Mon 24 Dec 00:58:39 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 2op5-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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/2op5-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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 00:58:43 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/2op5-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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 506 and 0 Target number of residues in the AU: 506 Target solvent content: 0.6053 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.4-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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.70 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: 73.087 3.400 Wilson plot Bfac: 54.52 10070 reflections ( 99.83 % complete ) and 0 restraints for refining 6196 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3224 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2444 (Rfree = 0.000) for 6196 atoms. Found 24 (46 requested) and removed 58 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 6266 seeds are put forward NCS extension: 0 residues added, 6266 seeds are put forward Round 1: 322 peptides, 60 chains. Longest chain 12 peptides. Score 0.375 Round 2: 359 peptides, 54 chains. Longest chain 17 peptides. Score 0.511 Round 3: 378 peptides, 52 chains. Longest chain 18 peptides. Score 0.564 Round 4: 389 peptides, 54 chains. Longest chain 18 peptides. Score 0.568 Round 5: 411 peptides, 56 chains. Longest chain 18 peptides. Score 0.591 Taking the results from Round 5 Chains 56, Residues 355, Estimated correctness of the model 25.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11593 restraints for refining 5103 atoms. 10229 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2700 (Rfree = 0.000) for 5103 atoms. Found 23 (38 requested) and removed 37 (19 requested) atoms. Cycle 2: After refmac, R = 0.2582 (Rfree = 0.000) for 5068 atoms. Found 12 (38 requested) and removed 21 (19 requested) atoms. Cycle 3: After refmac, R = 0.2525 (Rfree = 0.000) for 5050 atoms. Found 1 (38 requested) and removed 20 (19 requested) atoms. Cycle 4: After refmac, R = 0.2500 (Rfree = 0.000) for 5026 atoms. Found 6 (37 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2482 (Rfree = 0.000) for 5010 atoms. Found 7 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 5183 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5199 seeds are put forward Round 1: 337 peptides, 57 chains. Longest chain 18 peptides. Score 0.438 Round 2: 397 peptides, 57 chains. Longest chain 28 peptides. Score 0.558 Round 3: 411 peptides, 56 chains. Longest chain 26 peptides. Score 0.591 Round 4: 413 peptides, 56 chains. Longest chain 18 peptides. Score 0.594 Round 5: 403 peptides, 55 chains. Longest chain 27 peptides. Score 0.585 Taking the results from Round 4 Chains 56, Residues 357, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11654 restraints for refining 5104 atoms. 10282 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2542 (Rfree = 0.000) for 5104 atoms. Found 29 (38 requested) and removed 26 (19 requested) atoms. Cycle 7: After refmac, R = 0.2397 (Rfree = 0.000) for 5093 atoms. Found 11 (38 requested) and removed 25 (19 requested) atoms. Cycle 8: After refmac, R = 0.2345 (Rfree = 0.000) for 5071 atoms. Found 5 (38 requested) and removed 23 (19 requested) atoms. Cycle 9: After refmac, R = 0.2314 (Rfree = 0.000) for 5048 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.2276 (Rfree = 0.000) for 5028 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 5175 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5189 seeds are put forward Round 1: 343 peptides, 49 chains. Longest chain 19 peptides. Score 0.523 Round 2: 399 peptides, 54 chains. Longest chain 30 peptides. Score 0.585 Round 3: 402 peptides, 50 chains. Longest chain 21 peptides. Score 0.621 Round 4: 418 peptides, 51 chains. Longest chain 29 peptides. Score 0.639 Round 5: 428 peptides, 50 chains. Longest chain 30 peptides. Score 0.661 Taking the results from Round 5 Chains 51, Residues 378, Estimated correctness of the model 47.3 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11139 restraints for refining 5105 atoms. 