 0.000) for 6309 atoms. Found 31 (40 requested) and removed 47 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 6443 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6463 seeds are put forward Round 1: 409 peptides, 72 chains. Longest chain 19 peptides. Score 0.381 Round 2: 469 peptides, 71 chains. Longest chain 18 peptides. Score 0.478 Round 3: 460 peptides, 64 chains. Longest chain 22 peptides. Score 0.509 Round 4: 480 peptides, 64 chains. Longest chain 21 peptides. Score 0.536 Round 5: 499 peptides, 70 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 4 Chains 67, Residues 416, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14519 restraints for refining 6480 atoms. 12830 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2495 (Rfree = 0.000) for 6480 atoms. Found 40 (41 requested) and removed 51 (20 requested) atoms. Cycle 17: After refmac, R = 0.2383 (Rfree = 0.000) for 6430 atoms. Found 33 (41 requested) and removed 47 (20 requested) atoms. Cycle 18: After refmac, R = 0.2277 (Rfree = 0.000) for 6396 atoms. Found 22 (41 requested) and removed 46 (20 requested) atoms. Cycle 19: After refmac, R = 0.2109 (Rfree = 0.000) for 6357 atoms. Found 14 (40 requested) and removed 40 (20 requested) atoms. Cycle 20: After refmac, R = 0.2078 (Rfree = 0.000) for 6319 atoms. Found 6 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6479 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6503 seeds are put forward Round 1: 413 peptides, 73 chains. Longest chain 16 peptides. Score 0.381 Round 2: 471 peptides, 72 chains. Longest chain 23 peptides. Score 0.475 Round 3: 467 peptides, 66 chains. Longest chain 21 peptides. Score 0.506 Round 4: 482 peptides, 70 chains. Longest chain 31 peptides. Score 0.502 Round 5: 448 peptides, 65 chains. Longest chain 21 peptides. Score 0.486 Taking the results from Round 3 Chains 68, Residues 401, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14558 restraints for refining 6483 atoms. 12903 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2475 (Rfree = 0.000) for 6483 atoms. Found 41 (41 requested) and removed 57 (20 requested) atoms. Cycle 22: After refmac, R = 0.2530 (Rfree = 0.000) for 6431 atoms. Found 41 (41 requested) and removed 46 (20 requested) atoms. Cycle 23: After refmac, R = 0.2120 (Rfree = 0.000) for 6398 atoms. Found 10 (41 requested) and removed 39 (20 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 6358 atoms. Found 13 (40 requested) and removed 27 (20 requested) atoms. Cycle 25: After refmac, R = 0.2055 (Rfree = 0.000) for 6338 atoms. Found 8 (40 requested) and removed 33 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 6476 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6500 seeds are put forward Round 1: 408 peptides, 75 chains. Longest chain 13 peptides. Score 0.359 Round 2: 431 peptides, 67 chains. Longest chain 15 peptides. Score 0.448 Round 3: 448 peptides, 69 chains. Longest chain 14 peptides. Score 0.460 Round 4: 447 peptides, 69 chains. Longest chain 18 peptides. Score 0.459 Round 5: 462 peptides, 69 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 5 Chains 70, Residues 393, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14397 restraints for refining 6483 atoms. 12753 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2496 (Rfree = 0.000) for 6483 atoms. Found 38 (41 requested) and removed 33 (20 requested) atoms. Cycle 27: After refmac, R = 0.2450 (Rfree = 0.000) for 6454 atoms. Found 41 (41 requested) and removed 42 (20 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 6427 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Cycle 29: After refmac, R = 0.2288 (Rfree = 0.000) for 6411 atoms. Found 41 (41 requested) and removed 29 (20 requested) atoms. Cycle 30: After refmac, R = 0.2250 (Rfree = 0.000) for 6412 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 6636 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6659 seeds are put forward Round 1: 368 peptides, 71 chains. Longest chain 16 peptides. Score 0.321 Round 2: 421 peptides, 68 chains. Longest chain 19 peptides. Score 0.427 Round 3: 445 peptides, 68 chains. Longest chain 17 peptides. Score 0.463 Round 4: 454 peptides, 68 chains. Longest chain 16 peptides. Score 0.475 Round 5: 443 peptides, 65 chains. Longest chain 20 peptides. Score 0.479 Taking the results from Round 5 Chains 65, Residues 378, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14896 restraints for refining 6483 atoms. 