null Mon 24 Dec 07:39:58 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 1vrb-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-4.0-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/1vrb-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-4.0-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 07:40:02 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/1vrb-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-4.0-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 857 and 0 Target number of residues in the AU: 857 Target solvent content: 0.6729 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-4.0-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 10944 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: 48.979 4.000 Wilson plot Bfac: 94.96 12677 reflections ( 99.37 % complete ) and 0 restraints for refining 12128 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3670 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3450 (Rfree = 0.000) for 12128 atoms. Found 57 (57 requested) and removed 189 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 3.98 Search for helices and strands: 0 residues in 0 chains, 12212 seeds are put forward NCS extension: 0 residues added, 12212 seeds are put forward Round 1: 343 peptides, 69 chains. Longest chain 13 peptides. Score 0.267 Round 2: 466 peptides, 81 chains. Longest chain 15 peptides. Score 0.359 Round 3: 516 peptides, 85 chains. Longest chain 21 peptides. Score 0.397 Round 4: 530 peptides, 80 chains. Longest chain 22 peptides. Score 0.438 Round 5: 525 peptides, 79 chains. Longest chain 21 peptides. Score 0.437 Taking the results from Round 4 Chains 81, Residues 450, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 24499 restraints for refining 9879 atoms. 22738 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2881 (Rfree = 0.000) for 9879 atoms. Found 34 (46 requested) and removed 86 (23 requested) atoms. Cycle 2: After refmac, R = 0.2685 (Rfree = 0.000) for 9621 atoms. Found 35 (46 requested) and removed 83 (23 requested) atoms. Cycle 3: After refmac, R = 0.2658 (Rfree = 0.000) for 9465 atoms. Found 45 (45 requested) and removed 65 (22 requested) atoms. Cycle 4: After refmac, R = 0.2616 (Rfree = 0.000) for 9338 atoms. Found 44 (44 requested) and removed 80 (22 requested) atoms. Cycle 5: After refmac, R = 0.2173 (Rfree = 0.000) for 9229 atoms. Found 26 (44 requested) and removed 46 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.90 Search for helices and strands: 0 residues in 0 chains, 9526 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 9539 seeds are put forward Round 1: 439 peptides, 90 chains. Longest chain 9 peptides. Score 0.276 Round 2: 520 peptides, 92 chains. Longest chain 14 peptides. Score 0.366 Round 3: 544 peptides, 95 chains. Longest chain 13 peptides. Score 0.379 Round 4: 564 peptides, 91 chains. Longest chain 17 peptides. Score 0.422 Round 5: 534 peptides, 81 chains. Longest chain 18 peptides. Score 0.438 Taking the results from Round 5 Chains 81, Residues 453, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21591 restraints for refining 9158 atoms. 19844 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2569 (Rfree = 0.000) for 9158 atoms. Found 43 (43 requested) and removed 108 (21 requested) atoms. Cycle 7: After refmac, R = 0.2527 (Rfree = 0.000) for 9002 atoms. Found 43 (43 requested) and removed 73 (21 requested) atoms. Cycle 8: After refmac, R = 0.2514 (Rfree = 0.000) for 8889 atoms. Found 42 (42 requested) and removed 69 (21 requested) atoms. Cycle 9: After refmac, R = 0.2470 (Rfree = 0.000) for 8799 atoms. Found 42 (42 requested) and removed 56 (21 requested) atoms. Cycle 10: After refmac, R = 0.2450 (Rfree = 0.000) for 8750 atoms. Found 41 (41 requested) and removed 51 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 9109 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 9135 seeds are put forward Round 1: 436 peptides, 89 chains. Longest chain 12 peptides. Score 0.278 Round 2: 499 peptides, 84 chains. Longest chain 16 peptides. Score 0.383 Round 3: 493 peptides, 81 chains. Longest chain 13 peptides. Score 0.391 Round 4: 493 peptides, 77 chains. Longest chain 13 peptides. Score 0.411 Round 5: 521 peptides, 81 chains. Longest chain 17 peptides. Score 0.423 Taking the results from Round 5 Chains 81, Residues 440, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21015 restraints for refining 9057 atoms. 