Mon 24 Dec 00:24:05 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 2oh1-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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/2oh1-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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 00:24:10 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/2oh1-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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 517 and 0 Target number of residues in the AU: 517 Target solvent content: 0.6527 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: 2oh1-3.6-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: 2oh1-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5728 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: 77.501 3.600 Wilson plot Bfac: 79.82 9752 reflections ( 99.15 % complete ) and 0 restraints for refining 6405 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3193 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3117 (Rfree = 0.000) for 6405 atoms. Found 38 (41 requested) and removed 59 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 6520 seeds are put forward NCS extension: 0 residues added, 6520 seeds are put forward Round 1: 374 peptides, 67 chains. Longest chain 16 peptides. Score 0.398 Round 2: 413 peptides, 57 chains. Longest chain 19 peptides. Score 0.546 Round 3: 461 peptides, 55 chains. Longest chain 22 peptides. Score 0.632 Round 4: 470 peptides, 54 chains. Longest chain 29 peptides. Score 0.650 Round 5: 481 peptides, 56 chains. Longest chain 24 peptides. Score 0.653 Taking the results from Round 5 Chains 58, Residues 425, Estimated correctness of the model 34.2 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11230 restraints for refining 5191 atoms. 9544 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2581 (Rfree = 0.000) for 5191 atoms. Found 11 (33 requested) and removed 48 (16 requested) atoms. Cycle 2: After refmac, R = 0.2555 (Rfree = 0.000) for 5084 atoms. Found 11 (33 requested) and removed 32 (16 requested) atoms. Cycle 3: After refmac, R = 0.2394 (Rfree = 0.000) for 5034 atoms. Found 16 (32 requested) and removed 37 (16 requested) atoms. Cycle 4: After refmac, R = 0.2384 (Rfree = 0.000) for 4993 atoms. Found 8 (32 requested) and removed 31 (16 requested) atoms. Cycle 5: After refmac, R = 0.2305 (Rfree = 0.000) for 4949 atoms. Found 6 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 5132 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 5157 seeds are put forward Round 1: 378 peptides, 53 chains. Longest chain 18 peptides. Score 0.517 Round 2: 454 peptides, 53 chains. Longest chain 27 peptides. Score 0.635 Round 3: 461 peptides, 53 chains. Longest chain 22 peptides. Score 0.644 Round 4: 468 peptides, 50 chains. Longest chain 29 peptides. Score 0.672 Round 5: 433 peptides, 49 chains. Longest chain 21 peptides. Score 0.631 Taking the results from Round 4 Chains 53, Residues 418, Estimated correctness of the model 40.6 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11175 restraints for refining 5192 atoms. 9466 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2390 (Rfree = 0.000) for 5192 atoms. Found 13 (33 requested) and removed 45 (16 requested) atoms. Cycle 7: After refmac, R = 0.2264 (Rfree = 0.000) for 5137 atoms. Found 5 (33 requested) and removed 26 (16 requested) atoms. Cycle 8: After refmac, R = 0.2257 (Rfree = 0.000) for 5103 atoms. Found 11 (32 requested) and removed 34 (16 requested) atoms. Cycle 9: After refmac, R = 0.2541 (Rfree = 0.000) for 5069 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 10: After refmac, R = 0.2072 (Rfree = 0.000) for 5053 atoms. Found 2 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5187 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5199 seeds are put forward Round 1: 408 peptides, 66 chains. Longest chain 21 peptides. Score 0.470 Round 2: 438 peptides, 59 chains. Longest chain 22 peptides. Score 0.572 Round 3: 435 peptides, 54 chains. Longest chain 24 peptides. Score 0.601 Round 4: 443 peptides, 55 chains. Longest chain 21 peptides. Score 0.606 Round 5: 438 peptides, 52 chains. Longest chain 25 peptides. Score 0.619 Taking the results from Round 5 Chains 52, Residues 386, Estimated correctness of the model 21.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11458 restraints for refining 5191 atoms. 