null Mon 24 Dec 08:01:01 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 1vl5-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-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/1vl5-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-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 08:01:05 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/1vl5-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-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 753 and 0 Target number of residues in the AU: 753 Target solvent content: 0.6482 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.8-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: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 3.800 Wilson plot Bfac: 76.86 11385 reflections ( 99.89 % complete ) and 0 restraints for refining 9231 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3365 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3126 (Rfree = 0.000) for 9231 atoms. Found 50 (50 requested) and removed 76 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 9372 seeds are put forward NCS extension: 0 residues added, 9372 seeds are put forward Round 1: 362 peptides, 73 chains. Longest chain 11 peptides. Score 0.285 Round 2: 488 peptides, 83 chains. Longest chain 12 peptides. Score 0.408 Round 3: 494 peptides, 81 chains. Longest chain 17 peptides. Score 0.428 Round 4: 523 peptides, 78 chains. Longest chain 20 peptides. Score 0.482 Round 5: 515 peptides, 70 chains. Longest chain 24 peptides. Score 0.517 Taking the results from Round 5 Chains 72, Residues 445, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17485 restraints for refining 7524 atoms. 15671 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2496 (Rfree = 0.000) for 7524 atoms. Found 41 (41 requested) and removed 61 (20 requested) atoms. Cycle 2: After refmac, R = 0.2340 (Rfree = 0.000) for 7344 atoms. Found 21 (41 requested) and removed 43 (20 requested) atoms. Cycle 3: After refmac, R = 0.2240 (Rfree = 0.000) for 7240 atoms. Found 22 (40 requested) and removed 41 (20 requested) atoms. Cycle 4: After refmac, R = 0.2111 (Rfree = 0.000) for 7185 atoms. Found 24 (39 requested) and removed 27 (19 requested) atoms. Cycle 5: After refmac, R = 0.2077 (Rfree = 0.000) for 7161 atoms. Found 22 (39 requested) and removed 39 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 7408 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 7420 seeds are put forward Round 1: 450 peptides, 89 chains. Longest chain 11 peptides. Score 0.317 Round 2: 522 peptides, 83 chains. Longest chain 17 peptides. Score 0.453 Round 3: 522 peptides, 73 chains. Longest chain 18 peptides. Score 0.509 Round 4: 535 peptides, 72 chains. Longest chain 19 peptides. Score 0.530 Round 5: 543 peptides, 72 chains. Longest chain 21 peptides. Score 0.539 Taking the results from Round 5 Chains 79, Residues 471, Estimated correctness of the model 0.0 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 16775 restraints for refining 7488 atoms. 14779 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2310 (Rfree = 0.000) for 7488 atoms. Found 33 (41 requested) and removed 69 (20 requested) atoms. Cycle 7: After refmac, R = 0.2159 (Rfree = 0.000) for 7400 atoms. Found 22 (40 requested) and removed 48 (20 requested) atoms. Cycle 8: After refmac, R = 0.2151 (Rfree = 0.000) for 7349 atoms. Found 21 (40 requested) and removed 34 (20 requested) atoms. Cycle 9: After refmac, R = 0.2126 (Rfree = 0.000) for 7320 atoms. Found 27 (40 requested) and removed 48 (20 requested) atoms. Cycle 10: After refmac, R = 0.2005 (Rfree = 0.000) for 7281 atoms. Found 26 (40 requested) and removed 35 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 7545 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7558 seeds are put forward Round 1: 464 peptides, 83 chains. Longest chain 13 peptides. Score 0.374 Round 2: 520 peptides, 78 chains. Longest chain 19 peptides. Score 0.479 Round 3: 548 peptides, 79 chains. Longest chain 19 peptides. Score 0.508 Round 4: 572 peptides, 79 chains. Longest chain 27 peptides. Score 0.536 Round 5: 543 peptides, 73 chains. Longest chain 20 peptides. Score 0.534 Taking the results from Round 4 Chains 79, Residues 493, Estimated correctness of the model 0.0 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17010 restraints for refining 7525 atoms. 