null Tue 25 Dec 19:27:57 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 2oh1-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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/2oh1-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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 ============================================================ Tue 25 Dec 19:28:06 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/2oh1-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-3.6-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 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-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: 2oh1-3.6-parrot-hancs.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 6380 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3213 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3042 (Rfree = 0.000) for 6380 atoms. Found 31 (40 requested) and removed 64 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 6459 seeds are put forward NCS extension: 0 residues added, 6459 seeds are put forward Round 1: 343 peptides, 61 chains. Longest chain 11 peptides. Score 0.387 Round 2: 404 peptides, 56 chains. Longest chain 25 peptides. Score 0.539 Round 3: 416 peptides, 53 chains. Longest chain 18 peptides. Score 0.579 Round 4: 440 peptides, 54 chains. Longest chain 25 peptides. Score 0.609 Round 5: 456 peptides, 52 chains. Longest chain 25 peptides. Score 0.644 Taking the results from Round 5 Chains 52, Residues 404, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11448 restraints for refining 5188 atoms. 9884 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2485 (Rfree = 0.000) for 5188 atoms. Found 10 (33 requested) and removed 35 (16 requested) atoms. Cycle 2: After refmac, R = 0.2545 (Rfree = 0.000) for 5100 atoms. Found 14 (33 requested) and removed 35 (16 requested) atoms. Cycle 3: After refmac, R = 0.2499 (Rfree = 0.000) for 5049 atoms. Found 19 (32 requested) and removed 25 (16 requested) atoms. Cycle 4: After refmac, R = 0.2412 (Rfree = 0.000) for 5028 atoms. Found 16 (32 requested) and removed 39 (16 requested) atoms. Cycle 5: After refmac, R = 0.2361 (Rfree = 0.000) for 4983 atoms. Found 17 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.41 Search for helices and strands: 0 residues in 0 chains, 5147 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 5180 seeds are put forward Round 1: 402 peptides, 66 chains. Longest chain 16 peptides. Score 0.459 Round 2: 436 peptides, 54 chains. Longest chain 17 peptides. Score 0.603 Round 3: 438 peptides, 53 chains. Longest chain 20 peptides. Score 0.612 Round 4: 434 peptides, 47 chains. Longest chain 33 peptides. Score 0.645 Round 5: 453 peptides, 51 chains. Longest chain 28 peptides. Score 0.646 Taking the results from Round 5 Chains 51, Residues 402, Estimated correctness of the model 31.8 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 10940 restraints for refining 5190 atoms. 9240 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2544 (Rfree = 0.000) for 5190 atoms. Found 16 (33 requested) and removed 40 (16 requested) atoms. Cycle 7: After refmac, R = 0.2470 (Rfree = 0.000) for 5135 atoms. Found 8 (33 requested) and removed 28 (16 requested) atoms. Cycle 8: After refmac, R = 0.2441 (Rfree = 0.000) for 5095 atoms. Found 9 (32 requested) and removed 26 (16 requested) atoms. Cycle 9: After refmac, R = 0.2437 (Rfree = 0.000) for 5072 atoms. Found 10 (32 requested) and removed 32 (16 requested) atoms. Cycle 10: After refmac, R = 0.2294 (Rfree = 0.000) for 5044 atoms. Found 2 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 5208 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5228 seeds are put forward Round 1: 371 peptides, 60 chains. Longest chain 12 peptides. Score 0.450 Round 2: 416 peptides, 56 chains. Longest chain 21 peptides. Score 0.558 Round 3: 425 peptides, 57 chains. Longest chain 21 peptides. Score 0.565 Round 4: 414 peptides, 53 chains. Longest chain 24 peptides. Score 0.576 Round 5: 423 peptides, 50 chains. Longest chain 25 peptides. Score 0.610 Taking the results from Round 5 Chains 50, Residues 373, Estimated correctness of the model 18.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11466 restraints for refining 5193 atoms. 