null Sun 23 Dec 23:47:47 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqr-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-mrncs ############### 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 ============================================================ Sun 23 Dec 23:47:52 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-mrncs/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 923 and 0 Target number of residues in the AU: 923 Target solvent content: 0.6017 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-3.4-parrot-mrncs.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-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 53.18 15170 reflections ( 88.81 % complete ) and 0 restraints for refining 10482 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3563 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3032 (Rfree = 0.000) for 10482 atoms. Found 79 (79 requested) and removed 135 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 10606 seeds are put forward NCS extension: 0 residues added, 10606 seeds are put forward Round 1: 291 peptides, 68 chains. Longest chain 8 peptides. Score 0.199 Round 2: 395 peptides, 82 chains. Longest chain 9 peptides. Score 0.271 Round 3: 414 peptides, 84 chains. Longest chain 9 peptides. Score 0.287 Round 4: 438 peptides, 84 chains. Longest chain 10 peptides. Score 0.321 Round 5: 448 peptides, 88 chains. Longest chain 12 peptides. Score 0.311 Taking the results from Round 4 Chains 84, Residues 354, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20995 restraints for refining 8639 atoms. 19663 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2675 (Rfree = 0.000) for 8639 atoms. Found 28 (65 requested) and removed 59 (32 requested) atoms. Cycle 2: After refmac, R = 0.2505 (Rfree = 0.000) for 8512 atoms. Found 26 (64 requested) and removed 43 (32 requested) atoms. Cycle 3: After refmac, R = 0.2357 (Rfree = 0.000) for 8444 atoms. Found 29 (64 requested) and removed 39 (32 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 8398 atoms. Found 25 (63 requested) and removed 45 (31 requested) atoms. Cycle 5: After refmac, R = 0.2301 (Rfree = 0.000) for 8349 atoms. Found 26 (63 requested) and removed 42 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.08 Search for helices and strands: 0 residues in 0 chains, 8604 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 8615 seeds are put forward Round 1: 399 peptides, 86 chains. Longest chain 9 peptides. Score 0.252 Round 2: 483 peptides, 92 chains. Longest chain 13 peptides. Score 0.336 Round 3: 474 peptides, 84 chains. Longest chain 15 peptides. Score 0.370 Round 4: 480 peptides, 83 chains. Longest chain 18 peptides. Score 0.384 Round 5: 491 peptides, 81 chains. Longest chain 16 peptides. Score 0.409 Taking the results from Round 5 Chains 81, Residues 410, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 19700 restraints for refining 8406 atoms. 18062 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2320 (Rfree = 0.000) for 8406 atoms. Found 46 (63 requested) and removed 55 (31 requested) atoms. Cycle 7: After refmac, R = 0.2176 (Rfree = 0.000) for 8345 atoms. Found 22 (63 requested) and removed 48 (31 requested) atoms. Cycle 8: After refmac, R = 0.2131 (Rfree = 0.000) for 8294 atoms. Found 20 (62 requested) and removed 43 (31 requested) atoms. Cycle 9: After refmac, R = 0.2093 (Rfree = 0.000) for 8249 atoms. Found 13 (62 requested) and removed 37 (31 requested) atoms. Cycle 10: After refmac, R = 0.2057 (Rfree = 0.000) for 8216 atoms. Found 12 (62 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.11 Search for helices and strands: 0 residues in 0 chains, 8477 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8498 seeds are put forward Round 1: 452 peptides, 95 chains. Longest chain 9 peptides. Score 0.275 Round 2: 458 peptides, 80 chains. Longest chain 19 peptides. Score 0.372 Round 3: 487 peptides, 86 chains. Longest chain 15 peptides. Score 0.376 Round 4: 466 peptides, 78 chains. Longest chain 13 peptides. Score 0.394 Round 5: 467 peptides, 76 chains. Longest chain 17 peptides. Score 0.407 Taking the results from Round 5 Chains 76, Residues 391, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20315 restraints for refining 8583 atoms. 