Sun 23 Dec 22:23:07 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 2oh1-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-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/2oh1-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-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 22:23:17 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/2oh1-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.4-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 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-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: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.4-parrot-hancs.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 6303 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3118 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3007 (Rfree = 0.000) for 6303 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 6439 seeds are put forward NCS extension: 0 residues added, 6439 seeds are put forward Round 1: 369 peptides, 65 chains. Longest chain 12 peptides. Score 0.405 Round 2: 446 peptides, 62 chains. Longest chain 21 peptides. Score 0.564 Round 3: 466 peptides, 53 chains. Longest chain 38 peptides. Score 0.651 Round 4: 471 peptides, 44 chains. Longest chain 37 peptides. Score 0.709 Round 5: 465 peptides, 54 chains. Longest chain 32 peptides. Score 0.644 Taking the results from Round 4 Chains 46, Residues 427, Estimated correctness of the model 60.2 % 2 chains (46 residues) have been docked in sequence Building loops using Loopy2018 46 chains (427 residues) following loop building 2 chains (46 residues) in sequence following loop building ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10727 restraints for refining 5205 atoms. 8874 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2602 (Rfree = 0.000) for 5205 atoms. Found 20 (39 requested) and removed 51 (19 requested) atoms. Cycle 2: After refmac, R = 0.2460 (Rfree = 0.000) for 5094 atoms. Found 14 (38 requested) and removed 28 (19 requested) atoms. Cycle 3: After refmac, R = 0.2381 (Rfree = 0.000) for 5047 atoms. Found 10 (36 requested) and removed 31 (19 requested) atoms. Cycle 4: After refmac, R = 0.2275 (Rfree = 0.000) for 5013 atoms. Found 4 (35 requested) and removed 23 (18 requested) atoms. Cycle 5: After refmac, R = 0.2277 (Rfree = 0.000) for 4984 atoms. Found 4 (34 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 5112 seeds are put forward NCS extension: 38 residues added (33 deleted due to clashes), 5150 seeds are put forward Round 1: 438 peptides, 65 chains. Longest chain 19 peptides. Score 0.529 Round 2: 458 peptides, 53 chains. Longest chain 33 peptides. Score 0.640 Round 3: 488 peptides, 55 chains. Longest chain 37 peptides. Score 0.668 Round 4: 492 peptides, 54 chains. Longest chain 24 peptides. Score 0.678 Round 5: 499 peptides, 54 chains. Longest chain 33 peptides. Score 0.687 Taking the results from Round 5 Chains 54, Residues 445, Estimated correctness of the model 54.5 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10961 restraints for refining 5208 atoms. 9089 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2548 (Rfree = 0.000) for 5208 atoms. Found 26 (35 requested) and removed 55 (19 requested) atoms. Cycle 7: After refmac, R = 0.2448 (Rfree = 0.000) for 5149 atoms. Found 9 (35 requested) and removed 34 (19 requested) atoms. Cycle 8: After refmac, R = 0.2364 (Rfree = 0.000) for 5105 atoms. Found 7 (34 requested) and removed 30 (19 requested) atoms. Cycle 9: After refmac, R = 0.2286 (Rfree = 0.000) for 5072 atoms. Found 2 (34 requested) and removed 30 (19 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2197 (Rfree = 0.000) for 5030 atoms. Found 8 (34 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 5180 seeds are put forward NCS extension: 23 residues added (10 deleted due to clashes), 5203 seeds are put forward Round 1: 437 peptides, 64 chains. Longest chain 19 peptides. Score 0.535 Round 2: 480 peptides, 52 chains. Longest chain 40 peptides. Score 0.675 Round 3: 490 peptides, 58 chains. Longest chain 32 peptides. Score 0.653 Round 4: 491 peptides, 51 chains. Longest chain 40 peptides. Score 0.694 Round 5: 488 peptides, 52 chains. Longest chain 34 peptides. Score 0.685 Taking the results from Round 4 Chains 54, Residues 440, Estimated correctness of the model 56.3 % 3 chains (69 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10490 restraints for refining 5208 atoms. 