9992 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2383 (Rfree = 0.000) for 5193 atoms. Found 12 (33 requested) and removed 34 (16 requested) atoms. Cycle 12: After refmac, R = 0.2269 (Rfree = 0.000) for 5151 atoms. Found 8 (33 requested) and removed 26 (16 requested) atoms. Cycle 13: After refmac, R = 0.2289 (Rfree = 0.000) for 5123 atoms. Found 7 (32 requested) and removed 24 (16 requested) atoms. Cycle 14: After refmac, R = 0.2220 (Rfree = 0.000) for 5098 atoms. Found 10 (32 requested) and removed 25 (16 requested) atoms. Cycle 15: After refmac, R = 0.2241 (Rfree = 0.000) for 5075 atoms. Found 5 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 5218 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 5254 seeds are put forward Round 1: 389 peptides, 61 chains. Longest chain 17 peptides. Score 0.475 Round 2: 416 peptides, 56 chains. Longest chain 20 peptides. Score 0.558 Round 3: 402 peptides, 54 chains. Longest chain 24 peptides. Score 0.550 Round 4: 424 peptides, 53 chains. Longest chain 24 peptides. Score 0.592 Round 5: 410 peptides, 50 chains. Longest chain 24 peptides. Score 0.591 Taking the results from Round 4 Chains 54, Residues 371, Estimated correctness of the model 11.5 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11389 restraints for refining 5191 atoms. 9855 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2390 (Rfree = 0.000) for 5191 atoms. Found 24 (33 requested) and removed 35 (16 requested) atoms. Cycle 17: After refmac, R = 0.2205 (Rfree = 0.000) for 5163 atoms. Found 8 (33 requested) and removed 35 (16 requested) atoms. Cycle 18: After refmac, R = 0.2133 (Rfree = 0.000) for 5128 atoms. Found 7 (32 requested) and removed 25 (16 requested) atoms. Cycle 19: After refmac, R = 0.2125 (Rfree = 0.000) for 5104 atoms. Found 7 (32 requested) and removed 27 (16 requested) atoms. Cycle 20: After refmac, R = 0.2127 (Rfree = 0.000) for 5080 atoms. Found 6 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 5221 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5239 seeds are put forward Round 1: 346 peptides, 57 chains. Longest chain 22 peptides. Score 0.427 Round 2: 374 peptides, 49 chains. Longest chain 25 peptides. Score 0.541 Round 3: 385 peptides, 52 chains. Longest chain 21 peptides. Score 0.537 Round 4: 396 peptides, 52 chains. Longest chain 28 peptides. Score 0.555 Round 5: 389 peptides, 49 chains. Longest chain 30 peptides. Score 0.565 Taking the results from Round 5 Chains 52, Residues 340, Estimated correctness of the model 0.5 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11313 restraints for refining 5191 atoms. 9878 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2413 (Rfree = 0.000) for 5191 atoms. Found 15 (33 requested) and removed 34 (16 requested) atoms. Cycle 22: After refmac, R = 0.2317 (Rfree = 0.000) for 5150 atoms. Found 13 (33 requested) and removed 27 (16 requested) atoms. Cycle 23: After refmac, R = 0.2123 (Rfree = 0.000) for 5125 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. Cycle 24: After refmac, R = 0.2059 (Rfree = 0.000) for 5106 atoms. Found 2 (32 requested) and removed 24 (16 requested) atoms. Cycle 25: After refmac, R = 0.2340 (Rfree = 0.000) for 5082 atoms. Found 31 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5239 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5253 seeds are put forward Round 1: 336 peptides, 61 chains. Longest chain 11 peptides. Score 0.373 Round 2: 389 peptides, 61 chains. Longest chain 18 peptides. Score 0.475 Round 3: 388 peptides, 55 chains. Longest chain 17 peptides. Score 0.519 Round 4: 403 peptides, 57 chains. Longest chain 18 peptides. Score 0.530 Round 5: 384 peptides, 53 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 4 Chains 59, Residues 346, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11425 restraints for refining 5192 atoms. 10016 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2212 (Rfree = 0.000) for 5192 atoms. Found 21 (33 requested) and removed 25 (16 requested) atoms. Cycle 27: After refmac, R = 0.2113 (Rfree = 0.000) for 5178 atoms. Found 5 (33 requested) and removed 25 (16 requested) atoms. Cycle 28: After refmac, R = 0.2071 (Rfree = 0.000) for 5149 atoms. Found 10 (33 requested) and removed 21 (16 requested) atoms. Cycle 29: After refmac, R = 0.2015 (Rfree = 0.000) for 5132 atoms. Found 2 (32 requested) and removed 17 (16 requested) atoms. Cycle 30: After refmac, R = 0.1993 (Rfree = 0.000) for 5112 atoms. Found 11 (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, 5275 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5296 seeds are put forward Round 1: 312 peptides, 58 chains. Longest chain 16 peptides. Score 0.350 Round 2: 368 peptides, 53 chains. Longest chain 18 peptides. Score 0.500 Round 3: 370 peptides, 51 chains. Longest chain 21 peptides. Score 0.519 Round 4: 366 peptides, 52 chains. Longest chain 17 peptides. Score 0.504 Round 5: 384 peptides, 51 chains. Longest chain 22 peptides. Score 0.543 Taking the results from Round 5 Chains 53, Residues 333, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11503 restraints for refining 5193 atoms. 