9966 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2330 (Rfree = 0.000) for 5191 atoms. Found 15 (33 requested) and removed 33 (16 requested) atoms. Cycle 12: After refmac, R = 0.2425 (Rfree = 0.000) for 5152 atoms. Found 27 (33 requested) and removed 29 (16 requested) atoms. Cycle 13: After refmac, R = 0.2407 (Rfree = 0.000) for 5136 atoms. Found 20 (33 requested) and removed 34 (16 requested) atoms. Cycle 14: After refmac, R = 0.2049 (Rfree = 0.000) for 5108 atoms. Found 4 (32 requested) and removed 23 (16 requested) atoms. Cycle 15: After refmac, R = 0.2332 (Rfree = 0.000) for 5080 atoms. Found 23 (32 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5284 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5301 seeds are put forward Round 1: 358 peptides, 60 chains. Longest chain 14 peptides. Score 0.425 Round 2: 412 peptides, 54 chains. Longest chain 20 peptides. Score 0.566 Round 3: 421 peptides, 50 chains. Longest chain 30 peptides. Score 0.608 Round 4: 422 peptides, 49 chains. Longest chain 24 peptides. Score 0.616 Round 5: 420 peptides, 50 chains. Longest chain 26 peptides. Score 0.606 Taking the results from Round 4 Chains 50, Residues 373, Estimated correctness of the model 20.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11438 restraints for refining 5193 atoms. 9968 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2418 (Rfree = 0.000) for 5193 atoms. Found 15 (33 requested) and removed 41 (16 requested) atoms. Cycle 17: After refmac, R = 0.2313 (Rfree = 0.000) for 5149 atoms. Found 15 (33 requested) and removed 29 (16 requested) atoms. Cycle 18: After refmac, R = 0.2260 (Rfree = 0.000) for 5126 atoms. Found 20 (32 requested) and removed 29 (16 requested) atoms. Cycle 19: After refmac, R = 0.2175 (Rfree = 0.000) for 5107 atoms. Found 22 (32 requested) and removed 25 (16 requested) atoms. Cycle 20: After refmac, R = 0.2182 (Rfree = 0.000) for 5095 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.41 Search for helices and strands: 0 residues in 0 chains, 5267 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 5297 seeds are put forward Round 1: 368 peptides, 65 chains. Longest chain 14 peptides. Score 0.403 Round 2: 417 peptides, 62 chains. Longest chain 19 peptides. Score 0.516 Round 3: 397 peptides, 58 chains. Longest chain 21 peptides. Score 0.512 Round 4: 405 peptides, 62 chains. Longest chain 18 peptides. Score 0.495 Round 5: 423 peptides, 57 chains. Longest chain 22 peptides. Score 0.562 Taking the results from Round 5 Chains 60, Residues 366, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11501 restraints for refining 5192 atoms. 10026 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2317 (Rfree = 0.000) for 5192 atoms. Found 11 (33 requested) and removed 32 (16 requested) atoms. Cycle 22: After refmac, R = 0.2188 (Rfree = 0.000) for 5150 atoms. Found 9 (33 requested) and removed 21 (16 requested) atoms. Cycle 23: After refmac, R = 0.2076 (Rfree = 0.000) for 5132 atoms. Found 6 (32 requested) and removed 27 (16 requested) atoms. Cycle 24: After refmac, R = 0.2039 (Rfree = 0.000) for 5101 atoms. Found 8 (32 requested) and removed 28 (16 requested) atoms. Cycle 25: After refmac, R = 0.2005 (Rfree = 0.000) for 5074 atoms. Found 6 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5221 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5237 seeds are put forward Round 1: 386 peptides, 62 chains. Longest chain 18 peptides. Score 0.461 Round 2: 412 peptides, 58 chains. Longest chain 20 peptides. Score 0.537 Round 3: 397 peptides, 55 chains. Longest chain 18 peptides. Score 0.534 Round 4: 412 peptides, 55 chains. Longest chain 18 peptides. Score 0.559 Round 5: 414 peptides, 56 chains. Longest chain 19 peptides. Score 0.555 Taking the results from Round 4 Chains 60, Residues 357, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11313 restraints for refining 5191 atoms. 9819 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2217 (Rfree = 0.000) for 5191 atoms. Found 7 (33 requested) and removed 31 (16 requested) atoms. Cycle 27: After refmac, R = 0.2185 (Rfree = 0.000) for 5149 atoms. Found 6 (33 requested) and removed 22 (16 requested) atoms. Cycle 28: After refmac, R = 0.2098 (Rfree = 0.000) for 5122 atoms. Found 4 (32 requested) and removed 25 (16 requested) atoms. Cycle 29: After refmac, R = 0.2098 (Rfree = 0.000) for 5095 atoms. Found 8 (32 requested) and removed 27 (16 requested) atoms. Cycle 30: After refmac, R = 0.2028 (Rfree = 0.000) for 5070 atoms. Found 8 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5248 seeds are put forward Round 1: 321 peptides, 54 chains. Longest chain 16 peptides. Score 0.403 Round 2: 352 peptides, 53 chains. Longest chain 17 peptides. Score 0.471 Round 3: 362 peptides, 53 chains. Longest chain 17 peptides. Score 0.489 Round 4: 362 peptides, 51 chains. Longest chain 20 peptides. Score 0.505 Round 5: 358 peptides, 50 chains. Longest chain 18 peptides. Score 0.506 Taking the results from Round 5 Chains 52, Residues 308, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11898 restraints for refining 5193 atoms. 