18803 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2215 (Rfree = 0.000) for 8583 atoms. Found 38 (64 requested) and removed 61 (32 requested) atoms. Cycle 12: After refmac, R = 0.2089 (Rfree = 0.000) for 8532 atoms. Found 27 (64 requested) and removed 46 (32 requested) atoms. Cycle 13: After refmac, R = 0.2026 (Rfree = 0.000) for 8487 atoms. Found 27 (64 requested) and removed 42 (32 requested) atoms. Cycle 14: After refmac, R = 0.1986 (Rfree = 0.000) for 8460 atoms. Found 23 (63 requested) and removed 40 (31 requested) atoms. Cycle 15: After refmac, R = 0.1797 (Rfree = 0.000) for 8430 atoms. Found 9 (63 requested) and removed 33 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.13 Search for helices and strands: 0 residues in 0 chains, 8670 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8686 seeds are put forward Round 1: 406 peptides, 83 chains. Longest chain 10 peptides. Score 0.281 Round 2: 469 peptides, 82 chains. Longest chain 14 peptides. Score 0.375 Round 3: 484 peptides, 80 chains. Longest chain 14 peptides. Score 0.406 Round 4: 479 peptides, 84 chains. Longest chain 15 peptides. Score 0.377 Round 5: 503 peptides, 84 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 5 Chains 84, Residues 419, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20316 restraints for refining 8641 atoms. 18724 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2138 (Rfree = 0.000) for 8641 atoms. Found 33 (65 requested) and removed 50 (32 requested) atoms. Cycle 17: After refmac, R = 0.2017 (Rfree = 0.000) for 8603 atoms. Found 34 (65 requested) and removed 41 (32 requested) atoms. Cycle 18: After refmac, R = 0.1969 (Rfree = 0.000) for 8581 atoms. Found 26 (64 requested) and removed 40 (32 requested) atoms. Cycle 19: After refmac, R = 0.1917 (Rfree = 0.000) for 8553 atoms. Found 23 (64 requested) and removed 39 (32 requested) atoms. Cycle 20: After refmac, R = 0.1868 (Rfree = 0.000) for 8528 atoms. Found 24 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 8739 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 8759 seeds are put forward Round 1: 424 peptides, 85 chains. Longest chain 9 peptides. Score 0.295 Round 2: 485 peptides, 89 chains. Longest chain 13 peptides. Score 0.356 Round 3: 477 peptides, 87 chains. Longest chain 18 peptides. Score 0.357 Round 4: 460 peptides, 76 chains. Longest chain 16 peptides. Score 0.397 Round 5: 471 peptides, 78 chains. Longest chain 19 peptides. Score 0.400 Taking the results from Round 5 Chains 78, Residues 393, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20680 restraints for refining 8641 atoms. 19186 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2078 (Rfree = 0.000) for 8641 atoms. Found 43 (65 requested) and removed 37 (32 requested) atoms. Cycle 22: After refmac, R = 0.1968 (Rfree = 0.000) for 8615 atoms. Found 32 (65 requested) and removed 34 (32 requested) atoms. Cycle 23: After refmac, R = 0.1886 (Rfree = 0.000) for 8598 atoms. Found 18 (65 requested) and removed 37 (32 requested) atoms. Cycle 24: After refmac, R = 0.1794 (Rfree = 0.000) for 8567 atoms. Found 23 (64 requested) and removed 36 (32 requested) atoms. Cycle 25: After refmac, R = 0.1738 (Rfree = 0.000) for 8547 atoms. Found 12 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 8757 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 8780 seeds are put forward Round 1: 417 peptides, 86 chains. Longest chain 9 peptides. Score 0.279 Round 2: 446 peptides, 81 chains. Longest chain 12 peptides. Score 0.350 Round 3: 488 peptides, 82 chains. Longest chain 18 peptides. Score 0.400 Round 4: 492 peptides, 83 chains. Longest chain 16 peptides. Score 0.399 Round 5: 489 peptides, 81 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 5 Chains 81, Residues 408, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20225 restraints for refining 8641 atoms. 18637 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2077 (Rfree = 0.000) for 8641 atoms. Found 46 (65 requested) and removed 35 (32 requested) atoms. Cycle 27: After refmac, R = 0.1940 (Rfree = 0.000) for 8627 atoms. Found 17 (65 requested) and removed 35 (32 requested) atoms. Cycle 28: After refmac, R = 0.1947 (Rfree = 0.000) for 8589 atoms. Found 22 (65 requested) and removed 32 (32 requested) atoms. Cycle 29: After refmac, R = 0.1909 (Rfree = 0.000) for 8565 atoms. Found 24 (64 requested) and removed 36 (32 requested) atoms. Cycle 30: After refmac, R = 0.1846 (Rfree = 0.000) for 8549 atoms. Found 16 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 8770 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 8795 seeds are put forward Round 1: 378 peptides, 80 chains. Longest chain 12 peptides. Score 0.258 Round 2: 458 peptides, 82 chains. Longest chain 12 peptides. Score 0.360 Round 3: 446 peptides, 80 chains. Longest chain 13 peptides. Score 0.356 Round 4: 449 peptides, 76 chains. Longest chain 16 peptides. Score 0.383 Round 5: 460 peptides, 77 chains. Longest chain 13 peptides. Score 0.392 Taking the results from Round 5 Chains 78, Residues 383, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20383 restraints for refining 8640 atoms. 