Sun 23 Dec 23:48:16 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 1vrb-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-4.0-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/1vrb-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-4.0-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 23:48:21 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/1vrb-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-4.0-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 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-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-4.0-parrot-mrncs.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 12048 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3525 (Rfree = 0.000) for 12048 atoms. Found 57 (57 requested) and removed 327 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 3.95 Search for helices and strands: 0 residues in 0 chains, 11925 seeds are put forward NCS extension: 0 residues added, 11925 seeds are put forward Round 1: 283 peptides, 61 chains. Longest chain 9 peptides. Score 0.229 Round 2: 413 peptides, 79 chains. Longest chain 16 peptides. Score 0.303 Round 3: 450 peptides, 78 chains. Longest chain 16 peptides. Score 0.355 Round 4: 486 peptides, 85 chains. Longest chain 16 peptides. Score 0.362 Round 5: 502 peptides, 86 chains. Longest chain 19 peptides. Score 0.376 Taking the results from Round 5 Chains 90, Residues 416, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 24541 restraints for refining 9882 atoms. 22893 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2837 (Rfree = 0.000) for 9882 atoms. Found 38 (46 requested) and removed 102 (23 requested) atoms. Cycle 2: After refmac, R = 0.2671 (Rfree = 0.000) for 9641 atoms. Found 40 (46 requested) and removed 96 (23 requested) atoms. Cycle 3: After refmac, R = 0.2632 (Rfree = 0.000) for 9456 atoms. Found 45 (45 requested) and removed 70 (22 requested) atoms. Cycle 4: After refmac, R = 0.2578 (Rfree = 0.000) for 9345 atoms. Found 44 (44 requested) and removed 65 (22 requested) atoms. Cycle 5: After refmac, R = 0.2510 (Rfree = 0.000) for 9261 atoms. Found 44 (44 requested) and removed 54 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 9577 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 9597 seeds are put forward Round 1: 407 peptides, 81 chains. Longest chain 10 peptides. Score 0.284 Round 2: 520 peptides, 90 chains. Longest chain 16 peptides. Score 0.377 Round 3: 538 peptides, 89 chains. Longest chain 14 peptides. Score 0.403 Round 4: 538 peptides, 85 chains. Longest chain 16 peptides. Score 0.422 Round 5: 576 peptides, 88 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 5 Chains 88, Residues 488, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20217 restraints for refining 8823 atoms. 18291 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2524 (Rfree = 0.000) for 8823 atoms. Found 41 (41 requested) and removed 78 (20 requested) atoms. Cycle 7: After refmac, R = 0.2439 (Rfree = 0.000) for 8659 atoms. Found 37 (41 requested) and removed 54 (20 requested) atoms. Cycle 8: After refmac, R = 0.2290 (Rfree = 0.000) for 8566 atoms. Found 34 (41 requested) and removed 57 (20 requested) atoms. Cycle 9: After refmac, R = 0.2308 (Rfree = 0.000) for 8498 atoms. Found 37 (40 requested) and removed 47 (20 requested) atoms. Cycle 10: After refmac, R = 0.1893 (Rfree = 0.000) for 8458 atoms. Found 9 (40 requested) and removed 34 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 8778 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8794 seeds are put forward Round 1: 452 peptides, 87 chains. Longest chain 11 peptides. Score 0.309 Round 2: 567 peptides, 90 chains. Longest chain 19 peptides. Score 0.430 Round 3: 561 peptides, 79 chains. Longest chain 19 peptides. Score 0.476 Round 4: 556 peptides, 83 chains. Longest chain 20 peptides. Score 0.452 Round 5: 553 peptides, 77 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 5 Chains 77, Residues 476, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 19568 restraints for refining 8782 atoms. 