Mon 24 Dec 00:35:17 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 2gvh-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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 00:35:22 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/2gvh-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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 744 and 0 Target number of residues in the AU: 744 Target solvent content: 0.6651 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.85 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: 121.211 3.400 Wilson plot Bfac: 88.69 16460 reflections ( 99.72 % complete ) and 0 restraints for refining 7680 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3470 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2983 (Rfree = 0.000) for 7680 atoms. Found 56 (57 requested) and removed 139 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.08 Search for helices and strands: 0 residues in 0 chains, 7675 seeds are put forward NCS extension: 0 residues added, 7675 seeds are put forward Round 1: 464 peptides, 74 chains. Longest chain 20 peptides. Score 0.422 Round 2: 494 peptides, 61 chains. Longest chain 22 peptides. Score 0.531 Round 3: 514 peptides, 59 chains. Longest chain 28 peptides. Score 0.563 Round 4: 515 peptides, 55 chains. Longest chain 28 peptides. Score 0.585 Round 5: 521 peptides, 58 chains. Longest chain 25 peptides. Score 0.576 Taking the results from Round 4 Chains 61, Residues 460, Estimated correctness of the model 23.7 % 8 chains (98 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13242 restraints for refining 6285 atoms. 11123 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2680 (Rfree = 0.000) for 6285 atoms. Found 42 (47 requested) and removed 64 (23 requested) atoms. Cycle 2: After refmac, R = 0.2555 (Rfree = 0.000) for 6189 atoms. Found 26 (47 requested) and removed 37 (23 requested) atoms. Cycle 3: After refmac, R = 0.2491 (Rfree = 0.000) for 6156 atoms. Found 16 (46 requested) and removed 29 (23 requested) atoms. Cycle 4: After refmac, R = 0.2478 (Rfree = 0.000) for 6135 atoms. Found 9 (46 requested) and removed 26 (23 requested) atoms. Cycle 5: After refmac, R = 0.2441 (Rfree = 0.000) for 6108 atoms. Found 14 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.08 Search for helices and strands: 0 residues in 0 chains, 6280 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6303 seeds are put forward Round 1: 472 peptides, 68 chains. Longest chain 19 peptides. Score 0.466 Round 2: 504 peptides, 63 chains. Longest chain 20 peptides. Score 0.532 Round 3: 522 peptides, 57 chains. Longest chain 27 peptides. Score 0.582 Round 4: 520 peptides, 59 chains. Longest chain 21 peptides. Score 0.570 Round 5: 524 peptides, 52 chains. Longest chain 26 peptides. Score 0.608 Taking the results from Round 5 Chains 56, Residues 472, Estimated correctness of the model 31.3 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13480 restraints for refining 6285 atoms. 11447 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2643 (Rfree = 0.000) for 6285 atoms. Found 47 (47 requested) and removed 42 (23 requested) atoms. Cycle 7: After refmac, R = 0.2413 (Rfree = 0.000) for 6249 atoms. Found 16 (47 requested) and removed 33 (23 requested) atoms. Cycle 8: After refmac, R = 0.2342 (Rfree = 0.000) for 6212 atoms. Found 13 (47 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2305 (Rfree = 0.000) for 6180 atoms. Found 5 (46 requested) and removed 24 (23 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 6157 atoms. Found 4 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.08 Search for helices and strands: 0 residues in 0 chains, 6293 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 6309 seeds are put forward Round 1: 461 peptides, 68 chains. Longest chain 22 peptides. Score 0.452 Round 2: 500 peptides, 61 chains. Longest chain 28 peptides. Score 0.538 Round 3: 507 peptides, 64 chains. Longest chain 20 peptides. Score 0.530 Round 4: 527 peptides, 63 chains. Longest chain 24 peptides. Score 0.557 Round 5: 518 peptides, 54 chains. Longest chain 27 peptides. Score 0.593 Taking the results from Round 5 Chains 56, Residues 464, Estimated correctness of the model 26.4 % 6 chains (74 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13428 restraints for refining 6285 atoms. 