9559 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2589 (Rfree = 0.000) for 5105 atoms. Found 23 (38 requested) and removed 25 (19 requested) atoms. Cycle 12: After refmac, R = 0.2478 (Rfree = 0.000) for 5091 atoms. Found 13 (38 requested) and removed 23 (19 requested) atoms. Cycle 13: After refmac, R = 0.2396 (Rfree = 0.000) for 5072 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 14: After refmac, R = 0.2369 (Rfree = 0.000) for 5055 atoms. Found 13 (38 requested) and removed 19 (19 requested) atoms. Cycle 15: After refmac, R = 0.2301 (Rfree = 0.000) for 5044 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 5180 seeds are put forward NCS extension: 33 residues added (7 deleted due to clashes), 5213 seeds are put forward Round 1: 366 peptides, 59 chains. Longest chain 17 peptides. Score 0.481 Round 2: 416 peptides, 53 chains. Longest chain 30 peptides. Score 0.622 Round 3: 401 peptides, 52 chains. Longest chain 33 peptides. Score 0.604 Round 4: 429 peptides, 61 chains. Longest chain 23 peptides. Score 0.584 Round 5: 430 peptides, 52 chains. Longest chain 25 peptides. Score 0.651 Taking the results from Round 5 Chains 53, Residues 378, Estimated correctness of the model 44.4 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11149 restraints for refining 5105 atoms. 9580 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2484 (Rfree = 0.000) for 5105 atoms. Found 27 (38 requested) and removed 32 (19 requested) atoms. Cycle 17: After refmac, R = 0.2344 (Rfree = 0.000) for 5086 atoms. Found 9 (38 requested) and removed 22 (19 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2313 (Rfree = 0.000) for 5071 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 19: After refmac, R = 0.2296 (Rfree = 0.000) for 5057 atoms. Found 2 (38 requested) and removed 19 (19 requested) atoms. Cycle 20: After refmac, R = 0.2286 (Rfree = 0.000) for 5037 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 5178 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5192 seeds are put forward Round 1: 347 peptides, 55 chains. Longest chain 14 peptides. Score 0.477 Round 2: 398 peptides, 54 chains. Longest chain 15 peptides. Score 0.584 Round 3: 395 peptides, 53 chains. Longest chain 20 peptides. Score 0.586 Round 4: 411 peptides, 55 chains. Longest chain 21 peptides. Score 0.598 Round 5: 381 peptides, 50 chains. Longest chain 16 peptides. Score 0.585 Taking the results from Round 4 Chains 55, Residues 356, Estimated correctness of the model 28.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11678 restraints for refining 5104 atoms. 10309 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2544 (Rfree = 0.000) for 5104 atoms. Found 24 (38 requested) and removed 21 (19 requested) atoms. Cycle 22: After refmac, R = 0.2337 (Rfree = 0.000) for 5101 atoms. Found 6 (38 requested) and removed 21 (19 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2350 (Rfree = 0.000) for 5080 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. Cycle 24: After refmac, R = 0.2307 (Rfree = 0.000) for 5068 atoms. Found 3 (38 requested) and removed 19 (19 requested) atoms. Cycle 25: After refmac, R = 0.2310 (Rfree = 0.000) for 5049 atoms. Found 2 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 5186 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 5208 seeds are put forward Round 1: 326 peptides, 53 chains. Longest chain 16 peptides. Score 0.451 Round 2: 363 peptides, 53 chains. Longest chain 18 peptides. Score 0.527 Round 3: 355 peptides, 50 chains. Longest chain 19 peptides. Score 0.537 Round 4: 362 peptides, 49 chains. Longest chain 21 peptides. Score 0.559 Round 5: 359 peptides, 46 chains. Longest chain 18 peptides. Score 0.578 Taking the results from Round 5 Chains 46, Residues 313, Estimated correctness of the model 21.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11961 restraints for refining 5106 atoms. 10755 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2447 (Rfree = 0.000) for 5106 atoms. Found 18 (38 requested) and removed 21 (19 requested) atoms. Cycle 27: After refmac, R = 0.2357 (Rfree = 0.000) for 5096 atoms. Found 12 (38 requested) and removed 20 (19 requested) atoms. Cycle 28: After refmac, R = 0.2212 (Rfree = 0.000) for 5084 atoms. Found 5 (38 requested) and removed 20 (19 requested) atoms. Cycle 29: After refmac, R = 0.2394 (Rfree = 0.000) for 5065 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. Cycle 30: After refmac, R = 0.2273 (Rfree = 0.000) for 5048 atoms. Found 11 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 5184 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 5207 seeds are put forward Round 1: 335 peptides, 53 chains. Longest chain 18 peptides. Score 0.470 Round 2: 358 peptides, 48 chains. Longest chain 24 peptides. Score 0.560 Round 3: 335 peptides, 49 chains. Longest chain 20 peptides. Score 0.507 Round 4: 354 peptides, 49 chains. Longest chain 21 peptides. Score 0.544 Round 5: 359 peptides, 51 chains. Longest chain 20 peptides. Score 0.536 Taking the results from Round 2 Chains 48, Residues 310, Estimated correctness of the model 15.