Mon 24 Dec 00:32:00 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 1vp4-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-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/1vp4-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-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 00:32:05 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/1vp4-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-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 684 and 0 Target number of residues in the AU: 684 Target solvent content: 0.6562 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.8-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 3.800 Wilson plot Bfac: 82.24 10675 reflections ( 99.70 % complete ) and 0 restraints for refining 7481 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3580 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3275 (Rfree = 0.000) for 7481 atoms. Found 41 (41 requested) and removed 84 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 7576 seeds are put forward NCS extension: 0 residues added, 7576 seeds are put forward Round 1: 252 peptides, 52 chains. Longest chain 11 peptides. Score 0.254 Round 2: 373 peptides, 67 chains. Longest chain 21 peptides. Score 0.351 Round 3: 441 peptides, 78 chains. Longest chain 16 peptides. Score 0.384 Round 4: 461 peptides, 77 chains. Longest chain 22 peptides. Score 0.420 Round 5: 476 peptides, 73 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 73, Residues 403, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13566 restraints for refining 6030 atoms. 11987 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2906 (Rfree = 0.000) for 6030 atoms. Found 33 (33 requested) and removed 40 (16 requested) atoms. Cycle 2: After refmac, R = 0.2822 (Rfree = 0.000) for 5916 atoms. Found 32 (33 requested) and removed 37 (16 requested) atoms. Cycle 3: After refmac, R = 0.3095 (Rfree = 0.000) for 5828 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Cycle 4: After refmac, R = 0.2914 (Rfree = 0.000) for 5726 atoms. Found 31 (31 requested) and removed 57 (15 requested) atoms. Cycle 5: After refmac, R = 0.2836 (Rfree = 0.000) for 5652 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 5892 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5909 seeds are put forward Round 1: 389 peptides, 73 chains. Longest chain 10 peptides. Score 0.336 Round 2: 471 peptides, 74 chains. Longest chain 16 peptides. Score 0.453 Round 3: 468 peptides, 69 chains. Longest chain 14 peptides. Score 0.479 Round 4: 474 peptides, 69 chains. Longest chain 19 peptides. Score 0.487 Round 5: 479 peptides, 64 chains. Longest chain 17 peptides. Score 0.523 Taking the results from Round 5 Chains 64, Residues 415, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 12872 restraints for refining 5869 atoms. 11276 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 5869 atoms. Found 32 (32 requested) and removed 58 (16 requested) atoms. Cycle 7: After refmac, R = 0.2586 (Rfree = 0.000) for 5775 atoms. Found 23 (32 requested) and removed 50 (16 requested) atoms. Cycle 8: After refmac, R = 0.2430 (Rfree = 0.000) for 5689 atoms. Found 17 (31 requested) and removed 21 (15 requested) atoms. Cycle 9: After refmac, R = 0.2343 (Rfree = 0.000) for 5651 atoms. Found 10 (31 requested) and removed 26 (15 requested) atoms. Cycle 10: After refmac, R = 0.2309 (Rfree = 0.000) for 5614 atoms. Found 19 (30 requested) and removed 48 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 5844 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5859 seeds are put forward Round 1: 415 peptides, 77 chains. Longest chain 12 peptides. Score 0.350 Round 2: 482 peptides, 74 chains. Longest chain 19 peptides. Score 0.468 Round 3: 481 peptides, 69 chains. Longest chain 16 peptides. Score 0.496 Round 4: 478 peptides, 67 chains. Longest chain 28 peptides. Score 0.504 Round 5: 492 peptides, 70 chains. Longest chain 13 peptides. Score 0.505 Taking the results from Round 5 Chains 71, Residues 422, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13466 restraints for refining 6115 atoms. 