Mon 24 Dec 00:41:49 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 2okc-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-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/2okc-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-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 00:41:54 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/2okc-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-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 642 and 0 Target number of residues in the AU: 642 Target solvent content: 0.6476 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-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: 19 Cell parameters: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7120 target number of atoms Had to go as low as 0.75 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: 28.546 3.400 Wilson plot Bfac: 76.60 12678 reflections ( 89.55 % complete ) and 0 restraints for refining 7936 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3213 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3050 (Rfree = 0.000) for 7936 atoms. Found 59 (59 requested) and removed 80 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 8103 seeds are put forward NCS extension: 0 residues added, 8103 seeds are put forward Round 1: 363 peptides, 73 chains. Longest chain 12 peptides. Score 0.302 Round 2: 428 peptides, 72 chains. Longest chain 14 peptides. Score 0.419 Round 3: 474 peptides, 69 chains. Longest chain 24 peptides. Score 0.508 Round 4: 469 peptides, 65 chains. Longest chain 18 peptides. Score 0.525 Round 5: 485 peptides, 67 chains. Longest chain 22 peptides. Score 0.535 Taking the results from Round 5 Chains 71, Residues 418, Estimated correctness of the model 6.0 % 8 chains (58 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14389 restraints for refining 6469 atoms. 12612 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2520 (Rfree = 0.000) for 6469 atoms. Found 34 (48 requested) and removed 52 (24 requested) atoms. Cycle 2: After refmac, R = 0.2304 (Rfree = 0.000) for 6380 atoms. Found 22 (48 requested) and removed 35 (24 requested) atoms. Cycle 3: After refmac, R = 0.2299 (Rfree = 0.000) for 6339 atoms. Found 27 (48 requested) and removed 42 (24 requested) atoms. Cycle 4: After refmac, R = 0.2198 (Rfree = 0.000) for 6306 atoms. Found 24 (47 requested) and removed 32 (23 requested) atoms. Cycle 5: After refmac, R = 0.2114 (Rfree = 0.000) for 6284 atoms. Found 15 (47 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 6501 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6525 seeds are put forward Round 1: 434 peptides, 82 chains. Longest chain 12 peptides. Score 0.359 Round 2: 469 peptides, 71 chains. Longest chain 20 peptides. Score 0.488 Round 3: 448 peptides, 65 chains. Longest chain 21 peptides. Score 0.496 Round 4: 471 peptides, 60 chains. Longest chain 22 peptides. Score 0.558 Round 5: 485 peptides, 65 chains. Longest chain 20 peptides. Score 0.547 Taking the results from Round 4 Chains 61, Residues 411, Estimated correctness of the model 14.4 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14484 restraints for refining 6474 atoms. 12790 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2383 (Rfree = 0.000) for 6474 atoms. Found 32 (48 requested) and removed 48 (24 requested) atoms. Cycle 7: After refmac, R = 0.2260 (Rfree = 0.000) for 6419 atoms. Found 24 (48 requested) and removed 35 (24 requested) atoms. Cycle 8: After refmac, R = 0.2208 (Rfree = 0.000) for 6395 atoms. Found 30 (48 requested) and removed 37 (24 requested) atoms. Cycle 9: After refmac, R = 0.2185 (Rfree = 0.000) for 6378 atoms. Found 30 (48 requested) and removed 42 (24 requested) atoms. Cycle 10: After refmac, R = 0.1933 (Rfree = 0.000) for 6362 atoms. Found 8 (48 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 6552 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6574 seeds are put forward Round 1: 422 peptides, 77 chains. Longest chain 15 peptides. Score 0.374 Round 2: 485 peptides, 73 chains. Longest chain 20 peptides. Score 0.498 Round 3: 495 peptides, 75 chains. Longest chain 18 peptides. Score 0.500 Round 4: 466 peptides, 65 chains. Longest chain 20 peptides. Score 0.521 Round 5: 475 peptides, 65 chains. Longest chain 24 peptides. Score 0.534 Taking the results from Round 5 Chains 65, Residues 410, Estimated correctness of the model 5.7 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14711 restraints for refining 6474 atoms. 