19283 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2699 (Rfree = 0.000) for 9057 atoms. Found 43 (43 requested) and removed 102 (21 requested) atoms. Cycle 12: After refmac, R = 0.2627 (Rfree = 0.000) for 8889 atoms. Found 42 (42 requested) and removed 64 (21 requested) atoms. Cycle 13: After refmac, R = 0.2600 (Rfree = 0.000) for 8813 atoms. Found 42 (42 requested) and removed 59 (21 requested) atoms. Cycle 14: After refmac, R = 0.2474 (Rfree = 0.000) for 8753 atoms. Found 41 (41 requested) and removed 49 (20 requested) atoms. Cycle 15: After refmac, R = 0.2512 (Rfree = 0.000) for 8703 atoms. Found 41 (41 requested) and removed 41 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.94 Search for helices and strands: 0 residues in 0 chains, 8990 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 9009 seeds are put forward Round 1: 443 peptides, 87 chains. Longest chain 9 peptides. Score 0.298 Round 2: 528 peptides, 90 chains. Longest chain 18 peptides. Score 0.386 Round 3: 523 peptides, 87 chains. Longest chain 17 peptides. Score 0.395 Round 4: 500 peptides, 78 chains. Longest chain 26 peptides. Score 0.414 Round 5: 497 peptides, 74 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 5 Chains 74, Residues 423, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21114 restraints for refining 9060 atoms. 19496 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2695 (Rfree = 0.000) for 9060 atoms. Found 43 (43 requested) and removed 87 (21 requested) atoms. Cycle 17: After refmac, R = 0.2562 (Rfree = 0.000) for 8936 atoms. Found 42 (42 requested) and removed 70 (21 requested) atoms. Cycle 18: After refmac, R = 0.2563 (Rfree = 0.000) for 8837 atoms. Found 42 (42 requested) and removed 45 (21 requested) atoms. Cycle 19: After refmac, R = 0.2445 (Rfree = 0.000) for 8791 atoms. Found 41 (41 requested) and removed 45 (20 requested) atoms. Cycle 20: After refmac, R = 0.2555 (Rfree = 0.000) for 8761 atoms. Found 41 (41 requested) and removed 47 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.94 Search for helices and strands: 0 residues in 0 chains, 8992 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 9010 seeds are put forward Round 1: 407 peptides, 82 chains. Longest chain 10 peptides. Score 0.278 Round 2: 461 peptides, 79 chains. Longest chain 13 peptides. Score 0.363 Round 3: 493 peptides, 88 chains. Longest chain 12 peptides. Score 0.355 Round 4: 505 peptides, 81 chains. Longest chain 19 peptides. Score 0.405 Round 5: 502 peptides, 79 chains. Longest chain 16 peptides. Score 0.412 Taking the results from Round 5 Chains 81, Residues 423, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20801 restraints for refining 8971 atoms. 19140 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2618 (Rfree = 0.000) for 8971 atoms. Found 42 (42 requested) and removed 78 (21 requested) atoms. Cycle 22: After refmac, R = 0.2483 (Rfree = 0.000) for 8864 atoms. Found 42 (42 requested) and removed 67 (21 requested) atoms. Cycle 23: After refmac, R = 0.2446 (Rfree = 0.000) for 8791 atoms. Found 41 (41 requested) and removed 35 (20 requested) atoms. Cycle 24: After refmac, R = 0.2083 (Rfree = 0.000) for 8757 atoms. Found 21 (41 requested) and removed 33 (20 requested) atoms. Cycle 25: After refmac, R = 0.2040 (Rfree = 0.000) for 8710 atoms. Found 15 (41 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 8940 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8961 seeds are put forward Round 1: 399 peptides, 80 chains. Longest chain 11 peptides. Score 0.279 Round 2: 450 peptides, 76 chains. Longest chain 15 peptides. Score 0.366 Round 3: 480 peptides, 81 chains. Longest chain 13 peptides. Score 0.376 Round 4: 488 peptides, 80 chains. Longest chain 19 peptides. Score 0.390 Round 5: 472 peptides, 77 chains. Longest chain 16 peptides. Score 0.387 Taking the results from Round 4 Chains 80, Residues 408, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20905 restraints for refining 8989 atoms. 19348 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2565 (Rfree = 0.000) for 8989 atoms. Found 42 (42 requested) and removed 69 (21 requested) atoms. Cycle 27: After refmac, R = 0.2430 (Rfree = 0.000) for 8892 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Cycle 28: After refmac, R = 0.2396 (Rfree = 0.000) for 8835 atoms. Found 42 (42 requested) and removed 54 (21 requested) atoms. Cycle 29: After refmac, R = 0.2344 (Rfree = 0.000) for 8795 atoms. Found 41 (41 requested) and removed 34 (20 requested) atoms. Cycle 30: After refmac, R = 0.2389 (Rfree = 0.000) for 8770 atoms. Found 41 (41 requested) and removed 40 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.85 3.95 Search for helices and strands: 0 residues in 0 chains, 9015 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 9044 seeds are put forward Round 1: 354 peptides, 72 chains. Longest chain 11 peptides. Score 0.264 Round 2: 420 peptides, 74 chains. Longest chain 13 peptides. Score 0.340 Round 3: 433 peptides, 74 chains. Longest chain 14 peptides. Score 0.356 Round 4: 447 peptides, 72 chains. Longest chain 19 peptides. Score 0.384 Round 5: 475 peptides, 76 chains. Longest chain 21 peptides. Score 0.396 Taking the results from Round 5 Chains 78, Residues 399, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21113 restraints for refining 9063 atoms. 