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11761 restraints for refining 5104 atoms. 10569 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2342 (Rfree = 0.000) for 5104 atoms. Found 17 (38 requested) and removed 20 (19 requested) atoms. Cycle 32: After refmac, R = 0.2394 (Rfree = 0.000) for 5094 atoms. Found 14 (38 requested) and removed 21 (19 requested) atoms. Cycle 33: After refmac, R = 0.2306 (Rfree = 0.000) for 5085 atoms. Found 14 (38 requested) and removed 19 (19 requested) atoms. Cycle 34: After refmac, R = 0.2276 (Rfree = 0.000) for 5078 atoms. Found 12 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.2226 (Rfree = 0.000) for 5069 atoms. Found 11 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 5237 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 5263 seeds are put forward Round 1: 301 peptides, 54 chains. Longest chain 12 peptides. Score 0.385 Round 2: 344 peptides, 52 chains. Longest chain 17 peptides. Score 0.498 Round 3: 343 peptides, 52 chains. Longest chain 15 peptides. Score 0.496 Round 4: 346 peptides, 51 chains. Longest chain 15 peptides. Score 0.511 Round 5: 356 peptides, 55 chains. Longest chain 14 peptides. Score 0.496 Taking the results from Round 4 Chains 51, Residues 295, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11620 restraints for refining 5106 atoms. 10491 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2220 (Rfree = 0.000) for 5106 atoms. Found 16 (38 requested) and removed 22 (19 requested) atoms. Cycle 37: After refmac, R = 0.2015 (Rfree = 0.000) for 5096 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. Cycle 38: After refmac, R = 0.1995 (Rfree = 0.000) for 5074 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. Cycle 39: After refmac, R = 0.1992 (Rfree = 0.000) for 5060 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.1921 (Rfree = 0.000) for 5044 atoms. Found 5 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 5176 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 5200 seeds are put forward Round 1: 259 peptides, 47 chains. Longest chain 11 peptides. Score 0.357 Round 2: 303 peptides, 46 chains. Longest chain 22 peptides. Score 0.468 Round 3: 318 peptides, 46 chains. Longest chain 24 peptides. Score 0.499 Round 4: 317 peptides, 44 chains. Longest chain 24 peptides. Score 0.515 Round 5: 307 peptides, 43 chains. Longest chain 15 peptides. Score 0.504 Taking the results from Round 4 Chains 44, Residues 273, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11981 restraints for refining 5106 atoms. 10933 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2193 (Rfree = 0.000) for 5106 atoms. Found 16 (38 requested) and removed 21 (19 requested) atoms. Cycle 42: After refmac, R = 0.2098 (Rfree = 0.000) for 5100 atoms. Found 7 (38 requested) and removed 22 (19 requested) atoms. Cycle 43: After refmac, R = 0.2092 (Rfree = 0.000) for 5085 atoms. Found 3 (38 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.2064 (Rfree = 0.000) for 5068 atoms. Found 0 (38 requested) and removed 20 (19 requested) atoms. Cycle 45: After refmac, R = 0.2124 (Rfree = 0.000) for 5045 atoms. Found 8 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.38 Search for helices and strands: 0 residues in 0 chains, 5186 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 5217 seeds are put forward Round 1: 263 peptides, 47 chains. Longest chain 11 peptides. Score 0.367 Round 2: 302 peptides, 45 chains. Longest chain 12 peptides. Score 0.475 Round 3: 294 peptides, 44 chains. Longest chain 15 peptides. Score 0.467 Round 4: 299 peptides, 44 chains. Longest chain 15 peptides. Score 0.478 Round 5: 281 peptides, 44 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10070 reflections ( 99.83 % complete ) and 11990 restraints for refining 5106 atoms. 11014 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2151 (Rfree = 0.000) for 5106 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2136 (Rfree = 0.000) for 5081 atoms. Found 0 (38 requested) and removed 9 (19 requested) atoms. Cycle 48: After refmac, R = 0.2170 (Rfree = 0.000) for 5072 atoms. Found 0 (38 requested) and removed 4 (19 requested) atoms. Cycle 49: After refmac, R = 0.2197 (Rfree = 0.000) for 5067 atoms. TimeTaking 60.42