Sun 23 Dec 23:51:14 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 2oh1-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oh1-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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/2oh1-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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 ============================================================ Sun 23 Dec 23:51:19 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/2oh1-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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 491 and 0 Target number of residues in the AU: 491 Target solvent content: 0.6702 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: 2oh1-4.0-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: 2oh1-4.0-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 4.000 Wilson plot Bfac: 92.22 7165 reflections ( 99.07 % complete ) and 0 restraints for refining 6362 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3447 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3348 (Rfree = 0.000) for 6362 atoms. Found 30 (30 requested) and removed 52 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.87 3.77 Search for helices and strands: 0 residues in 0 chains, 6474 seeds are put forward NCS extension: 0 residues added, 6474 seeds are put forward Round 1: 276 peptides, 53 chains. Longest chain 14 peptides. Score 0.318 Round 2: 345 peptides, 43 chains. Longest chain 22 peptides. Score 0.538 Round 3: 351 peptides, 52 chains. Longest chain 16 peptides. Score 0.477 Round 4: 357 peptides, 43 chains. Longest chain 26 peptides. Score 0.558 Round 5: 371 peptides, 46 chains. Longest chain 26 peptides. Score 0.558 Taking the results from Round 5 Chains 46, Residues 325, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11998 restraints for refining 5172 atoms. 10744 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2886 (Rfree = 0.000) for 5172 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 2: After refmac, R = 0.2590 (Rfree = 0.000) for 5066 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 3: After refmac, R = 0.2518 (Rfree = 0.000) for 5027 atoms. Found 22 (24 requested) and removed 43 (12 requested) atoms. Cycle 4: After refmac, R = 0.2000 (Rfree = 0.000) for 4979 atoms. Found 10 (23 requested) and removed 31 (11 requested) atoms. Cycle 5: After refmac, R = 0.1897 (Rfree = 0.000) for 4953 atoms. Found 3 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 5106 seeds are put forward NCS extension: 41 residues added (5 deleted due to clashes), 5147 seeds are put forward Round 1: 310 peptides, 56 chains. Longest chain 13 peptides. Score 0.363 Round 2: 378 peptides, 56 chains. Longest chain 18 peptides. Score 0.494 Round 3: 365 peptides, 50 chains. Longest chain 20 peptides. Score 0.518 Round 4: 361 peptides, 46 chains. Longest chain 21 peptides. Score 0.542 Round 5: 350 peptides, 49 chains. Longest chain 21 peptides. Score 0.500 Taking the results from Round 4 Chains 51, Residues 315, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7165 reflections ( 99.07 % complete ) and 11862 restraints for refining 5173 atoms. 10556 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2733 (Rfree = 0.000) for 5173 atoms. Found 15 (24 requested) and removed 35 (12 requested) atoms. Cycle 7: After refmac, R = 0.2449 (Rfree = 0.000) for 5094 atoms. Found 22 (24 requested) and removed 40 (12 requested) atoms. Cycle 8: After refmac, R = 0.2193 (Rfree = 0.000) for 5032 atoms. Found 15 (24 requested) and removed 31 (12 requested) atoms. Cycle 9: After refmac, R = 0.1860 (Rfree = 0.000) for 4990 atoms. Found 4 (23 requested) and removed 22 (11 requested) atoms. Cycle 10: After refmac, R = 0.1711 (Rfree = 0.000) for 4967 atoms. Found 1 (23 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 5102 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5123 seeds are put forward Round 1: 320 peptides, 59 chains. Longest chain 14 peptides. Score 0.357 Round 2: 355 peptides, 53 chains. Longest chain 14 peptides. Score 0.477 Round 3: 371 peptides, 54 chains. Longest chain 18 peptides. Score 0.497 Round 4: 383 peptides, 55 chains. Longest chain 18 peptides. Score 0.511 Round 5: 391 peptides, 55 chains. Longest chain 19 peptides. Score 0.524 Taking the results from Round 5 Chains 55, Residues 336, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7165 reflections ( 99.07 % complete ) and 11932 restraints for refining 5173 atoms. 