19522 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2509 (Rfree = 0.000) for 9063 atoms. Found 43 (43 requested) and removed 66 (21 requested) atoms. Cycle 32: After refmac, R = 0.2429 (Rfree = 0.000) for 8948 atoms. Found 42 (42 requested) and removed 51 (21 requested) atoms. Cycle 33: After refmac, R = 0.2094 (Rfree = 0.000) for 8870 atoms. Found 30 (42 requested) and removed 42 (21 requested) atoms. Cycle 34: After refmac, R = 0.1951 (Rfree = 0.000) for 8821 atoms. Found 16 (42 requested) and removed 33 (21 requested) atoms. Cycle 35: After refmac, R = 0.1912 (Rfree = 0.000) for 8789 atoms. Found 14 (41 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.92 Search for helices and strands: 0 residues in 0 chains, 8999 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 9018 seeds are put forward Round 1: 340 peptides, 72 chains. Longest chain 11 peptides. Score 0.245 Round 2: 420 peptides, 78 chains. Longest chain 11 peptides. Score 0.318 Round 3: 432 peptides, 78 chains. Longest chain 15 peptides. Score 0.333 Round 4: 443 peptides, 73 chains. Longest chain 17 peptides. Score 0.373 Round 5: 423 peptides, 73 chains. Longest chain 16 peptides. Score 0.349 Taking the results from Round 4 Chains 73, Residues 370, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20893 restraints for refining 8935 atoms. 19469 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2462 (Rfree = 0.000) for 8935 atoms. Found 42 (42 requested) and removed 75 (21 requested) atoms. Cycle 37: After refmac, R = 0.2405 (Rfree = 0.000) for 8852 atoms. Found 42 (42 requested) and removed 54 (21 requested) atoms. Cycle 38: After refmac, R = 0.2276 (Rfree = 0.000) for 8801 atoms. Found 42 (42 requested) and removed 54 (21 requested) atoms. Cycle 39: After refmac, R = 0.2448 (Rfree = 0.000) for 8754 atoms. Found 41 (41 requested) and removed 83 (20 requested) atoms. Cycle 40: After refmac, R = 0.2247 (Rfree = 0.000) for 8687 atoms. Found 41 (41 requested) and removed 53 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 8918 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 8946 seeds are put forward Round 1: 341 peptides, 74 chains. Longest chain 8 peptides. Score 0.234 Round 2: 379 peptides, 73 chains. Longest chain 11 peptides. Score 0.292 Round 3: 385 peptides, 73 chains. Longest chain 11 peptides. Score 0.300 Round 4: 398 peptides, 68 chains. Longest chain 11 peptides. Score 0.345 Round 5: 390 peptides, 65 chains. Longest chain 16 peptides. Score 0.352 Taking the results from Round 5 Chains 65, Residues 325, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20386 restraints for refining 8703 atoms. 19128 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2424 (Rfree = 0.000) for 8703 atoms. Found 41 (41 requested) and removed 63 (20 requested) atoms. Cycle 42: After refmac, R = 0.2421 (Rfree = 0.000) for 8631 atoms. Found 41 (41 requested) and removed 57 (20 requested) atoms. Cycle 43: After refmac, R = 0.2327 (Rfree = 0.000) for 8593 atoms. Found 40 (40 requested) and removed 51 (20 requested) atoms. Cycle 44: After refmac, R = 0.2394 (Rfree = 0.000) for 8552 atoms. Found 40 (40 requested) and removed 45 (20 requested) atoms. Cycle 45: After refmac, R = 0.2391 (Rfree = 0.000) for 8527 atoms. Found 40 (40 requested) and removed 45 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.93 Search for helices and strands: 0 residues in 0 chains, 8735 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 8753 seeds are put forward Round 1: 317 peptides, 70 chains. Longest chain 8 peptides. Score 0.223 Round 2: 374 peptides, 69 chains. Longest chain 14 peptides. Score 0.309 Round 3: 370 peptides, 69 chains. Longest chain 10 peptides. Score 0.303 Round 4: 366 peptides, 63 chains. Longest chain 14 peptides. Score 0.333 Round 5: 372 peptides, 64 chains. Longest chain 16 peptides. Score 0.335 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 308, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vrb-4_warpNtrace.pdb as input Building loops using Loopy2018 64 chains (308 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12677 reflections ( 99.37 % complete ) and 19706 restraints for refining 8529 atoms. 18514 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2612 (Rfree = 0.000) for 8529 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2586 (Rfree = 0.000) for 8462 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2522 (Rfree = 0.000) for 8403 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2502 (Rfree = 0.000) for 8369 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:05:18 GMT 2018 Job finished. TimeTaking 85.35 Used memory is bytes: 17024424