null Mon 24 Dec 07:39:26 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 2oh1-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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/2oh1-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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 07:39:31 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/2oh1-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-4.0-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 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-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: 2oh1-4.0-parrot-noncs.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 6357 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3400 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3298 (Rfree = 0.000) for 6357 atoms. Found 30 (30 requested) and removed 63 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 6432 seeds are put forward NCS extension: 0 residues added, 6432 seeds are put forward Round 1: 281 peptides, 54 chains. Longest chain 14 peptides. Score 0.320 Round 2: 330 peptides, 55 chains. Longest chain 12 peptides. Score 0.413 Round 3: 352 peptides, 52 chains. Longest chain 15 peptides. Score 0.479 Round 4: 370 peptides, 50 chains. Longest chain 35 peptides. Score 0.527 Round 5: 367 peptides, 45 chains. Longest chain 21 peptides. Score 0.559 Taking the results from Round 5 Chains 45, Residues 322, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12208 restraints for refining 5172 atoms. 10958 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2693 (Rfree = 0.000) for 5172 atoms. Found 12 (24 requested) and removed 44 (12 requested) atoms. Cycle 2: After refmac, R = 0.2664 (Rfree = 0.000) for 5059 atoms. Found 22 (24 requested) and removed 56 (12 requested) atoms. Cycle 3: After refmac, R = 0.2443 (Rfree = 0.000) for 4987 atoms. Found 14 (23 requested) and removed 33 (11 requested) atoms. Cycle 4: After refmac, R = 0.2329 (Rfree = 0.000) for 4935 atoms. Found 12 (23 requested) and removed 34 (11 requested) atoms. Cycle 5: After refmac, R = 0.2486 (Rfree = 0.000) for 4880 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 5048 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5065 seeds are put forward Round 1: 289 peptides, 51 chains. Longest chain 12 peptides. Score 0.365 Round 2: 331 peptides, 49 chains. Longest chain 21 peptides. Score 0.465 Round 3: 340 peptides, 49 chains. Longest chain 14 peptides. Score 0.482 Round 4: 345 peptides, 47 chains. Longest chain 17 peptides. Score 0.507 Round 5: 358 peptides, 49 chains. Longest chain 23 peptides. Score 0.514 Taking the results from Round 5 Chains 50, Residues 309, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11899 restraints for refining 5173 atoms. 10679 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2395 (Rfree = 0.000) for 5173 atoms. Found 24 (24 requested) and removed 53 (12 requested) atoms. Cycle 7: After refmac, R = 0.2184 (Rfree = 0.000) for 5098 atoms. Found 11 (24 requested) and removed 33 (12 requested) atoms. Cycle 8: After refmac, R = 0.1821 (Rfree = 0.000) for 5047 atoms. Found 6 (24 requested) and removed 33 (12 requested) atoms. Cycle 9: After refmac, R = 0.1909 (Rfree = 0.000) for 5009 atoms. Found 10 (23 requested) and removed 29 (11 requested) atoms. Cycle 10: After refmac, R = 0.1696 (Rfree = 0.000) for 4982 atoms. Found 0 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 5135 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 5161 seeds are put forward Round 1: 306 peptides, 56 chains. Longest chain 11 peptides. Score 0.355 Round 2: 354 peptides, 52 chains. Longest chain 15 peptides. Score 0.483 Round 3: 349 peptides, 51 chains. Longest chain 16 peptides. Score 0.482 Round 4: 354 peptides, 47 chains. Longest chain 21 peptides. Score 0.522 Round 5: 360 peptides, 46 chains. Longest chain 19 peptides. Score 0.540 Taking the results from Round 5 Chains 46, Residues 314, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11938 restraints for refining 5173 atoms. 