Mon 24 Dec 01:08:36 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 1vp4-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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/1vp4-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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 01:08:40 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/1vp4-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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 700 and 0 Target number of residues in the AU: 700 Target solvent content: 0.6481 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: 1vp4-3.4-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.4-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 3.400 Wilson plot Bfac: 76.86 14842 reflections ( 99.78 % complete ) and 0 restraints for refining 7549 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3496 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3388 (Rfree = 0.000) for 7549 atoms. Found 56 (56 requested) and removed 124 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 7655 seeds are put forward NCS extension: 0 residues added, 7655 seeds are put forward Round 1: 361 peptides, 68 chains. Longest chain 10 peptides. Score 0.325 Round 2: 463 peptides, 75 chains. Longest chain 23 peptides. Score 0.435 Round 3: 483 peptides, 79 chains. Longest chain 19 peptides. Score 0.439 Round 4: 488 peptides, 77 chains. Longest chain 17 peptides. Score 0.458 Round 5: 501 peptides, 76 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 5 Chains 77, Residues 425, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13604 restraints for refining 6183 atoms. 11889 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2821 (Rfree = 0.000) for 6183 atoms. Found 43 (46 requested) and removed 57 (23 requested) atoms. Cycle 2: After refmac, R = 0.2691 (Rfree = 0.000) for 6104 atoms. Found 36 (46 requested) and removed 49 (23 requested) atoms. Cycle 3: After refmac, R = 0.2568 (Rfree = 0.000) for 6064 atoms. Found 37 (45 requested) and removed 41 (22 requested) atoms. Cycle 4: After refmac, R = 0.2354 (Rfree = 0.000) for 6039 atoms. Found 13 (45 requested) and removed 27 (22 requested) atoms. Cycle 5: After refmac, R = 0.2349 (Rfree = 0.000) for 6010 atoms. Found 7 (45 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 6253 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6281 seeds are put forward Round 1: 435 peptides, 77 chains. Longest chain 11 peptides. Score 0.381 Round 2: 506 peptides, 76 chains. Longest chain 15 peptides. Score 0.489 Round 3: 500 peptides, 70 chains. Longest chain 17 peptides. Score 0.516 Round 4: 496 peptides, 67 chains. Longest chain 17 peptides. Score 0.528 Round 5: 500 peptides, 68 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 4 Chains 67, Residues 429, Estimated correctness of the model 3.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13766 restraints for refining 6182 atoms. 12057 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2535 (Rfree = 0.000) for 6182 atoms. Found 35 (46 requested) and removed 36 (23 requested) atoms. Cycle 7: After refmac, R = 0.2437 (Rfree = 0.000) for 6159 atoms. Found 28 (46 requested) and removed 31 (23 requested) atoms. Cycle 8: After refmac, R = 0.2927 (Rfree = 0.000) for 6144 atoms. Found 46 (46 requested) and removed 43 (23 requested) atoms. Cycle 9: After refmac, R = 0.2334 (Rfree = 0.000) for 6123 atoms. Found 25 (46 requested) and removed 29 (23 requested) atoms. Cycle 10: After refmac, R = 0.2136 (Rfree = 0.000) for 6104 atoms. Found 7 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 6390 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6404 seeds are put forward Round 1: 443 peptides, 76 chains. Longest chain 15 peptides. Score 0.400 Round 2: 465 peptides, 70 chains. Longest chain 18 peptides. Score 0.469 Round 3: 479 peptides, 65 chains. Longest chain 16 peptides. Score 0.517 Round 4: 506 peptides, 67 chains. Longest chain 17 peptides. Score 0.540 Round 5: 500 peptides, 68 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 4 Chains 68, Residues 439, Estimated correctness of the model 7.9 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13708 restraints for refining 6183 atoms. 