11342 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2606 (Rfree = 0.000) for 6285 atoms. Found 45 (47 requested) and removed 38 (23 requested) atoms. Cycle 12: After refmac, R = 0.2532 (Rfree = 0.000) for 6241 atoms. Found 14 (47 requested) and removed 29 (23 requested) atoms. Cycle 13: After refmac, R = 0.2496 (Rfree = 0.000) for 6199 atoms. Found 22 (47 requested) and removed 28 (23 requested) atoms. Cycle 14: After refmac, R = 0.3010 (Rfree = 0.000) for 6177 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. Cycle 15: After refmac, R = 0.2401 (Rfree = 0.000) for 6160 atoms. Found 14 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.10 Search for helices and strands: 0 residues in 0 chains, 6352 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 6393 seeds are put forward Round 1: 480 peptides, 71 chains. Longest chain 22 peptides. Score 0.459 Round 2: 518 peptides, 64 chains. Longest chain 22 peptides. Score 0.542 Round 3: 498 peptides, 55 chains. Longest chain 25 peptides. Score 0.566 Round 4: 499 peptides, 56 chains. Longest chain 32 peptides. Score 0.562 Round 5: 515 peptides, 56 chains. Longest chain 27 peptides. Score 0.580 Taking the results from Round 5 Chains 61, Residues 459, Estimated correctness of the model 22.0 % 5 chains (67 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13586 restraints for refining 6285 atoms. 11563 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2668 (Rfree = 0.000) for 6285 atoms. Found 38 (47 requested) and removed 33 (23 requested) atoms. Cycle 17: After refmac, R = 0.2649 (Rfree = 0.000) for 6260 atoms. Found 36 (47 requested) and removed 44 (23 requested) atoms. Cycle 18: After refmac, R = 0.2990 (Rfree = 0.000) for 6237 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 19: After refmac, R = 0.2486 (Rfree = 0.000) for 6207 atoms. Found 18 (47 requested) and removed 29 (23 requested) atoms. Cycle 20: After refmac, R = 0.2378 (Rfree = 0.000) for 6175 atoms. Found 10 (46 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.11 Search for helices and strands: 0 residues in 0 chains, 6314 seeds are put forward NCS extension: 37 residues added (9 deleted due to clashes), 6351 seeds are put forward Round 1: 483 peptides, 66 chains. Longest chain 20 peptides. Score 0.491 Round 2: 501 peptides, 58 chains. Longest chain 24 peptides. Score 0.554 Round 3: 532 peptides, 61 chains. Longest chain 26 peptides. Score 0.573 Round 4: 528 peptides, 59 chains. Longest chain 23 peptides. Score 0.579 Round 5: 501 peptides, 56 chains. Longest chain 32 peptides. Score 0.565 Taking the results from Round 4 Chains 64, Residues 469, Estimated correctness of the model 21.7 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13913 restraints for refining 6283 atoms. 12011 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2635 (Rfree = 0.000) for 6283 atoms. Found 26 (47 requested) and removed 40 (23 requested) atoms. Cycle 22: After refmac, R = 0.2510 (Rfree = 0.000) for 6234 atoms. Found 17 (47 requested) and removed 36 (23 requested) atoms. Cycle 23: After refmac, R = 0.2452 (Rfree = 0.000) for 6195 atoms. Found 19 (46 requested) and removed 30 (23 requested) atoms. Cycle 24: After refmac, R = 0.2308 (Rfree = 0.000) for 6157 atoms. Found 15 (46 requested) and removed 28 (23 requested) atoms. Cycle 25: After refmac, R = 0.2302 (Rfree = 0.000) for 6125 atoms. Found 5 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.10 Search for helices and strands: 0 residues in 0 chains, 6233 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6252 seeds are put forward Round 1: 443 peptides, 64 chains. Longest chain 20 peptides. Score 0.452 Round 2: 476 peptides, 61 chains. Longest chain 21 peptides. Score 0.510 Round 3: 495 peptides, 61 chains. Longest chain 26 peptides. Score 0.532 Round 4: 504 peptides, 62 chains. Longest chain 26 peptides. Score 0.537 Round 5: 504 peptides, 59 chains. Longest chain 26 peptides. Score 0.552 Taking the results from Round 5 Chains 62, Residues 445, Estimated correctness of the model 12.2 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13921 restraints for refining 6285 atoms. 12041 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2431 (Rfree = 0.000) for 6285 atoms. Found 35 (47 requested) and removed 37 (23 requested) atoms. Cycle 27: After refmac, R = 0.2341 (Rfree = 0.000) for 6255 atoms. Found 21 (47 requested) and removed 37 (23 requested) atoms. Cycle 28: After refmac, R = 0.2179 (Rfree = 0.000) for 6216 atoms. Found 8 (47 requested) and removed 35 (23 requested) atoms. Cycle 29: After refmac, R = 0.2085 (Rfree = 0.000) for 6180 atoms. Found 8 (46 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2058 (Rfree = 0.000) for 6140 atoms. Found 5 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 6290 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6311 seeds are put forward Round 1: 435 peptides, 70 chains. Longest chain 21 peptides. Score 0.406 Round 2: 480 peptides, 61 chains. Longest chain 20 peptides. Score 0.514 Round 3: 492 peptides, 58 chains. Longest chain 30 peptides. Score 0.544 Round 4: 491 peptides, 55 chains. Longest chain 23 peptides. Score 0.559 Round 5: 513 peptides, 61 chains. Longest chain 28 peptides. Score 0.552 Taking the results from Round 4 Chains 61, Residues 436, Estimated correctness of the model 14.7 % 5 chains (57 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13768 restraints for refining 6285 atoms. 