11768 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2553 (Rfree = 0.000) for 6115 atoms. Found 33 (33 requested) and removed 46 (16 requested) atoms. Cycle 12: After refmac, R = 0.2364 (Rfree = 0.000) for 6043 atoms. Found 23 (33 requested) and removed 43 (16 requested) atoms. Cycle 13: After refmac, R = 0.2292 (Rfree = 0.000) for 5982 atoms. Found 17 (33 requested) and removed 28 (16 requested) atoms. Cycle 14: After refmac, R = 0.2398 (Rfree = 0.000) for 5950 atoms. Found 30 (32 requested) and removed 26 (16 requested) atoms. Cycle 15: After refmac, R = 0.2226 (Rfree = 0.000) for 5925 atoms. Found 14 (32 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 6150 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6168 seeds are put forward Round 1: 421 peptides, 77 chains. Longest chain 12 peptides. Score 0.359 Round 2: 468 peptides, 71 chains. Longest chain 22 peptides. Score 0.467 Round 3: 464 peptides, 65 chains. Longest chain 20 peptides. Score 0.498 Round 4: 488 peptides, 79 chains. Longest chain 16 peptides. Score 0.446 Round 5: 494 peptides, 69 chains. Longest chain 21 peptides. Score 0.514 Taking the results from Round 5 Chains 69, Residues 425, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13472 restraints for refining 6150 atoms. 11795 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2773 (Rfree = 0.000) for 6150 atoms. Found 33 (33 requested) and removed 65 (16 requested) atoms. Cycle 17: After refmac, R = 0.2634 (Rfree = 0.000) for 6056 atoms. Found 33 (33 requested) and removed 42 (16 requested) atoms. Cycle 18: After refmac, R = 0.2409 (Rfree = 0.000) for 5983 atoms. Found 22 (33 requested) and removed 29 (16 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2378 (Rfree = 0.000) for 5939 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 20: After refmac, R = 0.2215 (Rfree = 0.000) for 5924 atoms. Found 30 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 6152 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 6179 seeds are put forward Round 1: 368 peptides, 70 chains. Longest chain 19 peptides. Score 0.323 Round 2: 421 peptides, 71 chains. Longest chain 14 peptides. Score 0.399 Round 3: 419 peptides, 63 chains. Longest chain 16 peptides. Score 0.448 Round 4: 458 peptides, 70 chains. Longest chain 20 peptides. Score 0.459 Round 5: 439 peptides, 63 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 5 Chains 64, Residues 376, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13732 restraints for refining 6128 atoms. 12225 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2794 (Rfree = 0.000) for 6128 atoms. Found 33 (33 requested) and removed 50 (16 requested) atoms. Cycle 22: After refmac, R = 0.2618 (Rfree = 0.000) for 6042 atoms. Found 33 (33 requested) and removed 28 (16 requested) atoms. Cycle 23: After refmac, R = 0.2532 (Rfree = 0.000) for 5999 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 24: After refmac, R = 0.2437 (Rfree = 0.000) for 5963 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 25: After refmac, R = 0.2436 (Rfree = 0.000) for 5950 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 6147 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6163 seeds are put forward Round 1: 340 peptides, 65 chains. Longest chain 13 peptides. Score 0.312 Round 2: 411 peptides, 67 chains. Longest chain 16 peptides. Score 0.410 Round 3: 417 peptides, 65 chains. Longest chain 18 peptides. Score 0.432 Round 4: 440 peptides, 66 chains. Longest chain 22 peptides. Score 0.459 Round 5: 452 peptides, 63 chains. Longest chain 20 peptides. Score 0.493 Taking the results from Round 5 Chains 63, Residues 389, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13698 restraints for refining 6151 atoms. 12127 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2779 (Rfree = 0.000) for 6151 atoms. Found 33 (33 requested) and removed 41 (16 requested) atoms. Cycle 27: After refmac, R = 0.2514 (Rfree = 0.000) for 6098 atoms. Found 33 (33 requested) and removed 37 (16 requested) atoms. Cycle 28: After refmac, R = 0.2444 (Rfree = 0.000) for 6045 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. Cycle 29: After refmac, R = 0.2350 (Rfree = 0.000) for 6015 atoms. Found 33 (33 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 6006 atoms. Found 14 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 6199 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6219 seeds are put forward Round 1: 329 peptides, 69 chains. Longest chain 11 peptides. Score 0.264 Round 2: 381 peptides, 71 chains. Longest chain 12 peptides. Score 0.337 Round 3: 372 peptides, 63 chains. Longest chain 23 peptides. Score 0.377 Round 4: 386 peptides, 62 chains. Longest chain 15 peptides. Score 0.406 Round 5: 379 peptides, 60 chains. Longest chain 17 peptides. Score 0.408 Taking the results from Round 5 Chains 61, Residues 319, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14304 restraints for refining 6151 atoms. 