17658 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2475 (Rfree = 0.000) for 8782 atoms. Found 41 (41 requested) and removed 98 (20 requested) atoms. Cycle 12: After refmac, R = 0.2389 (Rfree = 0.000) for 8650 atoms. Found 41 (41 requested) and removed 57 (20 requested) atoms. Cycle 13: After refmac, R = 0.2343 (Rfree = 0.000) for 8584 atoms. Found 41 (41 requested) and removed 46 (20 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2317 (Rfree = 0.000) for 8550 atoms. Found 40 (40 requested) and removed 53 (20 requested) atoms. Cycle 15: After refmac, R = 0.2373 (Rfree = 0.000) for 8501 atoms. Found 40 (40 requested) and removed 64 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 8889 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8909 seeds are put forward Round 1: 467 peptides, 98 chains. Longest chain 15 peptides. Score 0.269 Round 2: 538 peptides, 93 chains. Longest chain 21 peptides. Score 0.382 Round 3: 560 peptides, 91 chains. Longest chain 27 peptides. Score 0.417 Round 4: 568 peptides, 89 chains. Longest chain 21 peptides. Score 0.436 Round 5: 577 peptides, 91 chains. Longest chain 21 peptides. Score 0.436 Taking the results from Round 5 Chains 93, Residues 486, Estimated correctness of the model 0.0 % 7 chains (39 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12677 reflections ( 99.37 % complete ) and 20209 restraints for refining 9085 atoms. 18227 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2458 (Rfree = 0.000) for 9085 atoms. Found 43 (43 requested) and removed 88 (21 requested) atoms. Cycle 17: After refmac, R = 0.2385 (Rfree = 0.000) for 8940 atoms. Found 42 (42 requested) and removed 77 (21 requested) atoms. Cycle 18: After refmac, R = 0.2349 (Rfree = 0.000) for 8849 atoms. Found 42 (42 requested) and removed 63 (21 requested) atoms. Cycle 19: After refmac, R = 0.2329 (Rfree = 0.000) for 8781 atoms. Found 41 (41 requested) and removed 59 (20 requested) atoms. Cycle 20: After refmac, R = 0.2299 (Rfree = 0.000) for 8727 atoms. Found 41 (41 requested) and removed 44 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 9074 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 9096 seeds are put forward Round 1: 428 peptides, 89 chains. Longest chain 13 peptides. Score 0.267 Round 2: 501 peptides, 88 chains. Longest chain 18 peptides. Score 0.364 Round 3: 515 peptides, 85 chains. Longest chain 18 peptides. Score 0.396 Round 4: 504 peptides, 77 chains. Longest chain 22 peptides. Score 0.424 Round 5: 510 peptides, 78 chains. Longest chain 20 peptides. Score 0.426 Taking the results from Round 5 Chains 81, Residues 432, Estimated correctness of the model 0.0 % 8 chains (46 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20546 restraints for refining 9137 atoms. 18731 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2320 (Rfree = 0.000) for 9137 atoms. Found 43 (43 requested) and removed 103 (21 requested) atoms. Cycle 22: After refmac, R = 0.2393 (Rfree = 0.000) for 9029 atoms. Found 43 (43 requested) and removed 73 (21 requested) atoms. Cycle 23: After refmac, R = 0.2275 (Rfree = 0.000) for 8956 atoms. Found 42 (42 requested) and removed 51 (21 requested) atoms. Cycle 24: After refmac, R = 0.2378 (Rfree = 0.000) for 8910 atoms. Found 42 (42 requested) and removed 63 (21 requested) atoms. Cycle 25: After refmac, R = 0.2317 (Rfree = 0.000) for 8845 atoms. Found 42 (42 requested) and removed 49 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 9147 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 9172 seeds are put forward Round 1: 432 peptides, 92 chains. Longest chain 10 peptides. Score 0.256 Round 2: 492 peptides, 88 chains. Longest chain 17 peptides. Score 0.353 Round 3: 495 peptides, 82 chains. Longest chain 20 peptides. Score 0.388 Round 4: 494 peptides, 85 chains. Longest chain 25 peptides. Score 0.372 Round 5: 501 peptides, 86 chains. Longest chain 17 peptides. Score 0.375 Taking the results from Round 3 Chains 82, Residues 413, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21154 restraints for refining 9130 atoms. 19584 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2404 (Rfree = 0.000) for 9130 atoms. Found 43 (43 requested) and removed 80 (21 requested) atoms. Cycle 27: After refmac, R = 0.2354 (Rfree = 0.000) for 9037 atoms. Found 43 (43 requested) and removed 63 (21 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2375 (Rfree = 0.000) for 8973 atoms. Found 42 (42 requested) and removed 53 (21 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2427 (Rfree = 0.000) for 8940 atoms. Found 42 (42 requested) and removed 60 (21 requested) atoms. Cycle 30: After refmac, R = 0.2433 (Rfree = 0.000) for 8896 atoms. Found 42 (42 requested) and removed 45 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 9231 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 9242 seeds are put forward Round 1: 381 peptides, 81 chains. Longest chain 15 peptides. Score 0.249 Round 2: 449 peptides, 80 chains. Longest chain 17 peptides. Score 0.343 Round 3: 457 peptides, 80 chains. Longest chain 15 peptides. Score 0.353 Round 4: 457 peptides, 72 chains. Longest chain 20 peptides. Score 0.396 Round 5: 432 peptides, 70 chains. Longest chain 17 peptides. Score 0.376 Taking the results from Round 4 Chains 73, Residues 385, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20966 restraints for refining 9081 atoms. 