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 2op5-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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/2op5-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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/2op5-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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 484 and 0 Target number of residues in the AU: 484 Target solvent content: 0.6225 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.6-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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5616 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: 73.087 3.600 Wilson plot Bfac: 62.34 8519 reflections ( 99.80 % complete ) and 0 restraints for refining 6193 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3325 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3072 (Rfree = 0.000) for 6193 atoms. Found 33 (39 requested) and removed 88 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 6287 seeds are put forward NCS extension: 0 residues added, 6287 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 13 peptides. Score 0.316 Round 2: 315 peptides, 49 chains. Longest chain 19 peptides. Score 0.465 Round 3: 316 peptides, 46 chains. Longest chain 19 peptides. Score 0.495 Round 4: 352 peptides, 47 chains. Longest chain 15 peptides. Score 0.557 Round 5: 346 peptides, 47 chains. Longest chain 19 peptides. Score 0.546 Taking the results from Round 4 Chains 47, Residues 305, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11882 restraints for refining 5091 atoms. 10709 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2389 (Rfree = 0.000) for 5091 atoms. Found 25 (32 requested) and removed 31 (16 requested) atoms. Cycle 2: After refmac, R = 0.2179 (Rfree = 0.000) for 5022 atoms. Found 13 (32 requested) and removed 31 (16 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2204 (Rfree = 0.000) for 4981 atoms. Found 8 (32 requested) and removed 27 (16 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2140 (Rfree = 0.000) for 4943 atoms. Found 6 (31 requested) and removed 23 (15 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2165 (Rfree = 0.000) for 4914 atoms. Found 11 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 5112 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5128 seeds are put forward Round 1: 314 peptides, 59 chains. Longest chain 17 peptides. Score 0.366 Round 2: 350 peptides, 57 chains. Longest chain 17 peptides. Score 0.466 Round 3: 349 peptides, 50 chains. Longest chain 26 peptides. Score 0.526 Round 4: 364 peptides, 52 chains. Longest chain 17 peptides. Score 0.538 Round 5: 394 peptides, 56 chains. Longest chain 17 peptides. Score 0.561 Taking the results from Round 5 Chains 56, Residues 338, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8519 reflections ( 99.80 % complete ) and 11499 restraints for refining 5075 atoms. 10203 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2354 (Rfree = 0.000) for 5075 atoms. Found 22 (32 requested) and removed 40 (16 requested) atoms. Cycle 7: After refmac, R = 0.2120 (Rfree = 0.000) for 5018 atoms. Found 8 (32 requested) and removed 35 (16 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1996 (Rfree = 0.000) for 4970 atoms. Found 9 (32 requested) and removed 20 (16 requested) atoms. Cycle 9: After refmac, R = 0.1993 (Rfree = 0.000) for 4937 atoms. Found 10 (31 requested) and removed 22 (15 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1929 (Rfree = 0.000) for 4916 atoms. Found 8 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 5112 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5128 seeds are put forward Round 1: 287 peptides, 51 chains. Longest chain 14 peptides. Score 0.383 Round 2: 318 peptides, 48 chains. Longest chain 16 peptides. Score 0.481 Round 3: 345 peptides, 51 chains. Longest chain 15 peptides. Score 0.509 Round 4: 342 peptides, 48 chains. Longest chain 14 peptides. Score 0.529 Round 5: 364 peptides, 52 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 52, Residues 312, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11606 restraints for refining 5090 atoms. 