13395 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2426 (Rfree = 0.000) for 6483 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 32: After refmac, R = 0.2145 (Rfree = 0.000) for 6439 atoms. Found 20 (41 requested) and removed 27 (20 requested) atoms. Cycle 33: After refmac, R = 0.2061 (Rfree = 0.000) for 6405 atoms. Found 27 (41 requested) and removed 31 (20 requested) atoms. Cycle 34: After refmac, R = 0.2059 (Rfree = 0.000) for 6382 atoms. Found 27 (41 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.2009 (Rfree = 0.000) for 6377 atoms. Found 26 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 6515 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6530 seeds are put forward Round 1: 343 peptides, 61 chains. Longest chain 15 peptides. Score 0.351 Round 2: 411 peptides, 67 chains. Longest chain 15 peptides. Score 0.418 Round 3: 439 peptides, 67 chains. Longest chain 17 peptides. Score 0.460 Round 4: 440 peptides, 67 chains. Longest chain 16 peptides. Score 0.462 Round 5: 445 peptides, 69 chains. Longest chain 19 peptides. Score 0.456 Taking the results from Round 4 Chains 67, Residues 373, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14588 restraints for refining 6481 atoms. 13031 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2144 (Rfree = 0.000) for 6481 atoms. Found 28 (41 requested) and removed 29 (20 requested) atoms. Cycle 37: After refmac, R = 0.1984 (Rfree = 0.000) for 6455 atoms. Found 24 (41 requested) and removed 32 (20 requested) atoms. Cycle 38: After refmac, R = 0.1930 (Rfree = 0.000) for 6438 atoms. Found 18 (41 requested) and removed 23 (20 requested) atoms. Cycle 39: After refmac, R = 0.1923 (Rfree = 0.000) for 6425 atoms. Found 20 (41 requested) and removed 23 (20 requested) atoms. Cycle 40: After refmac, R = 0.1893 (Rfree = 0.000) for 6417 atoms. Found 16 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 6547 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6564 seeds are put forward Round 1: 347 peptides, 69 chains. Longest chain 9 peptides. Score 0.299 Round 2: 383 peptides, 67 chains. Longest chain 15 peptides. Score 0.374 Round 3: 410 peptides, 70 chains. Longest chain 13 peptides. Score 0.396 Round 4: 426 peptides, 69 chains. Longest chain 14 peptides. Score 0.428 Round 5: 398 peptides, 62 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 5 Chains 62, Residues 336, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12391 reflections ( 99.37 % complete ) and 14990 restraints for refining 6481 atoms. 13602 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2105 (Rfree = 0.000) for 6481 atoms. Found 30 (41 requested) and removed 27 (20 requested) atoms. Cycle 42: After refmac, R = 0.2033 (Rfree = 0.000) for 6452 atoms. Found 36 (41 requested) and removed 27 (20 requested) atoms. Cycle 43: After refmac, R = 0.2037 (Rfree = 0.000) for 6438 atoms. Found 37 (41 requested) and removed 22 (20 requested) atoms. Cycle 44: After refmac, R = 0.1914 (Rfree = 0.000) for 6441 atoms. Found 20 (41 requested) and removed 26 (20 requested) atoms. Cycle 45: After refmac, R = 0.1959 (Rfree = 0.000) for 6423 atoms. Found 38 (41 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 6589 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6607 seeds are put forward Round 1: 346 peptides, 70 chains. Longest chain 13 peptides. Score 0.290 Round 2: 368 peptides, 64 chains. Longest chain 15 peptides. Score 0.371 Round 3: 399 peptides, 70 chains. Longest chain 15 peptides. Score 0.379 Round 4: 403 peptides, 68 chains. Longest chain 13 peptides. Score 0.399 Round 5: 406 peptides, 68 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 69, Residues 338, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 378 A and 388 A 67 chains (343 residues) following loop building 5 chains (44 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12391 reflections ( 99.37 % complete ) and 14685 restraints for refining 6483 atoms. 13257 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2168 (Rfree = 0.000) for 6483 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2202 (Rfree = 0.000) for 6426 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2136 (Rfree = 0.000) for 6386 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1900 (Rfree = 0.000) for 6352 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:13:18 GMT 2018 Job finished. TimeTaking 69.31 Used memory is bytes: 6943504