14999 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2248 (Rfree = 0.000) for 7525 atoms. Found 24 (41 requested) and removed 48 (20 requested) atoms. Cycle 12: After refmac, R = 0.2166 (Rfree = 0.000) for 7453 atoms. Found 17 (41 requested) and removed 44 (20 requested) atoms. Cycle 13: After refmac, R = 0.2086 (Rfree = 0.000) for 7396 atoms. Found 25 (40 requested) and removed 44 (20 requested) atoms. Cycle 14: After refmac, R = 0.2125 (Rfree = 0.000) for 7347 atoms. Found 35 (40 requested) and removed 39 (20 requested) atoms. Cycle 15: After refmac, R = 0.1749 (Rfree = 0.000) for 7328 atoms. Found 9 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 7593 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7607 seeds are put forward Round 1: 411 peptides, 81 chains. Longest chain 14 peptides. Score 0.309 Round 2: 489 peptides, 81 chains. Longest chain 15 peptides. Score 0.421 Round 3: 499 peptides, 73 chains. Longest chain 21 peptides. Score 0.480 Round 4: 514 peptides, 77 chains. Longest chain 21 peptides. Score 0.477 Round 5: 519 peptides, 78 chains. Longest chain 26 peptides. Score 0.477 Taking the results from Round 3 Chains 75, Residues 426, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17406 restraints for refining 7525 atoms. 15694 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2204 (Rfree = 0.000) for 7525 atoms. Found 21 (41 requested) and removed 47 (20 requested) atoms. Cycle 17: After refmac, R = 0.2128 (Rfree = 0.000) for 7452 atoms. Found 25 (41 requested) and removed 41 (20 requested) atoms. Cycle 18: After refmac, R = 0.2059 (Rfree = 0.000) for 7409 atoms. Found 28 (40 requested) and removed 42 (20 requested) atoms. Cycle 19: After refmac, R = 0.1702 (Rfree = 0.000) for 7373 atoms. Found 2 (40 requested) and removed 25 (20 requested) atoms. Cycle 20: After refmac, R = 0.1642 (Rfree = 0.000) for 7344 atoms. Found 4 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 7568 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7584 seeds are put forward Round 1: 402 peptides, 79 chains. Longest chain 10 peptides. Score 0.308 Round 2: 484 peptides, 79 chains. Longest chain 16 peptides. Score 0.426 Round 3: 483 peptides, 79 chains. Longest chain 19 peptides. Score 0.425 Round 4: 505 peptides, 78 chains. Longest chain 19 peptides. Score 0.460 Round 5: 480 peptides, 77 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 4 Chains 78, Residues 427, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17452 restraints for refining 7521 atoms. 15811 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2209 (Rfree = 0.000) for 7521 atoms. Found 32 (41 requested) and removed 37 (20 requested) atoms. Cycle 22: After refmac, R = 0.2136 (Rfree = 0.000) for 7467 atoms. Found 41 (41 requested) and removed 39 (20 requested) atoms. Cycle 23: After refmac, R = 0.1762 (Rfree = 0.000) for 7436 atoms. Found 7 (41 requested) and removed 31 (20 requested) atoms. Cycle 24: After refmac, R = 0.1701 (Rfree = 0.000) for 7396 atoms. Found 11 (40 requested) and removed 25 (20 requested) atoms. Cycle 25: After refmac, R = 0.1639 (Rfree = 0.000) for 7370 atoms. Found 2 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 7586 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7604 seeds are put forward Round 1: 399 peptides, 83 chains. Longest chain 11 peptides. Score 0.277 Round 2: 417 peptides, 71 chains. Longest chain 15 peptides. Score 0.381 Round 3: 458 peptides, 76 chains. Longest chain 16 peptides. Score 0.408 Round 4: 465 peptides, 69 chains. Longest chain 14 peptides. Score 0.459 Round 5: 455 peptides, 73 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 4 Chains 70, Residues 396, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17347 restraints for refining 7523 atoms. 15744 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2046 (Rfree = 0.000) for 7523 atoms. Found 41 (41 requested) and removed 40 (20 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 7489 atoms. Found 41 (41 requested) and removed 47 (20 requested) atoms. Cycle 28: After refmac, R = 0.2095 (Rfree = 0.000) for 7455 atoms. Found 41 (41 requested) and removed 31 (20 requested) atoms. Cycle 29: After refmac, R = 0.2049 (Rfree = 0.000) for 7437 atoms. Found 41 (41 requested) and removed 32 (20 requested) atoms. Cycle 30: After refmac, R = 0.1618 (Rfree = 0.000) for 7419 atoms. Found 13 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 7658 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7671 seeds are put forward Round 1: 347 peptides, 73 chains. Longest chain 9 peptides. Score 0.261 Round 2: 400 peptides, 70 chains. Longest chain 14 peptides. Score 0.363 Round 3: 419 peptides, 73 chains. Longest chain 14 peptides. Score 0.372 Round 4: 425 peptides, 71 chains. Longest chain 17 peptides. Score 0.393 Round 5: 410 peptides, 68 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 4 Chains 74, Residues 354, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17732 restraints for refining 7524 atoms. 