null Mon 24 Dec 07:30:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oh1-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-parrot-noncs ############### 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 07:30:12 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/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-parrot-noncs/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-noncs.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-noncs.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 6351 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3155 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2900 (Rfree = 0.000) for 6351 atoms. Found 42 (47 requested) and removed 60 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.30 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: 365 peptides, 62 chains. Longest chain 12 peptides. Score 0.422 Round 2: 452 peptides, 64 chains. Longest chain 19 peptides. Score 0.559 Round 3: 453 peptides, 55 chains. Longest chain 21 peptides. Score 0.621 Round 4: 451 peptides, 53 chains. Longest chain 23 peptides. Score 0.631 Round 5: 475 peptides, 54 chains. Longest chain 24 peptides. Score 0.657 Taking the results from Round 5 Chains 56, Residues 421, Estimated correctness of the model 46.2 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10919 restraints for refining 5207 atoms. 9168 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2555 (Rfree = 0.000) for 5207 atoms. Found 13 (39 requested) and removed 38 (19 requested) atoms. Cycle 2: After refmac, R = 0.2385 (Rfree = 0.000) for 5107 atoms. Found 10 (39 requested) and removed 36 (19 requested) atoms. Cycle 3: After refmac, R = 0.2374 (Rfree = 0.000) for 5042 atoms. Found 7 (38 requested) and removed 28 (19 requested) atoms. Cycle 4: After refmac, R = 0.2295 (Rfree = 0.000) for 4997 atoms. Found 8 (37 requested) and removed 26 (18 requested) atoms. Cycle 5: After refmac, R = 0.2251 (Rfree = 0.000) for 4968 atoms. Found 3 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 5088 seeds are put forward NCS extension: 11 residues added (10 deleted due to clashes), 5099 seeds are put forward Round 1: 417 peptides, 58 chains. Longest chain 24 peptides. Score 0.546 Round 2: 463 peptides, 57 chains. Longest chain 20 peptides. Score 0.622 Round 3: 495 peptides, 56 chains. Longest chain 35 peptides. Score 0.671 Round 4: 484 peptides, 52 chains. Longest chain 25 peptides. Score 0.680 Round 5: 474 peptides, 53 chains. Longest chain 32 peptides. Score 0.662 Taking the results from Round 4 Chains 53, Residues 432, Estimated correctness of the model 52.6 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11030 restraints for refining 5176 atoms. 9268 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2373 (Rfree = 0.000) for 5176 atoms. Found 20 (39 requested) and removed 45 (19 requested) atoms. Cycle 7: After refmac, R = 0.2116 (Rfree = 0.000) for 5129 atoms. Found 9 (38 requested) and removed 26 (19 requested) atoms. Cycle 8: After refmac, R = 0.2035 (Rfree = 0.000) for 5102 atoms. Found 1 (38 requested) and removed 24 (19 requested) atoms. Cycle 9: After refmac, R = 0.2084 (Rfree = 0.000) for 5072 atoms. Found 15 (38 requested) and removed 28 (19 requested) atoms. Cycle 10: After refmac, R = 0.2039 (Rfree = 0.000) for 5055 atoms. Found 1 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 5209 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 5222 seeds are put forward Round 1: 405 peptides, 57 chains. Longest chain 20 peptides. Score 0.533 Round 2: 440 peptides, 59 chains. Longest chain 22 peptides. Score 0.575 Round 3: 448 peptides, 52 chains. Longest chain 21 peptides. Score 0.633 Round 4: 466 peptides, 47 chains. Longest chain 32 peptides. Score 0.686 Round 5: 450 peptides, 54 chains. Longest chain 23 peptides. Score 0.623 Taking the results from Round 4 Chains 51, Residues 419, Estimated correctness of the model 54.2 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11023 restraints for refining 5208 atoms. 