13097 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2379 (Rfree = 0.000) for 6474 atoms. Found 35 (48 requested) and removed 36 (24 requested) atoms. Cycle 12: After refmac, R = 0.2283 (Rfree = 0.000) for 6443 atoms. Found 37 (48 requested) and removed 36 (24 requested) atoms. Cycle 13: After refmac, R = 0.2006 (Rfree = 0.000) for 6421 atoms. Found 16 (48 requested) and removed 33 (24 requested) atoms. Cycle 14: After refmac, R = 0.2107 (Rfree = 0.000) for 6392 atoms. Found 29 (48 requested) and removed 38 (24 requested) atoms. Cycle 15: After refmac, R = 0.1949 (Rfree = 0.000) for 6381 atoms. Found 15 (48 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 6606 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 6627 seeds are put forward Round 1: 395 peptides, 73 chains. Longest chain 12 peptides. Score 0.357 Round 2: 453 peptides, 70 chains. Longest chain 31 peptides. Score 0.471 Round 3: 451 peptides, 66 chains. Longest chain 17 peptides. Score 0.494 Round 4: 440 peptides, 66 chains. Longest chain 22 peptides. Score 0.477 Round 5: 470 peptides, 70 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 5 Chains 70, Residues 400, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14781 restraints for refining 6471 atoms. 13211 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2296 (Rfree = 0.000) for 6471 atoms. Found 31 (48 requested) and removed 37 (24 requested) atoms. Cycle 17: After refmac, R = 0.2213 (Rfree = 0.000) for 6440 atoms. Found 43 (48 requested) and removed 35 (24 requested) atoms. Cycle 18: After refmac, R = 0.2224 (Rfree = 0.000) for 6441 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. Cycle 19: After refmac, R = 0.1950 (Rfree = 0.000) for 6446 atoms. Found 16 (48 requested) and removed 58 (24 requested) atoms. Cycle 20: After refmac, R = 0.1917 (Rfree = 0.000) for 6399 atoms. Found 11 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 6572 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6594 seeds are put forward Round 1: 404 peptides, 74 chains. Longest chain 19 peptides. Score 0.365 Round 2: 455 peptides, 68 chains. Longest chain 21 peptides. Score 0.486 Round 3: 452 peptides, 64 chains. Longest chain 32 peptides. Score 0.508 Round 4: 457 peptides, 67 chains. Longest chain 18 peptides. Score 0.496 Round 5: 442 peptides, 60 chains. Longest chain 25 peptides. Score 0.519 Taking the results from Round 5 Chains 63, Residues 382, Estimated correctness of the model 0.0 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14561 restraints for refining 6473 atoms. 12938 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2340 (Rfree = 0.000) for 6473 atoms. Found 45 (48 requested) and removed 39 (24 requested) atoms. Cycle 22: After refmac, R = 0.2285 (Rfree = 0.000) for 6461 atoms. Found 40 (48 requested) and removed 37 (24 requested) atoms. Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 6447 atoms. Found 14 (48 requested) and removed 27 (24 requested) atoms. Cycle 24: After refmac, R = 0.2014 (Rfree = 0.000) for 6422 atoms. Found 8 (48 requested) and removed 29 (24 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 6392 atoms. Found 11 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 6566 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6590 seeds are put forward Round 1: 372 peptides, 72 chains. Longest chain 10 peptides. Score 0.325 Round 2: 412 peptides, 64 chains. Longest chain 16 peptides. Score 0.448 Round 3: 437 peptides, 64 chains. Longest chain 15 peptides. Score 0.486 Round 4: 436 peptides, 64 chains. Longest chain 16 peptides. Score 0.485 Round 5: 443 peptides, 64 chains. Longest chain 17 peptides. Score 0.495 Taking the results from Round 5 Chains 64, Residues 379, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14724 restraints for refining 6474 atoms. 13178 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2313 (Rfree = 0.000) for 6474 atoms. Found 34 (48 requested) and removed 36 (24 requested) atoms. Cycle 27: After refmac, R = 0.2272 (Rfree = 0.000) for 6452 atoms. Found 35 (48 requested) and removed 32 (24 requested) atoms. Cycle 28: After refmac, R = 0.2008 (Rfree = 0.000) for 6439 atoms. Found 13 (48 requested) and removed 25 (24 requested) atoms. Cycle 29: After refmac, R = 0.1999 (Rfree = 0.000) for 6409 atoms. Found 9 (48 requested) and removed 31 (24 requested) atoms. Cycle 30: After refmac, R = 0.2009 (Rfree = 0.000) for 6378 atoms. Found 13 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 6537 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6552 seeds are put forward Round 1: 376 peptides, 72 chains. Longest chain 16 peptides. Score 0.332 Round 2: 436 peptides, 74 chains. Longest chain 19 peptides. Score 0.418 Round 3: 440 peptides, 70 chains. Longest chain 15 peptides. Score 0.451 Round 4: 433 peptides, 66 chains. Longest chain 19 peptides. Score 0.467 Round 5: 416 peptides, 66 chains. Longest chain 20 peptides. Score 0.441 Taking the results from Round 4 Chains 68, Residues 367, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14369 restraints for refining 6474 atoms. 