18852 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2075 (Rfree = 0.000) for 8640 atoms. Found 50 (65 requested) and removed 35 (32 requested) atoms. Cycle 32: After refmac, R = 0.1912 (Rfree = 0.000) for 8632 atoms. Found 22 (65 requested) and removed 33 (32 requested) atoms. Cycle 33: After refmac, R = 0.1860 (Rfree = 0.000) for 8604 atoms. Found 24 (65 requested) and removed 36 (32 requested) atoms. Cycle 34: After refmac, R = 0.1819 (Rfree = 0.000) for 8584 atoms. Found 19 (64 requested) and removed 35 (32 requested) atoms. Cycle 35: After refmac, R = 0.1776 (Rfree = 0.000) for 8557 atoms. Found 19 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 8788 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8800 seeds are put forward Round 1: 374 peptides, 79 chains. Longest chain 12 peptides. Score 0.259 Round 2: 411 peptides, 79 chains. Longest chain 12 peptides. Score 0.313 Round 3: 430 peptides, 78 chains. Longest chain 14 peptides. Score 0.346 Round 4: 429 peptides, 77 chains. Longest chain 14 peptides. Score 0.350 Round 5: 440 peptides, 81 chains. Longest chain 16 peptides. Score 0.342 Taking the results from Round 4 Chains 77, Residues 352, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20327 restraints for refining 8639 atoms. 18972 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1940 (Rfree = 0.000) for 8639 atoms. Found 31 (65 requested) and removed 35 (32 requested) atoms. Cycle 37: After refmac, R = 0.1869 (Rfree = 0.000) for 8620 atoms. Found 15 (65 requested) and removed 32 (32 requested) atoms. Cycle 38: After refmac, R = 0.1860 (Rfree = 0.000) for 8596 atoms. Found 20 (64 requested) and removed 33 (32 requested) atoms. Cycle 39: After refmac, R = 0.1842 (Rfree = 0.000) for 8574 atoms. Found 22 (64 requested) and removed 32 (32 requested) atoms. Cycle 40: After refmac, R = 0.1771 (Rfree = 0.000) for 8562 atoms. Found 20 (64 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 8758 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8776 seeds are put forward Round 1: 368 peptides, 77 chains. Longest chain 11 peptides. Score 0.262 Round 2: 395 peptides, 75 chains. Longest chain 13 peptides. Score 0.314 Round 3: 399 peptides, 74 chains. Longest chain 14 peptides. Score 0.326 Round 4: 401 peptides, 70 chains. Longest chain 14 peptides. Score 0.353 Round 5: 404 peptides, 72 chains. Longest chain 14 peptides. Score 0.345 Taking the results from Round 4 Chains 72, Residues 331, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20474 restraints for refining 8640 atoms. 19112 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 8640 atoms. Found 21 (65 requested) and removed 39 (32 requested) atoms. Cycle 42: After refmac, R = 0.1807 (Rfree = 0.000) for 8602 atoms. Found 18 (65 requested) and removed 36 (32 requested) atoms. Cycle 43: After refmac, R = 0.1754 (Rfree = 0.000) for 8576 atoms. Found 17 (64 requested) and removed 34 (32 requested) atoms. Cycle 44: After refmac, R = 0.1714 (Rfree = 0.000) for 8556 atoms. Found 13 (64 requested) and removed 32 (32 requested) atoms. Cycle 45: After refmac, R = 0.1704 (Rfree = 0.000) for 8529 atoms. Found 11 (64 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.16 Search for helices and strands: 0 residues in 0 chains, 8738 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8753 seeds are put forward Round 1: 333 peptides, 74 chains. Longest chain 8 peptides. Score 0.227 Round 2: 380 peptides, 76 chains. Longest chain 12 peptides. Score 0.286 Round 3: 386 peptides, 76 chains. Longest chain 10 peptides. Score 0.295 Round 4: 390 peptides, 73 chains. Longest chain 14 peptides. Score 0.320 Round 5: 409 peptides, 75 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 334, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input Building loops using Loopy2018 75 chains (334 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15170 reflections ( 88.81 % complete ) and 20412 restraints for refining 8641 atoms. 19123 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1944 (Rfree = 0.000) for 8641 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1901 (Rfree = 0.000) for 8594 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 8558 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1808 (Rfree = 0.000) for 8514 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:26:02 GMT 2018 Job finished. TimeTaking 98.26 Used memory is bytes: 8737880