Mon 24 Dec 00:39:11 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 1vme-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-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/1vme-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-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 ============================================================ Mon 24 Dec 00:39:16 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/1vme-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-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 623 and 0 Target number of residues in the AU: 623 Target solvent content: 0.6451 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.70 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: 48.998 3.400 Wilson plot Bfac: 74.80 12971 reflections ( 99.85 % complete ) and 0 restraints for refining 7298 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3113 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2841 (Rfree = 0.000) for 7298 atoms. Found 55 (55 requested) and removed 63 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 7461 seeds are put forward NCS extension: 0 residues added, 7461 seeds are put forward Round 1: 442 peptides, 74 chains. Longest chain 13 peptides. Score 0.434 Round 2: 485 peptides, 65 chains. Longest chain 17 peptides. Score 0.557 Round 3: 534 peptides, 66 chains. Longest chain 19 peptides. Score 0.614 Round 4: 551 peptides, 64 chains. Longest chain 29 peptides. Score 0.645 Round 5: 575 peptides, 62 chains. Longest chain 24 peptides. Score 0.681 Taking the results from Round 5 Chains 62, Residues 513, Estimated correctness of the model 52.9 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12692 restraints for refining 5961 atoms. 10633 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 5961 atoms. Found 29 (45 requested) and removed 42 (22 requested) atoms. Cycle 2: After refmac, R = 0.2314 (Rfree = 0.000) for 5886 atoms. Found 19 (44 requested) and removed 39 (22 requested) atoms. Cycle 3: After refmac, R = 0.2265 (Rfree = 0.000) for 5832 atoms. Found 26 (44 requested) and removed 33 (22 requested) atoms. Cycle 4: After refmac, R = 0.2248 (Rfree = 0.000) for 5813 atoms. Found 10 (43 requested) and removed 31 (21 requested) atoms. Cycle 5: After refmac, R = 0.2221 (Rfree = 0.000) for 5782 atoms. Found 11 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 5924 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5946 seeds are put forward Round 1: 502 peptides, 68 chains. Longest chain 20 peptides. Score 0.562 Round 2: 530 peptides, 59 chains. Longest chain 28 peptides. Score 0.647 Round 3: 542 peptides, 59 chains. Longest chain 27 peptides. Score 0.660 Round 4: 552 peptides, 59 chains. Longest chain 30 peptides. Score 0.671 Round 5: 549 peptides, 61 chains. Longest chain 26 peptides. Score 0.658 Taking the results from Round 4 Chains 61, Residues 493, Estimated correctness of the model 50.1 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12254 restraints for refining 5964 atoms. 10096 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2375 (Rfree = 0.000) for 5964 atoms. Found 40 (45 requested) and removed 42 (22 requested) atoms. Cycle 7: After refmac, R = 0.2223 (Rfree = 0.000) for 5931 atoms. Found 14 (45 requested) and removed 32 (22 requested) atoms. Cycle 8: After refmac, R = 0.2207 (Rfree = 0.000) for 5898 atoms. Found 12 (44 requested) and removed 27 (22 requested) atoms. Cycle 9: After refmac, R = 0.2187 (Rfree = 0.000) for 5873 atoms. Found 9 (44 requested) and removed 23 (22 requested) atoms. Cycle 10: After refmac, R = 0.2143 (Rfree = 0.000) for 5854 atoms. Found 11 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 6035 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 6064 seeds are put forward Round 1: 484 peptides, 69 chains. Longest chain 18 peptides. Score 0.531 Round 2: 539 peptides, 62 chains. Longest chain 25 peptides. Score 0.642 Round 3: 534 peptides, 59 chains. Longest chain 22 peptides. Score 0.651 Round 4: 519 peptides, 63 chains. Longest chain 22 peptides. Score 0.612 Round 5: 539 peptides, 61 chains. Longest chain 19 peptides. Score 0.647 Taking the results from Round 3 Chains 64, Residues 475, Estimated correctness of the model 44.4 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12554 restraints for refining 5965 atoms. 