10728 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2372 (Rfree = 0.000) for 5173 atoms. Found 23 (24 requested) and removed 54 (12 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 5102 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 13: After refmac, R = 0.2006 (Rfree = 0.000) for 5075 atoms. Found 20 (24 requested) and removed 26 (12 requested) atoms. Cycle 14: After refmac, R = 0.2100 (Rfree = 0.000) for 5045 atoms. Found 21 (24 requested) and removed 37 (12 requested) atoms. Cycle 15: After refmac, R = 0.2080 (Rfree = 0.000) for 5013 atoms. Found 17 (23 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 5169 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 5203 seeds are put forward Round 1: 298 peptides, 56 chains. Longest chain 16 peptides. Score 0.338 Round 2: 320 peptides, 50 chains. Longest chain 15 peptides. Score 0.436 Round 3: 332 peptides, 50 chains. Longest chain 18 peptides. Score 0.459 Round 4: 329 peptides, 49 chains. Longest chain 18 peptides. Score 0.461 Round 5: 315 peptides, 46 chains. Longest chain 24 peptides. Score 0.460 Taking the results from Round 4 Chains 50, Residues 280, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11930 restraints for refining 5172 atoms. 10816 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2287 (Rfree = 0.000) for 5172 atoms. Found 12 (24 requested) and removed 42 (12 requested) atoms. Cycle 17: After refmac, R = 0.2205 (Rfree = 0.000) for 5111 atoms. Found 12 (24 requested) and removed 27 (12 requested) atoms. Cycle 18: After refmac, R = 0.2198 (Rfree = 0.000) for 5069 atoms. Found 9 (24 requested) and removed 27 (12 requested) atoms. Cycle 19: After refmac, R = 0.1785 (Rfree = 0.000) for 5041 atoms. Found 0 (23 requested) and removed 21 (11 requested) atoms. Cycle 20: After refmac, R = 0.1707 (Rfree = 0.000) for 5012 atoms. Found 2 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 5126 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5140 seeds are put forward Round 1: 295 peptides, 58 chains. Longest chain 10 peptides. Score 0.313 Round 2: 329 peptides, 53 chains. Longest chain 16 peptides. Score 0.428 Round 3: 298 peptides, 45 chains. Longest chain 12 peptides. Score 0.436 Round 4: 313 peptides, 45 chains. Longest chain 16 peptides. Score 0.465 Round 5: 329 peptides, 50 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 4 Chains 45, Residues 268, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12197 restraints for refining 5172 atoms. 11170 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2270 (Rfree = 0.000) for 5172 atoms. Found 15 (24 requested) and removed 36 (12 requested) atoms. Cycle 22: After refmac, R = 0.2143 (Rfree = 0.000) for 5120 atoms. Found 14 (24 requested) and removed 28 (12 requested) atoms. Cycle 23: After refmac, R = 0.2266 (Rfree = 0.000) for 5088 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 24: After refmac, R = 0.2200 (Rfree = 0.000) for 5059 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 25: After refmac, R = 0.2205 (Rfree = 0.000) for 5041 atoms. Found 21 (24 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 5166 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 5177 seeds are put forward Round 1: 244 peptides, 51 chains. Longest chain 9 peptides. Score 0.265 Round 2: 281 peptides, 53 chains. Longest chain 15 peptides. Score 0.329 Round 3: 288 peptides, 49 chains. Longest chain 13 peptides. Score 0.380 Round 4: 291 peptides, 48 chains. Longest chain 16 peptides. Score 0.396 Round 5: 283 peptides, 45 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 5 Chains 45, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12393 restraints for refining 5172 atoms. 11486 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2249 (Rfree = 0.000) for 5172 atoms. Found 24 (24 requested) and removed 45 (12 requested) atoms. Cycle 27: After refmac, R = 0.2373 (Rfree = 0.000) for 5122 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 28: After refmac, R = 0.2273 (Rfree = 0.000) for 5086 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 29: After refmac, R = 0.2112 (Rfree = 0.000) for 5064 atoms. Found 18 (24 requested) and removed 22 (12 requested) atoms. Cycle 30: After refmac, R = 0.2268 (Rfree = 0.000) for 5039 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 5177 seeds are put forward NCS extension: 0 residues added, 5177 seeds are put forward Round 1: 225 peptides, 46 chains. Longest chain 20 peptides. Score 0.270 Round 2: 270 peptides, 46 chains. Longest chain 22 peptides. Score 0.370 Round 3: 288 peptides, 51 chains. Longest chain 21 peptides. Score 0.362 Round 4: 285 peptides, 51 chains. Longest chain 12 peptides. Score 0.356 Round 5: 290 peptides, 45 chains. Longest chain 20 peptides. Score 0.420 Taking the results from Round 5 Chains 45, Residues 245, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12127 restraints for refining 5173 atoms. 