10653 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2252 (Rfree = 0.000) for 5193 atoms. Found 6 (33 requested) and removed 35 (16 requested) atoms. Cycle 32: After refmac, R = 0.2202 (Rfree = 0.000) for 5152 atoms. Found 6 (33 requested) and removed 29 (16 requested) atoms. Cycle 33: After refmac, R = 0.2140 (Rfree = 0.000) for 5125 atoms. Found 8 (32 requested) and removed 24 (16 requested) atoms. Cycle 34: After refmac, R = 0.2133 (Rfree = 0.000) for 5104 atoms. Found 10 (32 requested) and removed 24 (16 requested) atoms. Cycle 35: After refmac, R = 0.1909 (Rfree = 0.000) for 5085 atoms. Found 2 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 5232 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 5252 seeds are put forward Round 1: 302 peptides, 53 chains. Longest chain 19 peptides. Score 0.374 Round 2: 349 peptides, 57 chains. Longest chain 24 peptides. Score 0.433 Round 3: 355 peptides, 57 chains. Longest chain 17 peptides. Score 0.444 Round 4: 361 peptides, 57 chains. Longest chain 24 peptides. Score 0.455 Round 5: 380 peptides, 58 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 5 Chains 58, Residues 322, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11787 restraints for refining 5193 atoms. 10557 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2112 (Rfree = 0.000) for 5193 atoms. Found 7 (33 requested) and removed 29 (16 requested) atoms. Cycle 37: After refmac, R = 0.1976 (Rfree = 0.000) for 5157 atoms. Found 8 (33 requested) and removed 21 (16 requested) atoms. Cycle 38: After refmac, R = 0.2018 (Rfree = 0.000) for 5128 atoms. Found 11 (33 requested) and removed 19 (16 requested) atoms. Cycle 39: After refmac, R = 0.1968 (Rfree = 0.000) for 5116 atoms. Found 15 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 5104 atoms. Found 14 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 5263 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5278 seeds are put forward Round 1: 275 peptides, 51 chains. Longest chain 22 peptides. Score 0.335 Round 2: 311 peptides, 50 chains. Longest chain 16 peptides. Score 0.418 Round 3: 331 peptides, 48 chains. Longest chain 23 peptides. Score 0.473 Round 4: 323 peptides, 47 chains. Longest chain 15 peptides. Score 0.467 Round 5: 326 peptides, 47 chains. Longest chain 23 peptides. Score 0.472 Taking the results from Round 3 Chains 48, Residues 283, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11765 restraints for refining 5191 atoms. 10681 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2009 (Rfree = 0.000) for 5191 atoms. Found 12 (33 requested) and removed 26 (16 requested) atoms. Cycle 42: After refmac, R = 0.1986 (Rfree = 0.000) for 5169 atoms. Found 15 (33 requested) and removed 20 (16 requested) atoms. Cycle 43: After refmac, R = 0.1917 (Rfree = 0.000) for 5153 atoms. Found 12 (33 requested) and removed 19 (16 requested) atoms. Cycle 44: After refmac, R = 0.1886 (Rfree = 0.000) for 5138 atoms. Found 12 (33 requested) and removed 19 (16 requested) atoms. Cycle 45: After refmac, R = 0.1905 (Rfree = 0.000) for 5123 atoms. Found 15 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 5229 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5255 seeds are put forward Round 1: 262 peptides, 50 chains. Longest chain 14 peptides. Score 0.315 Round 2: 282 peptides, 44 chains. Longest chain 14 peptides. Score 0.413 Round 3: 294 peptides, 46 chains. Longest chain 14 peptides. Score 0.419 Round 4: 294 peptides, 46 chains. Longest chain 14 peptides. Score 0.419 Round 5: 273 peptides, 40 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 233, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9752 reflections ( 99.15 % complete ) and 11884 restraints for refining 5190 atoms. 10977 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1881 (Rfree = 0.000) for 5190 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1932 (Rfree = 0.000) for 5159 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1888 (Rfree = 0.000) for 5132 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1940 (Rfree = 0.000) for 5104 atoms. TimeTaking 53.53