null Sun 23 Dec 22:22:49 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 1vqs-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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/1vqs-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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 22:22:58 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/1vqs-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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 449 and 0 Target number of residues in the AU: 449 Target solvent content: 0.6429 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-4.0-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 4.000 Wilson plot Bfac: 73.36 6209 reflections ( 99.41 % complete ) and 0 restraints for refining 5104 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3496 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3422 (Rfree = 0.000) for 5104 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 5202 seeds are put forward NCS extension: 0 residues added, 5202 seeds are put forward Round 1: 212 peptides, 39 chains. Longest chain 13 peptides. Score 0.327 Round 2: 273 peptides, 40 chains. Longest chain 14 peptides. Score 0.464 Round 3: 274 peptides, 40 chains. Longest chain 14 peptides. Score 0.466 Round 4: 288 peptides, 39 chains. Longest chain 18 peptides. Score 0.506 Round 5: 285 peptides, 36 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 5 Chains 36, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9994 restraints for refining 4190 atoms. 9034 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3097 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.2821 (Rfree = 0.000) for 4080 atoms. Found 17 (19 requested) and removed 27 (9 requested) atoms. Cycle 3: After refmac, R = 0.2665 (Rfree = 0.000) for 4004 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 4: After refmac, R = 0.2533 (Rfree = 0.000) for 3963 atoms. Found 15 (18 requested) and removed 20 (9 requested) atoms. Cycle 5: After refmac, R = 0.2434 (Rfree = 0.000) for 3938 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 4043 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 4070 seeds are put forward Round 1: 249 peptides, 46 chains. Longest chain 12 peptides. Score 0.345 Round 2: 288 peptides, 47 chains. Longest chain 12 peptides. Score 0.428 Round 3: 295 peptides, 43 chains. Longest chain 15 peptides. Score 0.483 Round 4: 310 peptides, 44 chains. Longest chain 17 peptides. Score 0.505 Round 5: 306 peptides, 42 chains. Longest chain 15 peptides. Score 0.515 Taking the results from Round 5 Chains 42, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9515 restraints for refining 4102 atoms. 8501 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2710 (Rfree = 0.000) for 4102 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 7: After refmac, R = 0.2486 (Rfree = 0.000) for 4032 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 8: After refmac, R = 0.2335 (Rfree = 0.000) for 3984 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 3961 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 10: After refmac, R = 0.1973 (Rfree = 0.000) for 3945 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 4080 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4091 seeds are put forward Round 1: 270 peptides, 49 chains. Longest chain 11 peptides. Score 0.365 Round 2: 299 peptides, 43 chains. Longest chain 15 peptides. Score 0.491 Round 3: 315 peptides, 43 chains. Longest chain 24 peptides. Score 0.525 Round 4: 291 peptides, 40 chains. Longest chain 21 peptides. Score 0.503 Round 5: 300 peptides, 40 chains. Longest chain 19 peptides. Score 0.521 Taking the results from Round 3 Chains 43, Residues 272, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9057 restraints for refining 4039 atoms. 8012 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 4039 atoms. Found 18 (19 requested) and removed 26 (9 requested) atoms. Cycle 12: After refmac, R = 0.2175 (Rfree = 0.000) for 3993 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 13: After refmac, R = 0.2119 (Rfree = 0.000) for 3960 atoms. Found 17 (18 requested) and removed 23 (9 requested) atoms. Cycle 14: After refmac, R = 0.1994 (Rfree = 0.000) for 3934 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 15: After refmac, R = 0.1967 (Rfree = 0.000) for 3920 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 4087 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4101 seeds are put forward Round 1: 265 peptides, 50 chains. Longest chain 10 peptides. Score 0.343 Round 2: 292 peptides, 45 chains. Longest chain 15 peptides. Score 0.457 Round 3: 305 peptides, 43 chains. Longest chain 18 peptides. Score 0.504 Round 4: 294 peptides, 41 chains. Longest chain 18 peptides. Score 0.500 Round 5: 314 peptides, 45 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 5 Chains 46, Residues 269, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9313 restraints for refining 4190 atoms. 8196 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2315 (Rfree = 0.000) for 4190 atoms. Found 18 (19 requested) and removed 30 (9 requested) atoms. Cycle 17: After refmac, R = 0.2263 (Rfree = 0.000) for 4142 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 18: After refmac, R = 0.2135 (Rfree = 0.000) for 4107 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 19: After refmac, R = 0.1714 (Rfree = 0.000) for 4082 atoms. Found 2 (19 requested) and removed 16 (9 requested) atoms. Cycle 20: After refmac, R = 0.1611 (Rfree = 0.000) for 4055 atoms. Found 4 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 4204 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4221 seeds are put forward Round 1: 291 peptides, 57 chains. Longest chain 14 peptides. Score 0.334 Round 2: 319 peptides, 48 chains. Longest chain 18 peptides. Score 0.487 Round 3: 326 peptides, 46 chains. Longest chain 19 peptides. Score 0.520 Round 4: 320 peptides, 47 chains. Longest chain 16 peptides. Score 0.498 Round 5: 323 peptides, 49 chains. Longest chain 21 peptides. Score 0.486 Taking the results from Round 3 Chains 46, Residues 280, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9480 restraints for refining 4190 atoms. 