Mon 24 Dec 00:54:51 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 2oh1-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-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/2oh1-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-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 00:54:56 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/2oh1-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-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 530 and 0 Target number of residues in the AU: 530 Target solvent content: 0.6440 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-3.4-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: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5728 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: 77.501 3.400 Wilson plot Bfac: 74.13 11524 reflections ( 99.13 % complete ) and 0 restraints for refining 6338 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3130 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2947 (Rfree = 0.000) for 6338 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 6462 seeds are put forward NCS extension: 0 residues added, 6462 seeds are put forward Round 1: 353 peptides, 61 chains. Longest chain 12 peptides. Score 0.407 Round 2: 432 peptides, 61 chains. Longest chain 20 peptides. Score 0.548 Round 3: 466 peptides, 55 chains. Longest chain 36 peptides. Score 0.639 Round 4: 467 peptides, 59 chains. Longest chain 22 peptides. Score 0.615 Round 5: 468 peptides, 52 chains. Longest chain 24 peptides. Score 0.660 Taking the results from Round 5 Chains 55, Residues 416, Estimated correctness of the model 47.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10792 restraints for refining 5208 atoms. 9020 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2593 (Rfree = 0.000) for 5208 atoms. Found 7 (39 requested) and removed 47 (19 requested) atoms. Cycle 2: After refmac, R = 0.2592 (Rfree = 0.000) for 5079 atoms. Found 11 (39 requested) and removed 35 (19 requested) atoms. Cycle 3: After refmac, R = 0.2487 (Rfree = 0.000) for 5024 atoms. Found 7 (38 requested) and removed 31 (19 requested) atoms. Cycle 4: After refmac, R = 0.2407 (Rfree = 0.000) for 4968 atoms. Found 12 (37 requested) and removed 29 (18 requested) atoms. Cycle 5: After refmac, R = 0.2372 (Rfree = 0.000) for 4931 atoms. Found 9 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 5087 seeds are put forward NCS extension: 11 residues added (9 deleted due to clashes), 5098 seeds are put forward Round 1: 405 peptides, 62 chains. Longest chain 18 peptides. Score 0.495 Round 2: 449 peptides, 56 chains. Longest chain 18 peptides. Score 0.609 Round 3: 444 peptides, 54 chains. Longest chain 19 peptides. Score 0.614 Round 4: 458 peptides, 58 chains. Longest chain 19 peptides. Score 0.609 Round 5: 467 peptides, 50 chains. Longest chain 22 peptides. Score 0.670 Taking the results from Round 5 Chains 50, Residues 417, Estimated correctness of the model 49.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11282 restraints for refining 5174 atoms. 9664 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2356 (Rfree = 0.000) for 5174 atoms. Found 15 (39 requested) and removed 40 (19 requested) atoms. Cycle 7: After refmac, R = 0.2306 (Rfree = 0.000) for 5123 atoms. Found 12 (38 requested) and removed 31 (19 requested) atoms. Cycle 8: After refmac, R = 0.2261 (Rfree = 0.000) for 5096 atoms. Found 16 (38 requested) and removed 25 (19 requested) atoms. Cycle 9: After refmac, R = 0.2211 (Rfree = 0.000) for 5076 atoms. Found 9 (38 requested) and removed 28 (19 requested) atoms. Cycle 10: After refmac, R = 0.2138 (Rfree = 0.000) for 5048 atoms. Found 3 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 5202 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 5212 seeds are put forward Round 1: 400 peptides, 61 chains. Longest chain 17 peptides. Score 0.494 Round 2: 459 peptides, 55 chains. Longest chain 21 peptides. Score 0.629 Round 3: 460 peptides, 58 chains. Longest chain 19 peptides. Score 0.611 Round 4: 477 peptides, 59 chains. Longest chain 24 peptides. Score 0.629 Round 5: 474 peptides, 55 chains. Longest chain 22 peptides. Score 0.650 Taking the results from Round 5 Chains 56, Residues 419, Estimated correctness of the model 44.1 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11138 restraints for refining 5207 atoms. 9463 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2293 (Rfree = 0.000) for 5207 atoms. Found 7 (39 requested) and removed 29 (19 requested) atoms. Cycle 12: After refmac, R = 0.2178 (Rfree = 0.000) for 5167 atoms. Found 11 (39 requested) and removed 27 (19 requested) atoms. Cycle 13: After refmac, R = 0.2120 (Rfree = 0.000) for 5141 atoms. Found 9 (38 requested) and removed 29 (19 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 5120 atoms. Found 6 (38 requested) and removed 27 (19 requested) atoms. Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 5092 atoms. Found 8 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 5265 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 5276 seeds are put forward Round 1: 403 peptides, 65 chains. Longest chain 17 peptides. Score 0.469 Round 2: 438 peptides, 53 chains. Longest chain 21 peptides. Score 0.612 Round 3: 444 peptides, 52 chains. Longest chain 20 peptides. Score 0.627 Round 4: 434 peptides, 48 chains. Longest chain 19 peptides. Score 0.639 Round 5: 425 peptides, 56 chains. Longest chain 30 peptides. Score 0.573 Taking the results from Round 4 Chains 49, Residues 386, Estimated correctness of the model 40.9 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11157 restraints for refining 5208 atoms. 9580 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2345 (Rfree = 0.000) for 5208 atoms. Found 14 (39 requested) and removed 36 (19 requested) atoms. Cycle 17: After refmac, R = 0.2150 (Rfree = 0.000) for 5178 atoms. Found 10 (39 requested) and removed 31 (19 requested) atoms. Cycle 18: After refmac, R = 0.2068 (Rfree = 0.000) for 5150 atoms. Found 5 (38 requested) and removed 27 (19 requested) atoms. Cycle 19: After refmac, R = 0.1969 (Rfree = 0.000) for 5123 atoms. Found 11 (38 requested) and removed 27 (19 requested) atoms. Cycle 20: After refmac, R = 0.2267 (Rfree = 0.000) for 5101 atoms. Found 32 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 5239 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5262 seeds are put forward Round 1: 403 peptides, 58 chains. Longest chain 18 peptides. Score 0.522 Round 2: 423 peptides, 59 chains. Longest chain 21 peptides. Score 0.548 Round 3: 439 peptides, 57 chains. Longest chain 20 peptides. Score 0.587 Round 4: 452 peptides, 54 chains. Longest chain 19 peptides. Score 0.626 Round 5: 440 peptides, 55 chains. Longest chain 19 peptides. Score 0.602 Taking the results from Round 4 Chains 57, Residues 398, Estimated correctness of the model 36.9 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10994 restraints for refining 5208 atoms. 9300 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2204 (Rfree = 0.000) for 5208 atoms. Found 21 (39 requested) and removed 29 (19 requested) atoms. Cycle 22: After refmac, R = 0.2106 (Rfree = 0.000) for 5181 atoms. Found 4 (39 requested) and removed 21 (19 requested) atoms. Cycle 23: After refmac, R = 0.2062 (Rfree = 0.000) for 5153 atoms. Found 6 (38 requested) and removed 22 (19 requested) atoms. Cycle 24: After refmac, R = 0.2060 (Rfree = 0.000) for 5135 atoms. Found 15 (38 requested) and removed 22 (19 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1986 (Rfree = 0.000) for 5124 atoms. Found 4 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 5262 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5280 seeds are put forward Round 1: 384 peptides, 60 chains. Longest chain 18 peptides. Score 0.474 Round 2: 437 peptides, 55 chains. Longest chain 19 peptides. Score 0.598 Round 3: 439 peptides, 60 chains. Longest chain 18 peptides. Score 0.567 Round 4: 440 peptides, 56 chains. Longest chain 19 peptides. Score 0.595 Round 5: 418 peptides, 52 chains. Longest chain 20 peptides. Score 0.589 Taking the results from Round 2 Chains 57, Residues 382, Estimated correctness of the model 28.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11281 restraints for refining 5208 atoms. 9755 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2190 (Rfree = 0.000) for 5208 atoms. Found 8 (39 requested) and removed 27 (19 requested) atoms. Cycle 27: After refmac, R = 0.2144 (Rfree = 0.000) for 5180 atoms. Found 12 (39 requested) and removed 26 (19 requested) atoms. Cycle 28: After refmac, R = 0.1984 (Rfree = 0.000) for 5156 atoms. Found 6 (39 requested) and removed 23 (19 requested) atoms. Cycle 29: After refmac, R = 0.1965 (Rfree = 0.000) for 5134 atoms. Found 12 (38 requested) and removed 22 (19 requested) atoms. Cycle 30: After refmac, R = 0.1937 (Rfree = 0.000) for 5122 atoms. Found 11 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 5262 seeds are put forward NCS extension: 9 residues added (6 deleted due to clashes), 5271 seeds are put forward Round 1: 384 peptides, 65 chains. Longest chain 18 peptides. Score 0.433 Round 2: 409 peptides, 59 chains. Longest chain 20 peptides. Score 0.525 Round 3: 421 peptides, 55 chains. Longest chain 25 peptides. Score 0.573 Round 4: 423 peptides, 52 chains. Longest chain 28 peptides. Score 0.597 Round 5: 441 peptides, 53 chains. Longest chain 23 peptides. Score 0.617 Taking the results from Round 5 Chains 57, Residues 388, Estimated correctness of the model 34.1 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11023 restraints for refining 5208 atoms. 