10492 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2353 (Rfree = 0.000) for 5965 atoms. Found 32 (45 requested) and removed 34 (22 requested) atoms. Cycle 12: After refmac, R = 0.2250 (Rfree = 0.000) for 5948 atoms. Found 13 (45 requested) and removed 25 (22 requested) atoms. Cycle 13: After refmac, R = 0.2281 (Rfree = 0.000) for 5928 atoms. Found 7 (44 requested) and removed 23 (22 requested) atoms. Cycle 14: After refmac, R = 0.2305 (Rfree = 0.000) for 5904 atoms. Found 11 (44 requested) and removed 23 (22 requested) atoms. Cycle 15: After refmac, R = 0.2305 (Rfree = 0.000) for 5890 atoms. Found 9 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6035 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6051 seeds are put forward Round 1: 488 peptides, 67 chains. Longest chain 22 peptides. Score 0.549 Round 2: 513 peptides, 64 chains. Longest chain 20 peptides. Score 0.599 Round 3: 524 peptides, 59 chains. Longest chain 30 peptides. Score 0.640 Round 4: 533 peptides, 62 chains. Longest chain 26 peptides. Score 0.635 Round 5: 543 peptides, 63 chains. Longest chain 28 peptides. Score 0.641 Taking the results from Round 5 Chains 65, Residues 480, Estimated correctness of the model 41.5 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12960 restraints for refining 5965 atoms. 11012 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2397 (Rfree = 0.000) for 5965 atoms. Found 28 (45 requested) and removed 33 (22 requested) atoms. Cycle 17: After refmac, R = 0.2268 (Rfree = 0.000) for 5937 atoms. Found 9 (45 requested) and removed 26 (22 requested) atoms. Cycle 18: After refmac, R = 0.2235 (Rfree = 0.000) for 5908 atoms. Found 11 (44 requested) and removed 25 (22 requested) atoms. Cycle 19: After refmac, R = 0.2188 (Rfree = 0.000) for 5884 atoms. Found 9 (44 requested) and removed 26 (22 requested) atoms. Cycle 20: After refmac, R = 0.2167 (Rfree = 0.000) for 5864 atoms. Found 11 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6038 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6054 seeds are put forward Round 1: 455 peptides, 70 chains. Longest chain 18 peptides. Score 0.482 Round 2: 516 peptides, 59 chains. Longest chain 28 peptides. Score 0.631 Round 3: 509 peptides, 64 chains. Longest chain 26 peptides. Score 0.594 Round 4: 524 peptides, 59 chains. Longest chain 28 peptides. Score 0.640 Round 5: 513 peptides, 56 chains. Longest chain 28 peptides. Score 0.643 Taking the results from Round 5 Chains 59, Residues 457, Estimated correctness of the model 42.1 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12857 restraints for refining 5965 atoms. 10923 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2381 (Rfree = 0.000) for 5965 atoms. Found 34 (45 requested) and removed 32 (22 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2250 (Rfree = 0.000) for 5960 atoms. Found 10 (45 requested) and removed 25 (22 requested) atoms. Cycle 23: After refmac, R = 0.2208 (Rfree = 0.000) for 5937 atoms. Found 13 (44 requested) and removed 23 (22 requested) atoms. Cycle 24: After refmac, R = 0.2188 (Rfree = 0.000) for 5925 atoms. Found 11 (44 requested) and removed 23 (22 requested) atoms. Cycle 25: After refmac, R = 0.2166 (Rfree = 0.000) for 5911 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6068 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6085 seeds are put forward Round 1: 438 peptides, 62 chains. Longest chain 22 peptides. Score 0.509 Round 2: 494 peptides, 59 chains. Longest chain 24 peptides. Score 0.604 Round 3: 511 peptides, 56 chains. Longest chain 25 peptides. Score 0.641 Round 4: 507 peptides, 59 chains. Longest chain 20 peptides. Score 0.620 Round 5: 506 peptides, 55 chains. Longest chain 31 peptides. Score 0.641 Taking the results from Round 5 Chains 56, Residues 451, Estimated correctness of the model 41.5 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12767 restraints for refining 5963 atoms. 10827 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2421 (Rfree = 0.000) for 5963 atoms. Found 26 (45 requested) and removed 31 (22 requested) atoms. Cycle 27: After refmac, R = 0.2306 (Rfree = 0.000) for 5946 atoms. Found 21 (44 requested) and removed 26 (22 requested) atoms. Cycle 28: After refmac, R = 0.2286 (Rfree = 0.000) for 5932 atoms. Found 24 (44 requested) and removed 24 (22 requested) atoms. Cycle 29: After refmac, R = 0.2226 (Rfree = 0.000) for 5924 atoms. Found 25 (44 requested) and removed 26 (22 requested) atoms. Cycle 30: After refmac, R = 0.2223 (Rfree = 0.000) for 5917 atoms. Found 12 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6074 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 6093 seeds are put forward Round 1: 393 peptides, 63 chains. Longest chain 16 peptides. Score 0.432 Round 2: 447 peptides, 61 chains. Longest chain 23 peptides. Score 0.529 Round 3: 465 peptides, 59 chains. Longest chain 19 peptides. Score 0.566 Round 4: 464 peptides, 59 chains. Longest chain 24 peptides. Score 0.565 Round 5: 459 peptides, 55 chains. Longest chain 25 peptides. Score 0.582 Taking the results from Round 5 Chains 55, Residues 404, Estimated correctness of the model 22.7 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13163 restraints for refining 5965 atoms. 