Sun 23 Dec 22:22:52 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2op5-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:02 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/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.2-parrot-hancs/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 521 and 0 Target number of residues in the AU: 521 Target solvent content: 0.5936 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: 2op5-3.2-parrot-hancs.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: 2op5-3.2-parrot-hancs.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 3.200 Wilson plot Bfac: 49.79 12025 reflections ( 99.86 % complete ) and 0 restraints for refining 6227 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3266 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2627 (Rfree = 0.000) for 6227 atoms. Found 36 (55 requested) and removed 75 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 6309 seeds are put forward NCS extension: 0 residues added, 6309 seeds are put forward Round 1: 333 peptides, 62 chains. Longest chain 12 peptides. Score 0.381 Round 2: 401 peptides, 57 chains. Longest chain 17 peptides. Score 0.565 Round 3: 419 peptides, 55 chains. Longest chain 26 peptides. Score 0.612 Round 4: 422 peptides, 57 chains. Longest chain 22 peptides. Score 0.602 Round 5: 437 peptides, 54 chains. Longest chain 23 peptides. Score 0.648 Taking the results from Round 5 Chains 54, Residues 383, Estimated correctness of the model 53.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12025 reflections ( 99.86 % complete ) and 11238 restraints for refining 5127 atoms. 9760 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2555 (Rfree = 0.000) for 5127 atoms. Found 44 (46 requested) and removed 30 (23 requested) atoms. Cycle 2: After refmac, R = 0.2409 (Rfree = 0.000) for 5094 atoms. Found 9 (46 requested) and removed 32 (23 requested) atoms. Cycle 3: After refmac, R = 0.2422 (Rfree = 0.000) for 5047 atoms. Found 19 (45 requested) and removed 29 (22 requested) atoms. Cycle 4: After refmac, R = 0.2345 (Rfree = 0.000) for 5026 atoms. Found 11 (45 requested) and removed 28 (22 requested) atoms. Cycle 5: After refmac, R = 0.2367 (Rfree = 0.000) for 5000 atoms. Found 8 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 5188 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 5205 seeds are put forward Round 1: 416 peptides, 68 chains. Longest chain 14 peptides. Score 0.504 Round 2: 444 peptides, 61 chains. Longest chain 30 peptides. Score 0.609 Round 3: 447 peptides, 57 chains. Longest chain 26 peptides. Score 0.642 Round 4: 464 peptides, 56 chains. Longest chain 25 peptides. Score 0.674 Round 5: 435 peptides, 54 chains. Longest chain 19 peptides. Score 0.644 Taking the results from Round 4 Chains 56, Residues 408, Estimated correctness of the model 59.5 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11266 restraints for refining 5127 atoms. 9675 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2597 (Rfree = 0.000) for 5127 atoms. Found 31 (46 requested) and removed 38 (23 requested) atoms. Cycle 7: After refmac, R = 0.2469 (Rfree = 0.000) for 5105 atoms. Found 15 (45 requested) and removed 30 (22 requested) atoms. Cycle 8: After refmac, R = 0.2387 (Rfree = 0.000) for 5079 atoms. Found 13 (45 requested) and removed 27 (22 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 5057 atoms. Found 17 (45 requested) and removed 24 (22 requested) atoms. Cycle 10: After refmac, R = 0.2321 (Rfree = 0.000) for 5043 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 5242 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 5266 seeds are put forward Round 1: 380 peptides, 57 chains. Longest chain 16 peptides. Score 0.526 Round 2: 425 peptides, 57 chains. Longest chain 21 peptides. Score 0.607 Round 3: 426 peptides, 53 chains. Longest chain 21 peptides. Score 0.638 Round 4: 445 peptides, 57 chains. Longest chain 24 peptides. Score 0.639 Round 5: 428 peptides, 52 chains. Longest chain 21 peptides. Score 0.648 Taking the results from Round 5 Chains 53, Residues 376, Estimated correctness of the model 53.4 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11436 restraints for refining 5126 atoms. 