12867 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2260 (Rfree = 0.000) for 6474 atoms. Found 40 (48 requested) and removed 36 (24 requested) atoms. Cycle 32: After refmac, R = 0.2345 (Rfree = 0.000) for 6447 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Cycle 33: After refmac, R = 0.2270 (Rfree = 0.000) for 6427 atoms. Found 48 (48 requested) and removed 32 (24 requested) atoms. Cycle 34: After refmac, R = 0.1957 (Rfree = 0.000) for 6429 atoms. Found 24 (48 requested) and removed 31 (24 requested) atoms. Cycle 35: After refmac, R = 0.2283 (Rfree = 0.000) for 6409 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 6604 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 6633 seeds are put forward Round 1: 341 peptides, 67 chains. Longest chain 16 peptides. Score 0.308 Round 2: 380 peptides, 66 chains. Longest chain 18 peptides. Score 0.383 Round 3: 401 peptides, 69 chains. Longest chain 18 peptides. Score 0.396 Round 4: 395 peptides, 66 chains. Longest chain 22 peptides. Score 0.407 Round 5: 387 peptides, 62 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 63, Residues 325, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14816 restraints for refining 6474 atoms. 13521 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2253 (Rfree = 0.000) for 6474 atoms. Found 30 (48 requested) and removed 37 (24 requested) atoms. Cycle 37: After refmac, R = 0.2225 (Rfree = 0.000) for 6440 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. Cycle 38: After refmac, R = 0.2150 (Rfree = 0.000) for 6439 atoms. Found 48 (48 requested) and removed 26 (24 requested) atoms. Cycle 39: After refmac, R = 0.2112 (Rfree = 0.000) for 6447 atoms. Found 40 (48 requested) and removed 28 (24 requested) atoms. Cycle 40: After refmac, R = 0.2096 (Rfree = 0.000) for 6439 atoms. Found 39 (48 requested) and removed 36 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 6580 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6594 seeds are put forward Round 1: 300 peptides, 61 chains. Longest chain 12 peptides. Score 0.279 Round 2: 347 peptides, 60 chains. Longest chain 16 peptides. Score 0.371 Round 3: 344 peptides, 63 chains. Longest chain 12 peptides. Score 0.343 Round 4: 350 peptides, 61 chains. Longest chain 12 peptides. Score 0.369 Round 5: 353 peptides, 56 chains. Longest chain 16 peptides. Score 0.410 Taking the results from Round 5 Chains 57, Residues 297, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14698 restraints for refining 6474 atoms. 13468 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2183 (Rfree = 0.000) for 6474 atoms. Found 31 (48 requested) and removed 36 (24 requested) atoms. Cycle 42: After refmac, R = 0.2173 (Rfree = 0.000) for 6455 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 43: After refmac, R = 0.2122 (Rfree = 0.000) for 6452 atoms. Found 48 (48 requested) and removed 32 (24 requested) atoms. Cycle 44: After refmac, R = 0.2089 (Rfree = 0.000) for 6450 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 45: After refmac, R = 0.1775 (Rfree = 0.000) for 6452 atoms. Found 11 (48 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 6572 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6589 seeds are put forward Round 1: 270 peptides, 56 chains. Longest chain 16 peptides. Score 0.262 Round 2: 304 peptides, 55 chains. Longest chain 16 peptides. Score 0.334 Round 3: 331 peptides, 57 chains. Longest chain 16 peptides. Score 0.366 Round 4: 319 peptides, 60 chains. Longest chain 13 peptides. Score 0.322 Round 5: 314 peptides, 58 chains. Longest chain 12 peptides. Score 0.328 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 274, Estimated correctness of the model 0.0 % 6 chains (26 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (274 residues) following loop building 6 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12678 reflections ( 89.55 % complete ) and 14864 restraints for refining 6393 atoms. 13764 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2086 (Rfree = 0.000) for 6393 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2110 (Rfree = 0.000) for 6352 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2075 (Rfree = 0.000) for 6319 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2076 (Rfree = 0.000) for 6286 atoms. TimeTaking 66.17