16311 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2163 (Rfree = 0.000) for 7524 atoms. Found 33 (41 requested) and removed 40 (20 requested) atoms. Cycle 32: After refmac, R = 0.2097 (Rfree = 0.000) for 7478 atoms. Found 35 (41 requested) and removed 35 (20 requested) atoms. Cycle 33: After refmac, R = 0.1948 (Rfree = 0.000) for 7453 atoms. Found 25 (41 requested) and removed 29 (20 requested) atoms. Cycle 34: After refmac, R = 0.1918 (Rfree = 0.000) for 7432 atoms. Found 22 (40 requested) and removed 30 (20 requested) atoms. Cycle 35: After refmac, R = 0.1598 (Rfree = 0.000) for 7407 atoms. Found 6 (40 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 7582 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7602 seeds are put forward Round 1: 329 peptides, 68 chains. Longest chain 11 peptides. Score 0.266 Round 2: 369 peptides, 68 chains. Longest chain 12 peptides. Score 0.329 Round 3: 356 peptides, 62 chains. Longest chain 22 peptides. Score 0.349 Round 4: 356 peptides, 56 chains. Longest chain 14 peptides. Score 0.389 Round 5: 362 peptides, 57 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 5 Chains 57, Residues 305, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17923 restraints for refining 7525 atoms. 16719 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2209 (Rfree = 0.000) for 7525 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Cycle 37: After refmac, R = 0.2058 (Rfree = 0.000) for 7486 atoms. Found 32 (41 requested) and removed 37 (20 requested) atoms. Cycle 38: After refmac, R = 0.2056 (Rfree = 0.000) for 7460 atoms. Found 27 (41 requested) and removed 36 (20 requested) atoms. Cycle 39: After refmac, R = 0.1971 (Rfree = 0.000) for 7426 atoms. Found 24 (40 requested) and removed 29 (20 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 7397 atoms. Found 38 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 7607 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7623 seeds are put forward Round 1: 317 peptides, 67 chains. Longest chain 10 peptides. Score 0.253 Round 2: 367 peptides, 70 chains. Longest chain 10 peptides. Score 0.313 Round 3: 391 peptides, 71 chains. Longest chain 12 peptides. Score 0.343 Round 4: 383 peptides, 68 chains. Longest chain 13 peptides. Score 0.351 Round 5: 389 peptides, 68 chains. Longest chain 13 peptides. Score 0.359 Taking the results from Round 5 Chains 68, Residues 321, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17958 restraints for refining 7525 atoms. 16722 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2146 (Rfree = 0.000) for 7525 atoms. Found 39 (41 requested) and removed 47 (20 requested) atoms. Cycle 42: After refmac, R = 0.2072 (Rfree = 0.000) for 7479 atoms. Found 38 (41 requested) and removed 39 (20 requested) atoms. Cycle 43: After refmac, R = 0.1988 (Rfree = 0.000) for 7449 atoms. Found 30 (41 requested) and removed 29 (20 requested) atoms. Cycle 44: After refmac, R = 0.1565 (Rfree = 0.000) for 7428 atoms. Found 6 (40 requested) and removed 29 (20 requested) atoms. Cycle 45: After refmac, R = 0.1495 (Rfree = 0.000) for 7389 atoms. Found 6 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 7572 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7584 seeds are put forward Round 1: 326 peptides, 70 chains. Longest chain 11 peptides. Score 0.247 Round 2: 357 peptides, 67 chains. Longest chain 14 peptides. Score 0.317 Round 3: 367 peptides, 65 chains. Longest chain 14 peptides. Score 0.346 Round 4: 363 peptides, 64 chains. Longest chain 17 peptides. Score 0.347 Round 5: 354 peptides, 62 chains. Longest chain 12 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 299, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 64 chains (299 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11385 reflections ( 99.89 % complete ) and 17697 restraints for refining 7523 atoms. 16517 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2064 (Rfree = 0.000) for 7523 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1987 (Rfree = 0.000) for 7476 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1652 (Rfree = 0.000) for 7440 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1674 (Rfree = 0.000) for 7407 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:19:47 GMT 2018 Job finished. TimeTaking 78.77 Used memory is bytes: 9620952