11868 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2469 (Rfree = 0.000) for 6285 atoms. Found 47 (47 requested) and removed 30 (23 requested) atoms. Cycle 32: After refmac, R = 0.2279 (Rfree = 0.000) for 6277 atoms. Found 16 (47 requested) and removed 30 (23 requested) atoms. Cycle 33: After refmac, R = 0.2179 (Rfree = 0.000) for 6237 atoms. Found 14 (47 requested) and removed 25 (23 requested) atoms. Cycle 34: After refmac, R = 0.2112 (Rfree = 0.000) for 6211 atoms. Found 9 (47 requested) and removed 23 (23 requested) atoms. Cycle 35: After refmac, R = 0.2117 (Rfree = 0.000) for 6174 atoms. Found 10 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 6331 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 6353 seeds are put forward Round 1: 434 peptides, 67 chains. Longest chain 22 peptides. Score 0.423 Round 2: 480 peptides, 63 chains. Longest chain 20 peptides. Score 0.504 Round 3: 493 peptides, 59 chains. Longest chain 24 peptides. Score 0.540 Round 4: 492 peptides, 59 chains. Longest chain 23 peptides. Score 0.539 Round 5: 504 peptides, 58 chains. Longest chain 26 peptides. Score 0.558 Taking the results from Round 5 Chains 60, Residues 446, Estimated correctness of the model 14.4 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 16460 reflections ( 99.72 % complete ) and 13922 restraints for refining 6284 atoms. 12030 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2542 (Rfree = 0.000) for 6284 atoms. Found 41 (47 requested) and removed 40 (23 requested) atoms. Cycle 37: After refmac, R = 0.2422 (Rfree = 0.000) for 6261 atoms. Found 18 (47 requested) and removed 29 (23 requested) atoms. Cycle 38: After refmac, R = 0.2391 (Rfree = 0.000) for 6232 atoms. Found 10 (47 requested) and removed 28 (23 requested) atoms. Cycle 39: After refmac, R = 0.2298 (Rfree = 0.000) for 6203 atoms. Found 9 (46 requested) and removed 25 (23 requested) atoms. Cycle 40: After refmac, R = 0.2290 (Rfree = 0.000) for 6174 atoms. Found 9 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 6295 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6319 seeds are put forward Round 1: 410 peptides, 65 chains. Longest chain 19 peptides. Score 0.402 Round 2: 477 peptides, 66 chains. Longest chain 20 peptides. Score 0.483 Round 3: 475 peptides, 65 chains. Longest chain 24 peptides. Score 0.487 Round 4: 468 peptides, 60 chains. Longest chain 21 peptides. Score 0.506 Round 5: 484 peptides, 61 chains. Longest chain 24 peptides. Score 0.519 Taking the results from Round 5 Chains 63, Residues 423, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 16460 reflections ( 99.72 % complete ) and 14178 restraints for refining 6285 atoms. 12437 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2526 (Rfree = 0.000) for 6285 atoms. Found 29 (47 requested) and removed 32 (23 requested) atoms. Cycle 42: After refmac, R = 0.2380 (Rfree = 0.000) for 6266 atoms. Found 7 (47 requested) and removed 28 (23 requested) atoms. Cycle 43: After refmac, R = 0.2384 (Rfree = 0.000) for 6230 atoms. Found 8 (47 requested) and removed 27 (23 requested) atoms. Cycle 44: After refmac, R = 0.2285 (Rfree = 0.000) for 6206 atoms. Found 6 (46 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.2269 (Rfree = 0.000) for 6180 atoms. Found 4 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 6322 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6348 seeds are put forward Round 1: 400 peptides, 67 chains. Longest chain 19 peptides. Score 0.376 Round 2: 425 peptides, 57 chains. Longest chain 19 peptides. Score 0.470 Round 3: 450 peptides, 59 chains. Longest chain 19 peptides. Score 0.489 Round 4: 466 peptides, 60 chains. Longest chain 24 peptides. Score 0.503 Round 5: 460 peptides, 57 chains. Longest chain 19 peptides. Score 0.513 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 403, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input Building loops using Loopy2018 58 chains (403 residues) following loop building 2 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16460 reflections ( 99.72 % complete ) and 14283 restraints for refining 6284 atoms. 12636 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2441 (Rfree = 0.000) for 6284 atoms. Found 0 (47 requested) and removed 22 (23 requested) atoms. Cycle 47: After refmac, R = 0.2516 (Rfree = 0.000) for 6249 atoms. Found 0 (47 requested) and removed 15 (23 requested) atoms. Cycle 48: After refmac, R = 0.2595 (Rfree = 0.000) for 6229 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2527 (Rfree = 0.000) for 6183 atoms. TimeTaking 83.52