13053 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2653 (Rfree = 0.000) for 6151 atoms. Found 33 (33 requested) and removed 60 (16 requested) atoms. Cycle 32: After refmac, R = 0.2607 (Rfree = 0.000) for 6085 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Cycle 33: After refmac, R = 0.2526 (Rfree = 0.000) for 6054 atoms. Found 33 (33 requested) and removed 30 (16 requested) atoms. Cycle 34: After refmac, R = 0.2117 (Rfree = 0.000) for 6013 atoms. Found 16 (33 requested) and removed 23 (16 requested) atoms. Cycle 35: After refmac, R = 0.2153 (Rfree = 0.000) for 5980 atoms. Found 29 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 6170 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6190 seeds are put forward Round 1: 308 peptides, 64 chains. Longest chain 8 peptides. Score 0.264 Round 2: 382 peptides, 72 chains. Longest chain 15 peptides. Score 0.331 Round 3: 370 peptides, 66 chains. Longest chain 15 peptides. Score 0.354 Round 4: 368 peptides, 62 chains. Longest chain 17 peptides. Score 0.378 Round 5: 372 peptides, 60 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 5 Chains 61, Residues 312, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14204 restraints for refining 6151 atoms. 12962 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2401 (Rfree = 0.000) for 6151 atoms. Found 33 (33 requested) and removed 32 (16 requested) atoms. Cycle 37: After refmac, R = 0.2095 (Rfree = 0.000) for 6109 atoms. Found 17 (33 requested) and removed 26 (16 requested) atoms. Cycle 38: After refmac, R = 0.2117 (Rfree = 0.000) for 6074 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 39: After refmac, R = 0.1830 (Rfree = 0.000) for 6055 atoms. Found 10 (33 requested) and removed 18 (16 requested) atoms. Cycle 40: After refmac, R = 0.1925 (Rfree = 0.000) for 6035 atoms. Found 15 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 6230 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6252 seeds are put forward Round 1: 304 peptides, 61 chains. Longest chain 14 peptides. Score 0.279 Round 2: 346 peptides, 61 chains. Longest chain 12 peptides. Score 0.350 Round 3: 340 peptides, 58 chains. Longest chain 13 peptides. Score 0.361 Round 4: 359 peptides, 59 chains. Longest chain 17 peptides. Score 0.384 Round 5: 356 peptides, 59 chains. Longest chain 14 peptides. Score 0.380 Taking the results from Round 4 Chains 59, Residues 300, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14167 restraints for refining 6150 atoms. 12996 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2221 (Rfree = 0.000) for 6150 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 42: After refmac, R = 0.2065 (Rfree = 0.000) for 6136 atoms. Found 15 (33 requested) and removed 25 (16 requested) atoms. Cycle 43: After refmac, R = 0.2127 (Rfree = 0.000) for 6116 atoms. Found 25 (33 requested) and removed 20 (16 requested) atoms. Cycle 44: After refmac, R = 0.1970 (Rfree = 0.000) for 6110 atoms. Found 12 (33 requested) and removed 24 (16 requested) atoms. Cycle 45: After refmac, R = 0.1907 (Rfree = 0.000) for 6089 atoms. Found 3 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 6283 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6300 seeds are put forward Round 1: 301 peptides, 63 chains. Longest chain 9 peptides. Score 0.259 Round 2: 327 peptides, 57 chains. Longest chain 14 peptides. Score 0.347 Round 3: 327 peptides, 59 chains. Longest chain 14 peptides. Score 0.333 Round 4: 351 peptides, 55 chains. Longest chain 15 peptides. Score 0.399 Round 5: 343 peptides, 56 chains. Longest chain 18 peptides. Score 0.380 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 296, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (296 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10675 reflections ( 99.70 % complete ) and 14278 restraints for refining 6150 atoms. 13100 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2369 (Rfree = 0.000) for 6150 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2274 (Rfree = 0.000) for 6120 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2244 (Rfree = 0.000) for 6098 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2227 (Rfree = 0.000) for 6078 atoms. TimeTaking 77.72