9389 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2140 (Rfree = 0.000) for 5208 atoms. Found 16 (39 requested) and removed 30 (19 requested) atoms. Cycle 32: After refmac, R = 0.2060 (Rfree = 0.000) for 5178 atoms. Found 15 (39 requested) and removed 25 (19 requested) atoms. Cycle 33: After refmac, R = 0.2013 (Rfree = 0.000) for 5156 atoms. Found 16 (39 requested) and removed 22 (19 requested) atoms. Cycle 34: After refmac, R = 0.2023 (Rfree = 0.000) for 5144 atoms. Found 14 (38 requested) and removed 23 (19 requested) atoms. Cycle 35: After refmac, R = 0.1918 (Rfree = 0.000) for 5131 atoms. Found 6 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 5251 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 5277 seeds are put forward Round 1: 351 peptides, 57 chains. Longest chain 15 peptides. Score 0.436 Round 2: 396 peptides, 58 chains. Longest chain 18 peptides. Score 0.510 Round 3: 406 peptides, 58 chains. Longest chain 18 peptides. Score 0.527 Round 4: 393 peptides, 59 chains. Longest chain 18 peptides. Score 0.497 Round 5: 411 peptides, 51 chains. Longest chain 21 peptides. Score 0.586 Taking the results from Round 5 Chains 52, Residues 360, Estimated correctness of the model 24.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11193 restraints for refining 5208 atoms. 9699 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2136 (Rfree = 0.000) for 5208 atoms. Found 16 (39 requested) and removed 33 (19 requested) atoms. Cycle 37: After refmac, R = 0.2021 (Rfree = 0.000) for 5175 atoms. Found 8 (39 requested) and removed 25 (19 requested) atoms. Cycle 38: After refmac, R = 0.2009 (Rfree = 0.000) for 5158 atoms. Found 6 (38 requested) and removed 22 (19 requested) atoms. Cycle 39: After refmac, R = 0.1936 (Rfree = 0.000) for 5137 atoms. Found 7 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.1904 (Rfree = 0.000) for 5119 atoms. Found 5 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 5209 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5230 seeds are put forward Round 1: 312 peptides, 51 chains. Longest chain 17 peptides. Score 0.411 Round 2: 357 peptides, 52 chains. Longest chain 21 peptides. Score 0.488 Round 3: 363 peptides, 51 chains. Longest chain 24 peptides. Score 0.507 Round 4: 363 peptides, 50 chains. Longest chain 21 peptides. Score 0.515 Round 5: 370 peptides, 51 chains. Longest chain 17 peptides. Score 0.519 Taking the results from Round 5 Chains 51, Residues 319, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11472 restraints for refining 5208 atoms. 10161 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2088 (Rfree = 0.000) for 5208 atoms. Found 15 (39 requested) and removed 27 (19 requested) atoms. Cycle 42: After refmac, R = 0.1995 (Rfree = 0.000) for 5187 atoms. Found 9 (39 requested) and removed 22 (19 requested) atoms. Cycle 43: After refmac, R = 0.1984 (Rfree = 0.000) for 5170 atoms. Found 8 (39 requested) and removed 22 (19 requested) atoms. Cycle 44: After refmac, R = 0.1929 (Rfree = 0.000) for 5153 atoms. Found 6 (38 requested) and removed 21 (19 requested) atoms. Cycle 45: After refmac, R = 0.1914 (Rfree = 0.000) for 5136 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 5228 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 5256 seeds are put forward Round 1: 327 peptides, 56 chains. Longest chain 16 peptides. Score 0.398 Round 2: 340 peptides, 51 chains. Longest chain 18 peptides. Score 0.465 Round 3: 386 peptides, 53 chains. Longest chain 23 peptides. Score 0.531 Round 4: 368 peptides, 53 chains. Longest chain 19 peptides. Score 0.500 Round 5: 367 peptides, 48 chains. Longest chain 20 peptides. Score 0.537 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 319, Estimated correctness of the model 6.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11524 reflections ( 99.13 % complete ) and 11611 restraints for refining 5206 atoms. 10383 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2083 (Rfree = 0.000) for 5206 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2084 (Rfree = 0.000) for 5179 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2030 (Rfree = 0.000) for 5149 atoms. Found 0 (38 requested) and removed 17 (19 requested) atoms. Cycle 49: After refmac, R = 0.2010 (Rfree = 0.000) for 5128 atoms. TimeTaking 64.2