10410 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2428 (Rfree = 0.000) for 5090 atoms. Found 17 (32 requested) and removed 34 (16 requested) atoms. Cycle 12: After refmac, R = 0.2255 (Rfree = 0.000) for 5034 atoms. Found 14 (32 requested) and removed 40 (16 requested) atoms. Cycle 13: After refmac, R = 0.2046 (Rfree = 0.000) for 4987 atoms. Found 10 (32 requested) and removed 31 (16 requested) atoms. Cycle 14: After refmac, R = 0.2163 (Rfree = 0.000) for 4953 atoms. Found 19 (31 requested) and removed 28 (15 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1957 (Rfree = 0.000) for 4932 atoms. Found 12 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 5125 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5144 seeds are put forward Round 1: 261 peptides, 51 chains. Longest chain 10 peptides. Score 0.320 Round 2: 313 peptides, 52 chains. Longest chain 12 peptides. Score 0.432 Round 3: 354 peptides, 52 chains. Longest chain 21 peptides. Score 0.518 Round 4: 341 peptides, 51 chains. Longest chain 14 peptides. Score 0.501 Round 5: 333 peptides, 47 chains. Longest chain 20 peptides. Score 0.520 Taking the results from Round 5 Chains 47, Residues 286, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8519 reflections ( 99.80 % complete ) and 11788 restraints for refining 5090 atoms. 10691 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2246 (Rfree = 0.000) for 5090 atoms. Found 14 (32 requested) and removed 32 (16 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2130 (Rfree = 0.000) for 5042 atoms. Found 19 (32 requested) and removed 36 (16 requested) atoms. Cycle 18: After refmac, R = 0.2018 (Rfree = 0.000) for 5017 atoms. Found 10 (32 requested) and removed 23 (16 requested) atoms. Cycle 19: After refmac, R = 0.1707 (Rfree = 0.000) for 5000 atoms. Found 6 (32 requested) and removed 21 (16 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1650 (Rfree = 0.000) for 4978 atoms. Found 4 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5149 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5169 seeds are put forward Round 1: 258 peptides, 47 chains. Longest chain 12 peptides. Score 0.354 Round 2: 289 peptides, 46 chains. Longest chain 15 peptides. Score 0.437 Round 3: 322 peptides, 50 chains. Longest chain 17 peptides. Score 0.471 Round 4: 304 peptides, 50 chains. Longest chain 12 peptides. Score 0.431 Round 5: 290 peptides, 46 chains. Longest chain 15 peptides. Score 0.439 Taking the results from Round 3 Chains 50, Residues 272, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11829 restraints for refining 5090 atoms. 10791 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2177 (Rfree = 0.000) for 5090 atoms. Found 21 (32 requested) and removed 26 (16 requested) atoms. Cycle 22: After refmac, R = 0.2194 (Rfree = 0.000) for 5063 atoms. Found 25 (32 requested) and removed 28 (16 requested) atoms. Cycle 23: After refmac, R = 0.2038 (Rfree = 0.000) for 5052 atoms. Found 10 (32 requested) and removed 21 (16 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2008 (Rfree = 0.000) for 5028 atoms. Found 11 (32 requested) and removed 19 (16 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1882 (Rfree = 0.000) for 5012 atoms. Found 10 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5140 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5162 seeds are put forward Round 1: 257 peptides, 49 chains. Longest chain 11 peptides. Score 0.331 Round 2: 302 peptides, 48 chains. Longest chain 13 peptides. Score 0.446 Round 3: 283 peptides, 48 chains. Longest chain 11 peptides. Score 0.404 Round 4: 282 peptides, 44 chains. Longest chain 14 peptides. Score 0.441 Round 5: 295 peptides, 49 chains. Longest chain 12 peptides. Score 0.421 Taking the results from Round 2 Chains 48, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11708 restraints for refining 5091 atoms. 10740 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2120 (Rfree = 0.000) for 5091 atoms. Found 25 (32 requested) and removed 29 (16 requested) atoms. Cycle 27: After refmac, R = 0.1997 (Rfree = 0.000) for 5069 atoms. Found 11 (32 requested) and removed 21 (16 requested) atoms. Cycle 28: After refmac, R = 0.1885 (Rfree = 0.000) for 5055 atoms. Found 11 (32 requested) and removed 22 (16 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1864 (Rfree = 0.000) for 5034 atoms. Found 6 (32 requested) and removed 23 (16 requested) atoms. Cycle 30: After refmac, R = 0.1844 (Rfree = 0.000) for 5010 atoms. Found 12 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 5134 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5148 seeds are put forward Round 1: 273 peptides, 56 chains. Longest chain 11 peptides. Score 0.297 Round 2: 300 peptides, 53 chains. Longest chain 11 peptides. Score 0.393 Round 3: 295 peptides, 51 chains. Longest chain 17 peptides. Score 0.401 Round 4: 299 peptides, 47 chains. Longest chain 22 peptides. Score 0.449 Round 5: 302 peptides, 53 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 4 Chains 47, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11899 restraints for refining 5091 atoms. 