9934 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2501 (Rfree = 0.000) for 5126 atoms. Found 23 (46 requested) and removed 36 (23 requested) atoms. Cycle 12: After refmac, R = 0.2409 (Rfree = 0.000) for 5097 atoms. Found 18 (45 requested) and removed 26 (22 requested) atoms. Cycle 13: After refmac, R = 0.2328 (Rfree = 0.000) for 5080 atoms. Found 22 (45 requested) and removed 27 (22 requested) atoms. Cycle 14: After refmac, R = 0.2240 (Rfree = 0.000) for 5069 atoms. Found 13 (45 requested) and removed 22 (22 requested) atoms. Cycle 15: After refmac, R = 0.2186 (Rfree = 0.000) for 5054 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 5197 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 5225 seeds are put forward Round 1: 345 peptides, 54 chains. Longest chain 16 peptides. Score 0.482 Round 2: 377 peptides, 49 chains. Longest chain 23 peptides. Score 0.586 Round 3: 391 peptides, 49 chains. Longest chain 22 peptides. Score 0.610 Round 4: 414 peptides, 55 chains. Longest chain 24 peptides. Score 0.604 Round 5: 419 peptides, 50 chains. Longest chain 24 peptides. Score 0.648 Taking the results from Round 5 Chains 51, Residues 369, Estimated correctness of the model 53.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11398 restraints for refining 5125 atoms. 9943 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2383 (Rfree = 0.000) for 5125 atoms. Found 24 (46 requested) and removed 29 (23 requested) atoms. Cycle 17: After refmac, R = 0.2266 (Rfree = 0.000) for 5108 atoms. Found 17 (45 requested) and removed 22 (22 requested) atoms. Cycle 18: After refmac, R = 0.2191 (Rfree = 0.000) for 5098 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 19: After refmac, R = 0.2149 (Rfree = 0.000) for 5084 atoms. Found 9 (45 requested) and removed 23 (22 requested) atoms. Cycle 20: After refmac, R = 0.2095 (Rfree = 0.000) for 5067 atoms. Found 12 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 5198 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 5234 seeds are put forward Round 1: 362 peptides, 57 chains. Longest chain 14 peptides. Score 0.490 Round 2: 397 peptides, 59 chains. Longest chain 17 peptides. Score 0.542 Round 3: 406 peptides, 58 chains. Longest chain 25 peptides. Score 0.567 Round 4: 417 peptides, 58 chains. Longest chain 18 peptides. Score 0.586 Round 5: 418 peptides, 58 chains. Longest chain 17 peptides. Score 0.588 Taking the results from Round 5 Chains 58, Residues 360, Estimated correctness of the model 37.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11421 restraints for refining 5127 atoms. 10039 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2317 (Rfree = 0.000) for 5127 atoms. Found 19 (46 requested) and removed 25 (23 requested) atoms. Cycle 22: After refmac, R = 0.2185 (Rfree = 0.000) for 5114 atoms. Found 12 (45 requested) and removed 23 (22 requested) atoms. Cycle 23: After refmac, R = 0.2116 (Rfree = 0.000) for 5101 atoms. Found 10 (45 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2035 (Rfree = 0.000) for 5088 atoms. Found 5 (45 requested) and removed 22 (22 requested) atoms. Cycle 25: After refmac, R = 0.2009 (Rfree = 0.000) for 5070 atoms. Found 3 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.23 Search for helices and strands: 0 residues in 0 chains, 5204 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5219 seeds are put forward Round 1: 335 peptides, 57 chains. Longest chain 18 peptides. Score 0.433 Round 2: 389 peptides, 58 chains. Longest chain 24 peptides. Score 0.535 Round 3: 387 peptides, 57 chains. Longest chain 21 peptides. Score 0.540 Round 4: 394 peptides, 58 chains. Longest chain 19 peptides. Score 0.544 Round 5: 410 peptides, 60 chains. Longest chain 24 peptides. Score 0.558 Taking the results from Round 5 Chains 60, Residues 350, Estimated correctness of the model 29.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11473 restraints for refining 5126 atoms. 10133 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2161 (Rfree = 0.000) for 5126 atoms. Found 20 (46 requested) and removed 24 (23 requested) atoms. Cycle 27: After refmac, R = 0.2069 (Rfree = 0.000) for 5116 atoms. Found 13 (45 requested) and removed 23 (22 requested) atoms. Cycle 28: After refmac, R = 0.2039 (Rfree = 0.000) for 5097 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 29: After refmac, R = 0.1936 (Rfree = 0.000) for 5084 atoms. Found 6 (45 requested) and removed 23 (22 requested) atoms. Cycle 30: After refmac, R = 0.1904 (Rfree = 0.000) for 5064 atoms. Found 5 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 5207 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5232 seeds are put forward Round 1: 337 peptides, 60 chains. Longest chain 18 peptides. Score 0.409 Round 2: 383 peptides, 51 chains. Longest chain 33 peptides. Score 0.581 Round 3: 387 peptides, 53 chains. Longest chain 20 peptides. Score 0.572 Round 4: 388 peptides, 52 chains. Longest chain 19 peptides. Score 0.582 Round 5: 385 peptides, 60 chains. Longest chain 18 peptides. Score 0.510 Taking the results from Round 4 Chains 52, Residues 336, Estimated correctness of the model 36.