10643 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2453 (Rfree = 0.000) for 5173 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 12: After refmac, R = 0.2275 (Rfree = 0.000) for 5100 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 13: After refmac, R = 0.2156 (Rfree = 0.000) for 5072 atoms. Found 24 (24 requested) and removed 40 (12 requested) atoms. Cycle 14: After refmac, R = 0.1694 (Rfree = 0.000) for 5036 atoms. Found 8 (24 requested) and removed 27 (12 requested) atoms. Cycle 15: After refmac, R = 0.1590 (Rfree = 0.000) for 5008 atoms. Found 4 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 5184 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5204 seeds are put forward Round 1: 311 peptides, 62 chains. Longest chain 9 peptides. Score 0.312 Round 2: 344 peptides, 56 chains. Longest chain 13 peptides. Score 0.431 Round 3: 342 peptides, 52 chains. Longest chain 21 peptides. Score 0.461 Round 4: 362 peptides, 55 chains. Longest chain 14 peptides. Score 0.473 Round 5: 357 peptides, 54 chains. Longest chain 27 peptides. Score 0.472 Taking the results from Round 4 Chains 56, Residues 307, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11940 restraints for refining 5172 atoms. 10735 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 5172 atoms. Found 24 (24 requested) and removed 37 (12 requested) atoms. Cycle 17: After refmac, R = 0.2432 (Rfree = 0.000) for 5105 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 18: After refmac, R = 0.2378 (Rfree = 0.000) for 5060 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 5031 atoms. Found 5 (24 requested) and removed 16 (12 requested) atoms. Cycle 20: After refmac, R = 0.1806 (Rfree = 0.000) for 5006 atoms. Found 5 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5163 seeds are put forward Round 1: 275 peptides, 56 chains. Longest chain 10 peptides. Score 0.288 Round 2: 304 peptides, 48 chains. Longest chain 15 peptides. Score 0.422 Round 3: 314 peptides, 50 chains. Longest chain 16 peptides. Score 0.424 Round 4: 299 peptides, 46 chains. Longest chain 13 peptides. Score 0.429 Round 5: 292 peptides, 44 chains. Longest chain 12 peptides. Score 0.433 Taking the results from Round 5 Chains 44, Residues 248, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12299 restraints for refining 5173 atoms. 11351 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2280 (Rfree = 0.000) for 5173 atoms. Found 23 (24 requested) and removed 37 (12 requested) atoms. Cycle 22: After refmac, R = 0.2356 (Rfree = 0.000) for 5140 atoms. Found 24 (24 requested) and removed 37 (12 requested) atoms. Cycle 23: After refmac, R = 0.2252 (Rfree = 0.000) for 5105 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 24: After refmac, R = 0.2137 (Rfree = 0.000) for 5081 atoms. Found 21 (24 requested) and removed 26 (12 requested) atoms. Cycle 25: After refmac, R = 0.2210 (Rfree = 0.000) for 5062 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5226 seeds are put forward Round 1: 259 peptides, 56 chains. Longest chain 9 peptides. Score 0.251 Round 2: 300 peptides, 54 chains. Longest chain 10 peptides. Score 0.360 Round 3: 325 peptides, 54 chains. Longest chain 13 peptides. Score 0.411 Round 4: 334 peptides, 56 chains. Longest chain 14 peptides. Score 0.412 Round 5: 326 peptides, 53 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 5 Chains 53, Residues 273, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12060 restraints for refining 5173 atoms. 11021 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2242 (Rfree = 0.000) for 5173 atoms. Found 18 (24 requested) and removed 38 (12 requested) atoms. Cycle 27: After refmac, R = 0.2148 (Rfree = 0.000) for 5107 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 28: After refmac, R = 0.2199 (Rfree = 0.000) for 5078 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 29: After refmac, R = 0.2170 (Rfree = 0.000) for 5050 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 30: After refmac, R = 0.2039 (Rfree = 0.000) for 5021 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 5218 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5236 seeds are put forward Round 1: 234 peptides, 49 chains. Longest chain 11 peptides. Score 0.261 Round 2: 281 peptides, 50 chains. Longest chain 12 peptides. Score 0.357 Round 3: 281 peptides, 48 chains. Longest chain 14 peptides. Score 0.375 Round 4: 291 peptides, 48 chains. Longest chain 13 peptides. Score 0.396 Round 5: 293 peptides, 50 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 4 Chains 50, Residues 243, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11648 restraints for refining 5085 atoms. 