9258 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2265 (Rfree = 0.000) for 5208 atoms. Found 16 (39 requested) and removed 32 (19 requested) atoms. Cycle 12: After refmac, R = 0.2215 (Rfree = 0.000) for 5176 atoms. Found 22 (39 requested) and removed 28 (19 requested) atoms. Cycle 13: After refmac, R = 0.2122 (Rfree = 0.000) for 5163 atoms. Found 6 (39 requested) and removed 32 (19 requested) atoms. Cycle 14: After refmac, R = 0.2148 (Rfree = 0.000) for 5132 atoms. Found 12 (38 requested) and removed 22 (19 requested) atoms. Cycle 15: After refmac, R = 0.2059 (Rfree = 0.000) for 5117 atoms. Found 7 (38 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 5285 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5298 seeds are put forward Round 1: 389 peptides, 57 chains. Longest chain 20 peptides. Score 0.506 Round 2: 449 peptides, 58 chains. Longest chain 21 peptides. Score 0.595 Round 3: 451 peptides, 55 chains. Longest chain 21 peptides. Score 0.618 Round 4: 454 peptides, 56 chains. Longest chain 24 peptides. Score 0.616 Round 5: 461 peptides, 52 chains. Longest chain 24 peptides. Score 0.651 Taking the results from Round 5 Chains 52, Residues 409, Estimated correctness of the model 44.4 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11017 restraints for refining 5207 atoms. 9284 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2247 (Rfree = 0.000) for 5207 atoms. Found 12 (39 requested) and removed 30 (19 requested) atoms. Cycle 17: After refmac, R = 0.2130 (Rfree = 0.000) for 5174 atoms. Found 15 (39 requested) and removed 24 (19 requested) atoms. Cycle 18: After refmac, R = 0.2434 (Rfree = 0.000) for 5155 atoms. Found 28 (38 requested) and removed 35 (19 requested) atoms. Cycle 19: After refmac, R = 0.2086 (Rfree = 0.000) for 5141 atoms. Found 13 (38 requested) and removed 23 (19 requested) atoms. Cycle 20: After refmac, R = 0.2043 (Rfree = 0.000) for 5126 atoms. Found 9 (38 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 5273 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5286 seeds are put forward Round 1: 419 peptides, 63 chains. Longest chain 16 peptides. Score 0.512 Round 2: 435 peptides, 59 chains. Longest chain 18 peptides. Score 0.567 Round 3: 426 peptides, 54 chains. Longest chain 20 peptides. Score 0.588 Round 4: 421 peptides, 58 chains. Longest chain 17 peptides. Score 0.552 Round 5: 457 peptides, 56 chains. Longest chain 26 peptides. Score 0.620 Taking the results from Round 5 Chains 60, Residues 401, Estimated correctness of the model 35.1 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11326 restraints for refining 5208 atoms. 9652 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2243 (Rfree = 0.000) for 5208 atoms. Found 19 (39 requested) and removed 31 (19 requested) atoms. Cycle 22: After refmac, R = 0.2052 (Rfree = 0.000) for 5184 atoms. Found 3 (39 requested) and removed 26 (19 requested) atoms. Cycle 23: After refmac, R = 0.2106 (Rfree = 0.000) for 5148 atoms. Found 7 (38 requested) and removed 22 (19 requested) atoms. Cycle 24: After refmac, R = 0.2058 (Rfree = 0.000) for 5122 atoms. Found 8 (38 requested) and removed 21 (19 requested) atoms. Cycle 25: After refmac, R = 0.2098 (Rfree = 0.000) for 5098 atoms. Found 14 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 5238 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 5256 seeds are put forward Round 1: 358 peptides, 57 chains. Longest chain 17 peptides. Score 0.450 Round 2: 403 peptides, 58 chains. Longest chain 19 peptides. Score 0.522 Round 3: 416 peptides, 52 chains. Longest chain 21 peptides. Score 0.586 Round 4: 444 peptides, 56 chains. Longest chain 21 peptides. Score 0.601 Round 5: 421 peptides, 53 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 4 Chains 59, Residues 388, Estimated correctness of the model 29.0 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10929 restraints for refining 5206 atoms. 9233 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2239 (Rfree = 0.000) for 5206 atoms. Found 28 (39 requested) and removed 32 (19 requested) atoms. Cycle 27: After refmac, R = 0.2174 (Rfree = 0.000) for 5190 atoms. Found 11 (39 requested) and removed 25 (19 requested) atoms. Cycle 28: After refmac, R = 0.2855 (Rfree = 0.000) for 5170 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. Cycle 29: After refmac, R = 0.2890 (Rfree = 0.000) for 5151 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. Cycle 30: After refmac, R = 0.2766 (Rfree = 0.000) for 5133 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 5247 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 5266 seeds are put forward Round 1: 319 peptides, 60 chains. Longest chain 14 peptides. Score 0.347 Round 2: 346 peptides, 55 chains. Longest chain 13 peptides. Score 0.444 Round 3: 353 peptides, 52 chains. Longest chain 17 peptides. Score 0.481 Round 4: 360 peptides, 50 chains. Longest chain 22 peptides. Score 0.509 Round 5: 361 peptides, 52 chains. Longest chain 18 peptides. Score 0.495 Taking the results from Round 4 Chains 50, Residues 310, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11820 restraints for refining 5208 atoms. 