10167 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2232 (Rfree = 0.000) for 5193 atoms. Found 9 (33 requested) and removed 24 (16 requested) atoms. Cycle 32: After refmac, R = 0.2173 (Rfree = 0.000) for 5169 atoms. Found 10 (33 requested) and removed 24 (16 requested) atoms. Cycle 33: After refmac, R = 0.2102 (Rfree = 0.000) for 5146 atoms. Found 7 (33 requested) and removed 21 (16 requested) atoms. Cycle 34: After refmac, R = 0.2091 (Rfree = 0.000) for 5128 atoms. Found 6 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.2061 (Rfree = 0.000) for 5115 atoms. Found 4 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 5235 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5256 seeds are put forward Round 1: 309 peptides, 52 chains. Longest chain 19 peptides. Score 0.397 Round 2: 335 peptides, 46 chains. Longest chain 27 peptides. Score 0.497 Round 3: 342 peptides, 53 chains. Longest chain 14 peptides. Score 0.453 Round 4: 356 peptides, 54 chains. Longest chain 23 peptides. Score 0.470 Round 5: 356 peptides, 50 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 5 Chains 50, Residues 306, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 11844 restraints for refining 5193 atoms. 10659 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2321 (Rfree = 0.000) for 5193 atoms. Found 12 (33 requested) and removed 24 (16 requested) atoms. Cycle 37: After refmac, R = 0.2289 (Rfree = 0.000) for 5165 atoms. Found 32 (33 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 5165 atoms. Found 23 (33 requested) and removed 21 (16 requested) atoms. Cycle 39: After refmac, R = 0.1986 (Rfree = 0.000) for 5161 atoms. Found 5 (33 requested) and removed 21 (16 requested) atoms. Cycle 40: After refmac, R = 0.2143 (Rfree = 0.000) for 5141 atoms. Found 10 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5252 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5274 seeds are put forward Round 1: 285 peptides, 57 chains. Longest chain 10 peptides. Score 0.301 Round 2: 293 peptides, 48 chains. Longest chain 19 peptides. Score 0.400 Round 3: 296 peptides, 45 chains. Longest chain 29 peptides. Score 0.432 Round 4: 323 peptides, 50 chains. Longest chain 18 peptides. Score 0.442 Round 5: 315 peptides, 47 chains. Longest chain 20 peptides. Score 0.452 Taking the results from Round 5 Chains 47, Residues 268, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9752 reflections ( 99.15 % complete ) and 12122 restraints for refining 5192 atoms. 11097 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2278 (Rfree = 0.000) for 5192 atoms. Found 23 (33 requested) and removed 31 (16 requested) atoms. Cycle 42: After refmac, R = 0.2117 (Rfree = 0.000) for 5173 atoms. Found 32 (33 requested) and removed 20 (16 requested) atoms. Cycle 43: After refmac, R = 0.2053 (Rfree = 0.000) for 5181 atoms. Found 20 (33 requested) and removed 21 (16 requested) atoms. Cycle 44: After refmac, R = 0.1988 (Rfree = 0.000) for 5172 atoms. Found 19 (33 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.1739 (Rfree = 0.000) for 5163 atoms. Found 6 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 5305 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5325 seeds are put forward Round 1: 248 peptides, 46 chains. Longest chain 16 peptides. Score 0.323 Round 2: 279 peptides, 46 chains. Longest chain 20 peptides. Score 0.389 Round 3: 300 peptides, 49 chains. Longest chain 15 peptides. Score 0.405 Round 4: 307 peptides, 48 chains. Longest chain 22 peptides. Score 0.428 Round 5: 313 peptides, 52 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % 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 12161 restraints for refining 5193 atoms. 11173 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2043 (Rfree = 0.000) for 5193 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1962 (Rfree = 0.000) for 5166 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2008 (Rfree = 0.000) for 5144 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2017 (Rfree = 0.000) for 5122 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:46:11 GMT 2018 Job finished. TimeTaking 78.23 Used memory is bytes: 6120016