8486 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2411 (Rfree = 0.000) for 5208 atoms. Found 19 (35 requested) and removed 38 (19 requested) atoms. Cycle 12: After refmac, R = 0.2213 (Rfree = 0.000) for 5168 atoms. Found 7 (35 requested) and removed 25 (19 requested) atoms. Cycle 13: After refmac, R = 0.2162 (Rfree = 0.000) for 5142 atoms. Found 9 (34 requested) and removed 25 (19 requested) atoms. Cycle 14: After refmac, R = 0.2137 (Rfree = 0.000) for 5118 atoms. Found 3 (34 requested) and removed 21 (19 requested) atoms. Cycle 15: After refmac, R = 0.2127 (Rfree = 0.000) for 5094 atoms. Found 6 (34 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 5203 seeds are put forward NCS extension: 32 residues added (12 deleted due to clashes), 5235 seeds are put forward Round 1: 397 peptides, 58 chains. Longest chain 20 peptides. Score 0.512 Round 2: 436 peptides, 53 chains. Longest chain 20 peptides. Score 0.609 Round 3: 440 peptides, 50 chains. Longest chain 21 peptides. Score 0.635 Round 4: 452 peptides, 51 chains. Longest chain 21 peptides. Score 0.645 Round 5: 441 peptides, 53 chains. Longest chain 33 peptides. Score 0.617 Taking the results from Round 4 Chains 54, Residues 401, Estimated correctness of the model 42.7 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 10970 restraints for refining 5207 atoms. 9235 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2399 (Rfree = 0.000) for 5207 atoms. Found 11 (35 requested) and removed 37 (19 requested) atoms. Cycle 17: After refmac, R = 0.2256 (Rfree = 0.000) for 5152 atoms. Found 8 (35 requested) and removed 27 (19 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 5116 atoms. Found 10 (34 requested) and removed 29 (19 requested) atoms. Cycle 19: After refmac, R = 0.2174 (Rfree = 0.000) for 5087 atoms. Found 12 (34 requested) and removed 24 (19 requested) atoms. Cycle 20: After refmac, R = 0.2140 (Rfree = 0.000) for 5066 atoms. Found 7 (34 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 5230 seeds are put forward Round 1: 417 peptides, 58 chains. Longest chain 26 peptides. Score 0.546 Round 2: 447 peptides, 53 chains. Longest chain 26 peptides. Score 0.625 Round 3: 460 peptides, 57 chains. Longest chain 21 peptides. Score 0.618 Round 4: 466 peptides, 54 chains. Longest chain 20 peptides. Score 0.645 Round 5: 448 peptides, 55 chains. Longest chain 21 peptides. Score 0.614 Taking the results from Round 4 Chains 55, Residues 412, Estimated correctness of the model 42.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11372 restraints for refining 5208 atoms. 9720 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2297 (Rfree = 0.000) for 5208 atoms. Found 28 (35 requested) and removed 31 (19 requested) atoms. Cycle 22: After refmac, R = 0.2251 (Rfree = 0.000) for 5190 atoms. Found 24 (35 requested) and removed 28 (19 requested) atoms. Cycle 23: After refmac, R = 0.2189 (Rfree = 0.000) for 5178 atoms. Found 11 (35 requested) and removed 30 (19 requested) atoms. Cycle 24: After refmac, R = 0.2174 (Rfree = 0.000) for 5152 atoms. Found 14 (34 requested) and removed 33 (19 requested) atoms. Cycle 25: After refmac, R = 0.2088 (Rfree = 0.000) for 5127 atoms. Found 8 (34 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 5262 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5276 seeds are put forward Round 1: 410 peptides, 59 chains. Longest chain 23 peptides. Score 0.527 Round 2: 427 peptides, 57 chains. Longest chain 23 peptides. Score 0.569 Round 3: 447 peptides, 57 chains. Longest chain 35 peptides. Score 0.599 Round 4: 463 peptides, 59 chains. Longest chain 21 peptides. Score 0.609 Round 5: 444 peptides, 58 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 4 Chains 59, Residues 404, Estimated correctness of the model 31.6 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11156 restraints for refining 5207 atoms. 9527 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2340 (Rfree = 0.000) for 5207 atoms. Found 21 (35 requested) and removed 36 (19 requested) atoms. Cycle 27: After refmac, R = 0.2232 (Rfree = 0.000) for 5178 atoms. Found 11 (35 requested) and removed 30 (19 requested) atoms. Cycle 28: After refmac, R = 0.2150 (Rfree = 0.000) for 5148 atoms. Found 5 (34 requested) and removed 28 (19 requested) atoms. Cycle 29: After refmac, R = 0.2189 (Rfree = 0.000) for 5115 atoms. Found 8 (34 requested) and removed 23 (19 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 5098 atoms. Found 2 (34 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 5224 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 5239 seeds are put forward Round 1: 368 peptides, 57 chains. Longest chain 16 peptides. Score 0.468 Round 2: 401 peptides, 53 chains. Longest chain 19 peptides. Score 0.556 Round 3: 408 peptides, 53 chains. Longest chain 19 peptides. Score 0.567 Round 4: 407 peptides, 54 chains. Longest chain 18 peptides. Score 0.558 Round 5: 405 peptides, 56 chains. Longest chain 26 peptides. Score 0.540 Taking the results from Round 3 Chains 53, Residues 355, Estimated correctness of the model 17.5 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11600 restraints for refining 5208 atoms. 