10618 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2449 (Rfree = 0.000) for 5208 atoms. Found 22 (39 requested) and removed 30 (19 requested) atoms. Cycle 32: After refmac, R = 0.2308 (Rfree = 0.000) for 5187 atoms. Found 25 (39 requested) and removed 28 (19 requested) atoms. Cycle 33: After refmac, R = 0.2228 (Rfree = 0.000) for 5170 atoms. Found 14 (39 requested) and removed 21 (19 requested) atoms. Cycle 34: After refmac, R = 0.2157 (Rfree = 0.000) for 5149 atoms. Found 27 (38 requested) and removed 22 (19 requested) atoms. Cycle 35: After refmac, R = 0.2140 (Rfree = 0.000) for 5146 atoms. Found 18 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 5297 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5310 seeds are put forward Round 1: 303 peptides, 56 chains. Longest chain 15 peptides. Score 0.349 Round 2: 358 peptides, 52 chains. Longest chain 22 peptides. Score 0.490 Round 3: 380 peptides, 55 chains. Longest chain 20 peptides. Score 0.506 Round 4: 378 peptides, 55 chains. Longest chain 19 peptides. Score 0.502 Round 5: 371 peptides, 51 chains. Longest chain 26 peptides. Score 0.521 Taking the results from Round 5 Chains 54, Residues 320, Estimated correctness of the model 0.8 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11092 restraints for refining 5207 atoms. 9690 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2279 (Rfree = 0.000) for 5207 atoms. Found 29 (39 requested) and removed 26 (19 requested) atoms. Cycle 37: After refmac, R = 0.2101 (Rfree = 0.000) for 5194 atoms. Found 8 (39 requested) and removed 20 (19 requested) atoms. Cycle 38: After refmac, R = 0.2080 (Rfree = 0.000) for 5173 atoms. Found 10 (39 requested) and removed 22 (19 requested) atoms. Cycle 39: After refmac, R = 0.2064 (Rfree = 0.000) for 5153 atoms. Found 15 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.1986 (Rfree = 0.000) for 5140 atoms. Found 8 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 5237 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5251 seeds are put forward Round 1: 330 peptides, 56 chains. Longest chain 13 peptides. Score 0.404 Round 2: 352 peptides, 53 chains. Longest chain 20 peptides. Score 0.471 Round 3: 384 peptides, 55 chains. Longest chain 17 peptides. Score 0.512 Round 4: 376 peptides, 52 chains. Longest chain 25 peptides. Score 0.522 Round 5: 380 peptides, 54 chains. Longest chain 20 peptides. Score 0.513 Taking the results from Round 4 Chains 54, Residues 324, Estimated correctness of the model 1.2 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11225 restraints for refining 5208 atoms. 9835 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2159 (Rfree = 0.000) for 5208 atoms. Found 22 (39 requested) and removed 27 (19 requested) atoms. Cycle 42: After refmac, R = 0.2038 (Rfree = 0.000) for 5185 atoms. Found 7 (39 requested) and removed 25 (19 requested) atoms. Cycle 43: After refmac, R = 0.2053 (Rfree = 0.000) for 5161 atoms. Found 11 (39 requested) and removed 23 (19 requested) atoms. Cycle 44: After refmac, R = 0.2025 (Rfree = 0.000) for 5145 atoms. Found 10 (38 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.2003 (Rfree = 0.000) for 5132 atoms. Found 7 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 5241 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5255 seeds are put forward Round 1: 326 peptides, 57 chains. Longest chain 16 peptides. Score 0.387 Round 2: 365 peptides, 54 chains. Longest chain 17 peptides. Score 0.487 Round 3: 363 peptides, 55 chains. Longest chain 16 peptides. Score 0.475 Round 4: 362 peptides, 50 chains. Longest chain 23 peptides. Score 0.513 Round 5: 368 peptides, 49 chains. Longest chain 18 peptides. Score 0.531 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 319, Estimated correctness of the model 4.6 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (319 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11524 reflections ( 99.13 % complete ) and 11327 restraints for refining 5208 atoms. 10028 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2206 (Rfree = 0.000) for 5208 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2200 (Rfree = 0.000) for 5175 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2173 (Rfree = 0.000) for 5151 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 5129 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:28:19 GMT 2018 Job finished. TimeTaking 58.19 Used memory is bytes: 21524336