10938 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2075 (Rfree = 0.000) for 5091 atoms. Found 21 (32 requested) and removed 27 (16 requested) atoms. Cycle 32: After refmac, R = 0.1957 (Rfree = 0.000) for 5065 atoms. Found 14 (32 requested) and removed 19 (16 requested) atoms. Cycle 33: After refmac, R = 0.1928 (Rfree = 0.000) for 5055 atoms. Found 24 (32 requested) and removed 20 (16 requested) atoms. Cycle 34: After refmac, R = 0.1938 (Rfree = 0.000) for 5052 atoms. Found 21 (32 requested) and removed 22 (16 requested) atoms. Cycle 35: After refmac, R = 0.1854 (Rfree = 0.000) for 5043 atoms. Found 24 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5178 seeds are put forward NCS extension: 38 residues added (0 deleted due to clashes), 5216 seeds are put forward Round 1: 250 peptides, 50 chains. Longest chain 10 peptides. Score 0.303 Round 2: 292 peptides, 49 chains. Longest chain 16 peptides. Score 0.414 Round 3: 294 peptides, 50 chains. Longest chain 11 peptides. Score 0.409 Round 4: 295 peptides, 50 chains. Longest chain 13 peptides. Score 0.411 Round 5: 283 peptides, 46 chains. Longest chain 17 peptides. Score 0.423 Taking the results from Round 5 Chains 46, Residues 237, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11898 restraints for refining 5091 atoms. 10996 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 5091 atoms. Found 24 (32 requested) and removed 24 (16 requested) atoms. Cycle 37: After refmac, R = 0.2016 (Rfree = 0.000) for 5078 atoms. Found 13 (32 requested) and removed 25 (16 requested) atoms. Cycle 38: After refmac, R = 0.1871 (Rfree = 0.000) for 5058 atoms. Found 8 (32 requested) and removed 20 (16 requested) atoms. Cycle 39: After refmac, R = 0.1870 (Rfree = 0.000) for 5037 atoms. Found 5 (32 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.1813 (Rfree = 0.000) for 5021 atoms. Found 5 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 5161 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 5184 seeds are put forward Round 1: 257 peptides, 49 chains. Longest chain 10 peptides. Score 0.331 Round 2: 273 peptides, 45 chains. Longest chain 12 peptides. Score 0.411 Round 3: 267 peptides, 46 chains. Longest chain 12 peptides. Score 0.386 Round 4: 264 peptides, 42 chains. Longest chain 18 peptides. Score 0.420 Round 5: 265 peptides, 44 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 4 Chains 42, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12081 restraints for refining 5091 atoms. 11235 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2112 (Rfree = 0.000) for 5091 atoms. Found 14 (32 requested) and removed 18 (16 requested) atoms. Cycle 42: After refmac, R = 0.1950 (Rfree = 0.000) for 5077 atoms. Found 19 (32 requested) and removed 23 (16 requested) atoms. Cycle 43: After refmac, R = 0.1860 (Rfree = 0.000) for 5061 atoms. Found 15 (32 requested) and removed 18 (16 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1665 (Rfree = 0.000) for 5053 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1758 (Rfree = 0.000) for 5038 atoms. Found 8 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5165 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5187 seeds are put forward Round 1: 201 peptides, 42 chains. Longest chain 8 peptides. Score 0.262 Round 2: 225 peptides, 38 chains. Longest chain 10 peptides. Score 0.369 Round 3: 238 peptides, 42 chains. Longest chain 11 peptides. Score 0.358 Round 4: 247 peptides, 40 chains. Longest chain 14 peptides. Score 0.401 Round 5: 227 peptides, 37 chains. Longest chain 20 peptides. Score 0.385 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 207, 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 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 8519 reflections ( 99.80 % complete ) and 12054 restraints for refining 5091 atoms. 11266 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1979 (Rfree = 0.000) for 5091 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1938 (Rfree = 0.000) for 5066 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1877 (Rfree = 0.000) for 5044 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1821 (Rfree = 0.000) for 5026 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB TimeTaking 75.32