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11534 restraints for refining 5127 atoms. 10242 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2089 (Rfree = 0.000) for 5127 atoms. Found 26 (46 requested) and removed 24 (23 requested) atoms. Cycle 32: After refmac, R = 0.1996 (Rfree = 0.000) for 5122 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. Cycle 33: After refmac, R = 0.1994 (Rfree = 0.000) for 5106 atoms. Found 10 (45 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.1936 (Rfree = 0.000) for 5090 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.1913 (Rfree = 0.000) for 5075 atoms. Found 5 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.27 Search for helices and strands: 0 residues in 0 chains, 5200 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5222 seeds are put forward Round 1: 310 peptides, 52 chains. Longest chain 19 peptides. Score 0.426 Round 2: 328 peptides, 46 chains. Longest chain 23 peptides. Score 0.519 Round 3: 361 peptides, 50 chains. Longest chain 34 peptides. Score 0.549 Round 4: 331 peptides, 47 chains. Longest chain 23 peptides. Score 0.516 Round 5: 342 peptides, 46 chains. Longest chain 33 peptides. Score 0.546 Taking the results from Round 3 Chains 50, Residues 311, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11501 restraints for refining 5127 atoms. 10307 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2046 (Rfree = 0.000) for 5127 atoms. Found 20 (46 requested) and removed 23 (23 requested) atoms. Cycle 37: After refmac, R = 0.1983 (Rfree = 0.000) for 5121 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 38: After refmac, R = 0.1949 (Rfree = 0.000) for 5104 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.1888 (Rfree = 0.000) for 5084 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.1846 (Rfree = 0.000) for 5069 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 5167 seeds are put forward NCS extension: 34 residues added (5 deleted due to clashes), 5201 seeds are put forward Round 1: 318 peptides, 58 chains. Longest chain 13 peptides. Score 0.385 Round 2: 355 peptides, 53 chains. Longest chain 27 peptides. Score 0.511 Round 3: 356 peptides, 56 chains. Longest chain 17 peptides. Score 0.487 Round 4: 366 peptides, 53 chains. Longest chain 33 peptides. Score 0.533 Round 5: 352 peptides, 51 chains. Longest chain 23 peptides. Score 0.523 Taking the results from Round 4 Chains 53, Residues 313, Estimated correctness of the model 21.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12025 reflections ( 99.86 % complete ) and 11401 restraints for refining 5127 atoms. 10187 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2065 (Rfree = 0.000) for 5127 atoms. Found 26 (46 requested) and removed 27 (23 requested) atoms. Cycle 42: After refmac, R = 0.1976 (Rfree = 0.000) for 5116 atoms. Found 19 (46 requested) and removed 25 (23 requested) atoms. Cycle 43: After refmac, R = 0.1913 (Rfree = 0.000) for 5106 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.1873 (Rfree = 0.000) for 5093 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.1825 (Rfree = 0.000) for 5075 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 5231 seeds are put forward Round 1: 301 peptides, 53 chains. Longest chain 22 peptides. Score 0.395 Round 2: 327 peptides, 51 chains. Longest chain 19 peptides. Score 0.472 Round 3: 322 peptides, 50 chains. Longest chain 23 peptides. Score 0.471 Round 4: 332 peptides, 48 chains. Longest chain 22 peptides. Score 0.509 Round 5: 329 peptides, 51 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 284, Estimated correctness of the model 14.2 % 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. 12025 reflections ( 99.86 % complete ) and 11607 restraints for refining 5126 atoms. 10519 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1978 (Rfree = 0.000) for 5126 atoms. Found 0 (46 requested) and removed 19 (23 requested) atoms. Cycle 47: After refmac, R = 0.1931 (Rfree = 0.000) for 5103 atoms. Found 0 (45 requested) and removed 4 (22 requested) atoms. Cycle 48: After refmac, R = 0.1892 (Rfree = 0.000) for 5094 atoms. Found 0 (45 requested) and removed 13 (22 requested) atoms. Cycle 49: After refmac, R = 0.1866 (Rfree = 0.000) for 5076 atoms. Found 0 (45 requested) and removed 7 (22 requested) atoms. Writing output files ... TimeTaking 69.72