10221 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2271 (Rfree = 0.000) for 5208 atoms. Found 14 (35 requested) and removed 29 (19 requested) atoms. Cycle 32: After refmac, R = 0.2151 (Rfree = 0.000) for 5181 atoms. Found 6 (35 requested) and removed 27 (19 requested) atoms. Cycle 33: After refmac, R = 0.2125 (Rfree = 0.000) for 5156 atoms. Found 13 (34 requested) and removed 22 (19 requested) atoms. Cycle 34: After refmac, R = 0.2264 (Rfree = 0.000) for 5141 atoms. Found 18 (34 requested) and removed 25 (19 requested) atoms. Cycle 35: After refmac, R = 0.2332 (Rfree = 0.000) for 5126 atoms. Found 19 (34 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 5281 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 5294 seeds are put forward Round 1: 318 peptides, 54 chains. Longest chain 14 peptides. Score 0.397 Round 2: 393 peptides, 57 chains. Longest chain 20 peptides. Score 0.513 Round 3: 385 peptides, 50 chains. Longest chain 21 peptides. Score 0.552 Round 4: 408 peptides, 57 chains. Longest chain 18 peptides. Score 0.538 Round 5: 401 peptides, 56 chains. Longest chain 18 peptides. Score 0.534 Taking the results from Round 3 Chains 52, Residues 335, Estimated correctness of the model 12.2 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11455 restraints for refining 5208 atoms. 10116 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2209 (Rfree = 0.000) for 5208 atoms. Found 17 (35 requested) and removed 27 (19 requested) atoms. Cycle 37: After refmac, R = 0.2196 (Rfree = 0.000) for 5187 atoms. Found 15 (35 requested) and removed 30 (19 requested) atoms. Cycle 38: After refmac, R = 0.2595 (Rfree = 0.000) for 5167 atoms. Found 35 (35 requested) and removed 34 (19 requested) atoms. Cycle 39: After refmac, R = 0.2116 (Rfree = 0.000) for 5161 atoms. Found 18 (35 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.2240 (Rfree = 0.000) for 5152 atoms. Found 34 (34 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 5302 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 5325 seeds are put forward Round 1: 325 peptides, 59 chains. Longest chain 16 peptides. Score 0.368 Round 2: 367 peptides, 55 chains. Longest chain 18 peptides. Score 0.482 Round 3: 379 peptides, 56 chains. Longest chain 18 peptides. Score 0.496 Round 4: 383 peptides, 55 chains. Longest chain 18 peptides. Score 0.511 Round 5: 377 peptides, 51 chains. Longest chain 20 peptides. Score 0.531 Taking the results from Round 5 Chains 51, Residues 326, Estimated correctness of the model 4.6 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 11524 reflections ( 99.13 % complete ) and 11149 restraints for refining 5208 atoms. 9732 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2239 (Rfree = 0.000) for 5208 atoms. Found 19 (35 requested) and removed 25 (19 requested) atoms. Cycle 42: After refmac, R = 0.2175 (Rfree = 0.000) for 5182 atoms. Found 7 (35 requested) and removed 25 (19 requested) atoms. Cycle 43: After refmac, R = 0.2185 (Rfree = 0.000) for 5156 atoms. Found 7 (34 requested) and removed 24 (19 requested) atoms. Cycle 44: After refmac, R = 0.2113 (Rfree = 0.000) for 5133 atoms. Found 5 (34 requested) and removed 21 (19 requested) atoms. Cycle 45: After refmac, R = 0.2111 (Rfree = 0.000) for 5115 atoms. Found 7 (34 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 5241 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 5258 seeds are put forward Round 1: 324 peptides, 61 chains. Longest chain 13 peptides. Score 0.348 Round 2: 354 peptides, 54 chains. Longest chain 21 peptides. Score 0.467 Round 3: 371 peptides, 57 chains. Longest chain 21 peptides. Score 0.474 Round 4: 361 peptides, 53 chains. Longest chain 22 peptides. Score 0.488 Round 5: 370 peptides, 53 chains. Longest chain 22 peptides. Score 0.503 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 317, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input Building loops using Loopy2018 53 chains (317 residues) following loop building 3 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11524 reflections ( 99.13 % complete ) and 11605 restraints for refining 5208 atoms. 10302 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2248 (Rfree = 0.000) for 5208 atoms. Found 0 (35 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2227 (Rfree = 0.000) for 5178 atoms. Found 0 (35 requested) and removed 11 (19 requested) atoms. Cycle 48: After refmac, R = 0.2210 (Rfree = 0.000) for 5161 atoms. Found 0 (35 requested) and removed 9 (19 requested) atoms. Cycle 49: After refmac, R = 0.2173 (Rfree = 0.000) for 5151 atoms. Found 0 (34 requested) and removed 11 (19 requested) atoms. Writing output files ... TimeTaking 73.72