11943 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2703 (Rfree = 0.000) for 6183 atoms. Found 46 (46 requested) and removed 35 (23 requested) atoms. Cycle 12: After refmac, R = 0.2507 (Rfree = 0.000) for 6166 atoms. Found 35 (46 requested) and removed 34 (23 requested) atoms. Cycle 13: After refmac, R = 0.2433 (Rfree = 0.000) for 6146 atoms. Found 30 (46 requested) and removed 33 (23 requested) atoms. Cycle 14: After refmac, R = 0.2341 (Rfree = 0.000) for 6131 atoms. Found 30 (46 requested) and removed 29 (23 requested) atoms. Cycle 15: After refmac, R = 0.2145 (Rfree = 0.000) for 6127 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 6331 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6347 seeds are put forward Round 1: 436 peptides, 71 chains. Longest chain 15 peptides. Score 0.421 Round 2: 464 peptides, 70 chains. Longest chain 23 peptides. Score 0.467 Round 3: 495 peptides, 65 chains. Longest chain 31 peptides. Score 0.538 Round 4: 482 peptides, 64 chains. Longest chain 16 peptides. Score 0.527 Round 5: 465 peptides, 65 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 3 Chains 65, Residues 430, Estimated correctness of the model 7.2 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13701 restraints for refining 6182 atoms. 11957 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2438 (Rfree = 0.000) for 6182 atoms. Found 35 (46 requested) and removed 29 (23 requested) atoms. Cycle 17: After refmac, R = 0.2403 (Rfree = 0.000) for 6160 atoms. Found 29 (46 requested) and removed 27 (23 requested) atoms. Cycle 18: After refmac, R = 0.2381 (Rfree = 0.000) for 6150 atoms. Found 32 (46 requested) and removed 26 (23 requested) atoms. Cycle 19: After refmac, R = 0.2335 (Rfree = 0.000) for 6151 atoms. Found 27 (46 requested) and removed 25 (23 requested) atoms. Cycle 20: After refmac, R = 0.2158 (Rfree = 0.000) for 6146 atoms. Found 7 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 6380 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 6406 seeds are put forward Round 1: 409 peptides, 70 chains. Longest chain 15 peptides. Score 0.387 Round 2: 452 peptides, 62 chains. Longest chain 22 peptides. Score 0.499 Round 3: 503 peptides, 65 chains. Longest chain 33 peptides. Score 0.548 Round 4: 473 peptides, 67 chains. Longest chain 21 peptides. Score 0.498 Round 5: 488 peptides, 64 chains. Longest chain 28 peptides. Score 0.535 Taking the results from Round 3 Chains 67, Residues 438, Estimated correctness of the model 10.8 % 3 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13355 restraints for refining 6181 atoms. 11427 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2592 (Rfree = 0.000) for 6181 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 22: After refmac, R = 0.2529 (Rfree = 0.000) for 6160 atoms. Found 27 (46 requested) and removed 30 (23 requested) atoms. Cycle 23: After refmac, R = 0.2395 (Rfree = 0.000) for 6152 atoms. Found 21 (46 requested) and removed 29 (23 requested) atoms. Cycle 24: After refmac, R = 0.2392 (Rfree = 0.000) for 6135 atoms. Found 15 (46 requested) and removed 26 (23 requested) atoms. Cycle 25: After refmac, R = 0.2296 (Rfree = 0.000) for 6122 atoms. Found 8 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 6364 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6383 seeds are put forward Round 1: 406 peptides, 74 chains. Longest chain 11 peptides. Score 0.356 Round 2: 466 peptides, 68 chains. Longest chain 20 peptides. Score 0.482 Round 3: 454 peptides, 70 chains. Longest chain 17 peptides. Score 0.453 Round 4: 453 peptides, 60 chains. Longest chain 27 peptides. Score 0.513 Round 5: 444 peptides, 63 chains. Longest chain 20 peptides. Score 0.483 Taking the results from Round 4 Chains 61, Residues 393, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14050 restraints for refining 6181 atoms. 12501 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2434 (Rfree = 0.000) for 6181 atoms. Found 28 (46 requested) and removed 30 (23 requested) atoms. Cycle 27: After refmac, R = 0.2340 (Rfree = 0.000) for 6153 atoms. Found 20 (46 requested) and removed 27 (23 requested) atoms. Cycle 28: After refmac, R = 0.2288 (Rfree = 0.000) for 6133 atoms. Found 28 (46 requested) and removed 26 (23 requested) atoms. Cycle 29: After refmac, R = 0.2298 (Rfree = 0.000) for 6122 atoms. Found 32 (46 requested) and removed 29 (23 requested) atoms. Cycle 30: After refmac, R = 0.2367 (Rfree = 0.000) for 6120 atoms. Found 41 (46 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 6351 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 6384 seeds are put forward Round 1: 400 peptides, 77 chains. Longest chain 12 peptides. Score 0.326 Round 2: 428 peptides, 66 chains. Longest chain 18 peptides. Score 0.441 Round 3: 455 peptides, 70 chains. Longest chain 15 peptides. Score 0.455 Round 4: 462 peptides, 72 chains. Longest chain 21 peptides. Score 0.452 Round 5: 463 peptides, 65 chains. Longest chain 24 peptides. Score 0.496 Taking the results from Round 5 Chains 65, Residues 398, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14282 restraints for refining 6183 atoms. 