10695 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2309 (Rfree = 0.000) for 5085 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 32: After refmac, R = 0.2056 (Rfree = 0.000) for 5032 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 33: After refmac, R = 0.2161 (Rfree = 0.000) for 4993 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 34: After refmac, R = 0.2172 (Rfree = 0.000) for 4972 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 35: After refmac, R = 0.1741 (Rfree = 0.000) for 4963 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 5079 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5097 seeds are put forward Round 1: 223 peptides, 47 chains. Longest chain 9 peptides. Score 0.255 Round 2: 271 peptides, 50 chains. Longest chain 10 peptides. Score 0.335 Round 3: 282 peptides, 48 chains. Longest chain 12 peptides. Score 0.377 Round 4: 281 peptides, 47 chains. Longest chain 15 peptides. Score 0.384 Round 5: 277 peptides, 46 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 5 Chains 46, Residues 231, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11494 restraints for refining 5010 atoms. 10595 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2123 (Rfree = 0.000) for 5010 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 37: After refmac, R = 0.2092 (Rfree = 0.000) for 4974 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 38: After refmac, R = 0.2090 (Rfree = 0.000) for 4952 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 39: After refmac, R = 0.2057 (Rfree = 0.000) for 4933 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 40: After refmac, R = 0.1624 (Rfree = 0.000) for 4927 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 5055 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5073 seeds are put forward Round 1: 226 peptides, 46 chains. Longest chain 10 peptides. Score 0.272 Round 2: 246 peptides, 42 chains. Longest chain 12 peptides. Score 0.356 Round 3: 263 peptides, 44 chains. Longest chain 16 peptides. Score 0.374 Round 4: 269 peptides, 43 chains. Longest chain 15 peptides. Score 0.396 Round 5: 289 peptides, 49 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 4 Chains 44, Residues 226, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11428 restraints for refining 5082 atoms. 10532 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2089 (Rfree = 0.000) for 5082 atoms. Found 24 (24 requested) and removed 49 (12 requested) atoms. Cycle 42: After refmac, R = 0.2113 (Rfree = 0.000) for 5028 atoms. Found 24 (24 requested) and removed 46 (12 requested) atoms. Cycle 43: After refmac, R = 0.2108 (Rfree = 0.000) for 4995 atoms. Found 23 (23 requested) and removed 49 (11 requested) atoms. Cycle 44: After refmac, R = 0.1508 (Rfree = 0.000) for 4953 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 45: After refmac, R = 0.1362 (Rfree = 0.000) for 4939 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 5068 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5084 seeds are put forward Round 1: 206 peptides, 46 chains. Longest chain 7 peptides. Score 0.224 Round 2: 254 peptides, 49 chains. Longest chain 8 peptides. Score 0.307 Round 3: 268 peptides, 49 chains. Longest chain 11 peptides. Score 0.338 Round 4: 274 peptides, 50 chains. Longest chain 9 peptides. Score 0.342 Round 5: 260 peptides, 44 chains. Longest chain 15 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 216, 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 2oh1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7165 reflections ( 99.07 % complete ) and 11860 restraints for refining 5092 atoms. 11026 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2121 (Rfree = 0.000) for 5092 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1980 (Rfree = 0.000) for 5053 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1997 (Rfree = 0.000) for 5030 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1518 (Rfree = 0.000) for 5005 atoms. TimeTaking 60.38