11494 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2273 (Rfree = 0.000) for 5965 atoms. Found 26 (45 requested) and removed 34 (22 requested) atoms. Cycle 32: After refmac, R = 0.2131 (Rfree = 0.000) for 5944 atoms. Found 12 (44 requested) and removed 25 (22 requested) atoms. Cycle 33: After refmac, R = 0.2110 (Rfree = 0.000) for 5928 atoms. Found 10 (44 requested) and removed 24 (22 requested) atoms. Cycle 34: After refmac, R = 0.2067 (Rfree = 0.000) for 5911 atoms. Found 8 (44 requested) and removed 23 (22 requested) atoms. Cycle 35: After refmac, R = 0.2051 (Rfree = 0.000) for 5893 atoms. Found 10 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6036 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 6071 seeds are put forward Round 1: 413 peptides, 71 chains. Longest chain 14 peptides. Score 0.408 Round 2: 445 peptides, 62 chains. Longest chain 20 peptides. Score 0.519 Round 3: 438 peptides, 61 chains. Longest chain 19 peptides. Score 0.516 Round 4: 462 peptides, 63 chains. Longest chain 20 peptides. Score 0.537 Round 5: 452 peptides, 63 chains. Longest chain 21 peptides. Score 0.523 Taking the results from Round 4 Chains 65, Residues 399, Estimated correctness of the model 6.8 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13094 restraints for refining 5965 atoms. 11354 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2243 (Rfree = 0.000) for 5965 atoms. Found 38 (45 requested) and removed 37 (22 requested) atoms. Cycle 37: After refmac, R = 0.2053 (Rfree = 0.000) for 5951 atoms. Found 9 (45 requested) and removed 23 (22 requested) atoms. Cycle 38: After refmac, R = 0.2010 (Rfree = 0.000) for 5932 atoms. Found 10 (44 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.1954 (Rfree = 0.000) for 5915 atoms. Found 5 (44 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.1959 (Rfree = 0.000) for 5897 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6033 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6058 seeds are put forward Round 1: 387 peptides, 64 chains. Longest chain 16 peptides. Score 0.415 Round 2: 425 peptides, 57 chains. Longest chain 20 peptides. Score 0.523 Round 3: 425 peptides, 55 chains. Longest chain 17 peptides. Score 0.536 Round 4: 441 peptides, 56 chains. Longest chain 20 peptides. Score 0.552 Round 5: 442 peptides, 56 chains. Longest chain 19 peptides. Score 0.553 Taking the results from Round 5 Chains 58, Residues 386, Estimated correctness of the model 12.6 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13337 restraints for refining 5965 atoms. 11746 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2160 (Rfree = 0.000) for 5965 atoms. Found 20 (45 requested) and removed 24 (22 requested) atoms. Cycle 42: After refmac, R = 0.2151 (Rfree = 0.000) for 5948 atoms. Found 24 (45 requested) and removed 26 (22 requested) atoms. Cycle 43: After refmac, R = 0.2047 (Rfree = 0.000) for 5939 atoms. Found 13 (44 requested) and removed 23 (22 requested) atoms. Cycle 44: After refmac, R = 0.2035 (Rfree = 0.000) for 5921 atoms. Found 9 (44 requested) and removed 26 (22 requested) atoms. Cycle 45: After refmac, R = 0.1972 (Rfree = 0.000) for 5902 atoms. Found 11 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6055 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6070 seeds are put forward Round 1: 376 peptides, 62 chains. Longest chain 15 peptides. Score 0.411 Round 2: 386 peptides, 51 chains. Longest chain 20 peptides. Score 0.505 Round 3: 402 peptides, 56 chains. Longest chain 18 peptides. Score 0.495 Round 4: 424 peptides, 58 chains. Longest chain 17 peptides. Score 0.515 Round 5: 413 peptides, 53 chains. Longest chain 18 peptides. Score 0.532 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 360, Estimated correctness of the model 4.9 % 4 chains (27 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (360 residues) following loop building 4 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12971 reflections ( 99.85 % complete ) and 13291 restraints for refining 5964 atoms. 11813 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2125 (Rfree = 0.000) for 5964 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2084 (Rfree = 0.000) for 5930 atoms. Found 0 (44 requested) and removed 20 (22 requested) atoms. Cycle 48: After refmac, R = 0.2066 (Rfree = 0.000) for 5896 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2046 (Rfree = 0.000) for 5869 atoms. TimeTaking 73.95