11166 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2296 (Rfree = 0.000) for 5173 atoms. Found 18 (24 requested) and removed 54 (12 requested) atoms. Cycle 32: After refmac, R = 0.2138 (Rfree = 0.000) for 5113 atoms. Found 22 (24 requested) and removed 33 (12 requested) atoms. Cycle 33: After refmac, R = 0.2158 (Rfree = 0.000) for 5081 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 34: After refmac, R = 0.2024 (Rfree = 0.000) for 5053 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 35: After refmac, R = 0.2074 (Rfree = 0.000) for 5046 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 5180 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 5217 seeds are put forward Round 1: 234 peptides, 51 chains. Longest chain 8 peptides. Score 0.241 Round 2: 264 peptides, 49 chains. Longest chain 9 peptides. Score 0.329 Round 3: 276 peptides, 50 chains. Longest chain 11 peptides. Score 0.346 Round 4: 287 peptides, 50 chains. Longest chain 13 peptides. Score 0.369 Round 5: 299 peptides, 52 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Chains 52, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 11952 restraints for refining 5172 atoms. 11016 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2137 (Rfree = 0.000) for 5172 atoms. Found 19 (24 requested) and removed 36 (12 requested) atoms. Cycle 37: After refmac, R = 0.2141 (Rfree = 0.000) for 5128 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 38: After refmac, R = 0.2201 (Rfree = 0.000) for 5110 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 39: After refmac, R = 0.2148 (Rfree = 0.000) for 5100 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 40: After refmac, R = 0.2078 (Rfree = 0.000) for 5091 atoms. Found 20 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 5241 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 5251 seeds are put forward Round 1: 232 peptides, 52 chains. Longest chain 9 peptides. Score 0.227 Round 2: 265 peptides, 49 chains. Longest chain 10 peptides. Score 0.332 Round 3: 246 peptides, 46 chains. Longest chain 10 peptides. Score 0.318 Round 4: 247 peptides, 45 chains. Longest chain 12 peptides. Score 0.330 Round 5: 249 peptides, 44 chains. Longest chain 11 peptides. Score 0.344 Taking the results from Round 5 Chains 44, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7165 reflections ( 99.07 % complete ) and 12367 restraints for refining 5173 atoms. 11591 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2555 (Rfree = 0.000) for 5173 atoms. Found 24 (24 requested) and removed 40 (12 requested) atoms. Cycle 42: After refmac, R = 0.2118 (Rfree = 0.000) for 5133 atoms. Found 21 (24 requested) and removed 32 (12 requested) atoms. Cycle 43: After refmac, R = 0.2278 (Rfree = 0.000) for 5109 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 44: After refmac, R = 0.2142 (Rfree = 0.000) for 5102 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 45: After refmac, R = 0.2134 (Rfree = 0.000) for 5090 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 5204 seeds are put forward Round 1: 218 peptides, 47 chains. Longest chain 8 peptides. Score 0.243 Round 2: 244 peptides, 44 chains. Longest chain 10 peptides. Score 0.333 Round 3: 242 peptides, 42 chains. Longest chain 11 peptides. Score 0.348 Round 4: 256 peptides, 47 chains. Longest chain 11 peptides. Score 0.331 Round 5: 277 peptides, 49 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 228, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2oh1-4_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (228 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7165 reflections ( 99.07 % complete ) and 12310 restraints for refining 5172 atoms. 11418 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2321 (Rfree = 0.000) for 5172 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2103 (Rfree = 0.000) for 5140 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2034 (Rfree = 0.000) for 5123 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1583 (Rfree = 0.000) for 5105 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:37:49 GMT 2018 Job finished. TimeTaking 58.39 Used memory is bytes: 21422808