12755 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2268 (Rfree = 0.000) for 6183 atoms. Found 28 (46 requested) and removed 30 (23 requested) atoms. Cycle 32: After refmac, R = 0.2148 (Rfree = 0.000) for 6158 atoms. Found 30 (46 requested) and removed 26 (23 requested) atoms. Cycle 33: After refmac, R = 0.2045 (Rfree = 0.000) for 6148 atoms. Found 17 (46 requested) and removed 27 (23 requested) atoms. Cycle 34: After refmac, R = 0.1969 (Rfree = 0.000) for 6133 atoms. Found 15 (46 requested) and removed 28 (23 requested) atoms. Cycle 35: After refmac, R = 0.1942 (Rfree = 0.000) for 6113 atoms. Found 20 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 6374 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6399 seeds are put forward Round 1: 364 peptides, 70 chains. Longest chain 12 peptides. Score 0.316 Round 2: 420 peptides, 63 chains. Longest chain 15 peptides. Score 0.449 Round 3: 432 peptides, 60 chains. Longest chain 26 peptides. Score 0.485 Round 4: 436 peptides, 65 chains. Longest chain 20 peptides. Score 0.459 Round 5: 444 peptides, 64 chains. Longest chain 23 peptides. Score 0.476 Taking the results from Round 3 Chains 60, Residues 372, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13822 restraints for refining 6181 atoms. 12313 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2146 (Rfree = 0.000) for 6181 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. Cycle 37: After refmac, R = 0.2023 (Rfree = 0.000) for 6185 atoms. Found 19 (46 requested) and removed 24 (23 requested) atoms. Cycle 38: After refmac, R = 0.1992 (Rfree = 0.000) for 6170 atoms. Found 14 (46 requested) and removed 25 (23 requested) atoms. Cycle 39: After refmac, R = 0.1953 (Rfree = 0.000) for 6153 atoms. Found 16 (46 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.1917 (Rfree = 0.000) for 6143 atoms. Found 13 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 6353 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 6389 seeds are put forward Round 1: 355 peptides, 60 chains. Longest chain 16 peptides. Score 0.371 Round 2: 402 peptides, 52 chains. Longest chain 20 peptides. Score 0.493 Round 3: 406 peptides, 59 chains. Longest chain 33 peptides. Score 0.455 Round 4: 417 peptides, 59 chains. Longest chain 18 peptides. Score 0.470 Round 5: 411 peptides, 57 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 2 Chains 52, Residues 350, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14006 restraints for refining 6183 atoms. 12604 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2057 (Rfree = 0.000) for 6183 atoms. Found 46 (46 requested) and removed 25 (23 requested) atoms. Cycle 42: After refmac, R = 0.1935 (Rfree = 0.000) for 6186 atoms. Found 15 (46 requested) and removed 24 (23 requested) atoms. Cycle 43: After refmac, R = 0.1864 (Rfree = 0.000) for 6169 atoms. Found 7 (46 requested) and removed 24 (23 requested) atoms. Cycle 44: After refmac, R = 0.1801 (Rfree = 0.000) for 6145 atoms. Found 7 (46 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.1760 (Rfree = 0.000) for 6127 atoms. Found 6 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 6288 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6313 seeds are put forward Round 1: 346 peptides, 66 chains. Longest chain 14 peptides. Score 0.314 Round 2: 382 peptides, 57 chains. Longest chain 20 peptides. Score 0.433 Round 3: 388 peptides, 57 chains. Longest chain 18 peptides. Score 0.442 Round 4: 375 peptides, 55 chains. Longest chain 19 peptides. Score 0.436 Round 5: 401 peptides, 52 chains. Longest chain 22 peptides. Score 0.492 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 349, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14842 reflections ( 99.78 % complete ) and 14156 restraints for refining 6182 atoms. 12784 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2042 (Rfree = 0.000) for 6182 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2055 (Rfree = 0.000) for 6146 atoms. Found 0 (46 requested) and removed 20 (23 requested) atoms. Cycle 48: After refmac, R = 0.1946 (Rfree = 0.000) for 6121 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1891 (Rfree = 0.000) for 6085 atoms. TimeTaking 70.88