19439 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2478 (Rfree = 0.000) for 9081 atoms. Found 43 (43 requested) and removed 73 (21 requested) atoms. Cycle 32: After refmac, R = 0.2432 (Rfree = 0.000) for 9017 atoms. Found 43 (43 requested) and removed 71 (21 requested) atoms. Cycle 33: After refmac, R = 0.2433 (Rfree = 0.000) for 8956 atoms. Found 42 (42 requested) and removed 58 (21 requested) atoms. Cycle 34: After refmac, R = 0.2153 (Rfree = 0.000) for 8912 atoms. Found 14 (42 requested) and removed 42 (21 requested) atoms. Cycle 35: After refmac, R = 0.2057 (Rfree = 0.000) for 8864 atoms. Found 9 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 9135 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 9161 seeds are put forward Round 1: 347 peptides, 73 chains. Longest chain 8 peptides. Score 0.249 Round 2: 437 peptides, 81 chains. Longest chain 10 peptides. Score 0.323 Round 3: 440 peptides, 75 chains. Longest chain 19 peptides. Score 0.359 Round 4: 459 peptides, 78 chains. Longest chain 12 peptides. Score 0.366 Round 5: 433 peptides, 75 chains. Longest chain 16 peptides. Score 0.351 Taking the results from Round 4 Chains 78, Residues 381, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 20633 restraints for refining 9073 atoms. 19077 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2480 (Rfree = 0.000) for 9073 atoms. Found 43 (43 requested) and removed 73 (21 requested) atoms. Cycle 37: After refmac, R = 0.2440 (Rfree = 0.000) for 9000 atoms. Found 42 (42 requested) and removed 51 (21 requested) atoms. Cycle 38: After refmac, R = 0.2394 (Rfree = 0.000) for 8967 atoms. Found 42 (42 requested) and removed 47 (21 requested) atoms. Cycle 39: After refmac, R = 0.2318 (Rfree = 0.000) for 8931 atoms. Found 42 (42 requested) and removed 42 (21 requested) atoms. Cycle 40: After refmac, R = 0.2087 (Rfree = 0.000) for 8913 atoms. Found 13 (42 requested) and removed 34 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 9155 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 9168 seeds are put forward Round 1: 347 peptides, 72 chains. Longest chain 8 peptides. Score 0.254 Round 2: 441 peptides, 81 chains. Longest chain 13 peptides. Score 0.328 Round 3: 435 peptides, 77 chains. Longest chain 12 peptides. Score 0.342 Round 4: 424 peptides, 74 chains. Longest chain 14 peptides. Score 0.345 Round 5: 414 peptides, 75 chains. Longest chain 14 peptides. Score 0.327 Taking the results from Round 4 Chains 74, Residues 350, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12677 reflections ( 99.37 % complete ) and 21303 restraints for refining 9088 atoms. 19965 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2665 (Rfree = 0.000) for 9088 atoms. Found 43 (43 requested) and removed 79 (21 requested) atoms. Cycle 42: After refmac, R = 0.2559 (Rfree = 0.000) for 9006 atoms. Found 43 (43 requested) and removed 54 (21 requested) atoms. Cycle 43: After refmac, R = 0.2207 (Rfree = 0.000) for 8965 atoms. Found 27 (42 requested) and removed 46 (21 requested) atoms. Cycle 44: After refmac, R = 0.2085 (Rfree = 0.000) for 8927 atoms. Found 19 (42 requested) and removed 33 (21 requested) atoms. Cycle 45: After refmac, R = 0.2210 (Rfree = 0.000) for 8899 atoms. Found 15 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.95 Search for helices and strands: 0 residues in 0 chains, 9130 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 9148 seeds are put forward Round 1: 333 peptides, 71 chains. Longest chain 9 peptides. Score 0.241 Round 2: 352 peptides, 67 chains. Longest chain 15 peptides. Score 0.291 Round 3: 363 peptides, 63 chains. Longest chain 14 peptides. Score 0.329 Round 4: 346 peptides, 60 chains. Longest chain 15 peptides. Score 0.324 Round 5: 364 peptides, 60 chains. Longest chain 13 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 304, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vrb-4_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (304 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12677 reflections ( 99.37 % complete ) and 21590 restraints for refining 9124 atoms. 20404 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2617 (Rfree = 0.000) for 9124 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2643 (Rfree = 0.000) for 9066 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2468 (Rfree = 0.000) for 9021 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2560 (Rfree = 0.000) for 8977 atoms. TimeTaking 104.82