8406 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2280 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 22: After refmac, R = 0.2192 (Rfree = 0.000) for 4141 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 23: After refmac, R = 0.2246 (Rfree = 0.000) for 4126 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 24: After refmac, R = 0.2088 (Rfree = 0.000) for 4105 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 25: After refmac, R = 0.2156 (Rfree = 0.000) for 4086 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 4249 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4267 seeds are put forward Round 1: 243 peptides, 47 chains. Longest chain 9 peptides. Score 0.319 Round 2: 287 peptides, 51 chains. Longest chain 16 peptides. Score 0.386 Round 3: 273 peptides, 44 chains. Longest chain 16 peptides. Score 0.424 Round 4: 267 peptides, 38 chains. Longest chain 19 peptides. Score 0.471 Round 5: 270 peptides, 41 chains. Longest chain 17 peptides. Score 0.447 Taking the results from Round 4 Chains 38, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9879 restraints for refining 4189 atoms. 9001 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2191 (Rfree = 0.000) for 4189 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 4173 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 28: After refmac, R = 0.2227 (Rfree = 0.000) for 4148 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 29: After refmac, R = 0.2124 (Rfree = 0.000) for 4128 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 30: After refmac, R = 0.2026 (Rfree = 0.000) for 4112 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 4263 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4283 seeds are put forward Round 1: 224 peptides, 47 chains. Longest chain 9 peptides. Score 0.269 Round 2: 268 peptides, 46 chains. Longest chain 15 peptides. Score 0.392 Round 3: 278 peptides, 46 chains. Longest chain 19 peptides. Score 0.415 Round 4: 294 peptides, 47 chains. Longest chain 15 peptides. Score 0.442 Round 5: 282 peptides, 43 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 5 Chains 44, Residues 239, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9556 restraints for refining 4190 atoms. 8595 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2252 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 32: After refmac, R = 0.1980 (Rfree = 0.000) for 4155 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 33: After refmac, R = 0.1929 (Rfree = 0.000) for 4137 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 34: After refmac, R = 0.2000 (Rfree = 0.000) for 4125 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 35: After refmac, R = 0.1948 (Rfree = 0.000) for 4115 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4243 seeds are put forward Round 1: 212 peptides, 41 chains. Longest chain 13 peptides. Score 0.305 Round 2: 244 peptides, 41 chains. Longest chain 14 peptides. Score 0.386 Round 3: 257 peptides, 43 chains. Longest chain 19 peptides. Score 0.397 Round 4: 243 peptides, 39 chains. Longest chain 18 peptides. Score 0.405 Round 5: 250 peptides, 41 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 4 Chains 39, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9926 restraints for refining 4190 atoms. 9149 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2189 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 37: After refmac, R = 0.2108 (Rfree = 0.000) for 4138 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 38: After refmac, R = 0.2292 (Rfree = 0.000) for 4127 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 39: After refmac, R = 0.2179 (Rfree = 0.000) for 4103 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 40: After refmac, R = 0.2179 (Rfree = 0.000) for 4086 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 4256 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4276 seeds are put forward Round 1: 169 peptides, 39 chains. Longest chain 7 peptides. Score 0.207 Round 2: 218 peptides, 43 chains. Longest chain 9 peptides. Score 0.298 Round 3: 207 peptides, 40 chains. Longest chain 10 peptides. Score 0.303 Round 4: 205 peptides, 38 chains. Longest chain 11 peptides. Score 0.320 Round 5: 205 peptides, 36 chains. Longest chain 12 peptides. Score 0.343 Taking the results from Round 5 Chains 36, Residues 169, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9977 restraints for refining 4190 atoms. 9309 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2254 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 42: After refmac, R = 0.2121 (Rfree = 0.000) for 4162 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 43: After refmac, R = 0.2310 (Rfree = 0.000) for 4142 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 44: After refmac, R = 0.2130 (Rfree = 0.000) for 4120 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 45: After refmac, R = 0.2232 (Rfree = 0.000) for 4108 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 4243 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 4246 seeds are put forward Round 1: 155 peptides, 35 chains. Longest chain 6 peptides. Score 0.214 Round 2: 187 peptides, 35 chains. Longest chain 11 peptides. Score 0.307 Round 3: 186 peptides, 35 chains. Longest chain 13 peptides. Score 0.304 Round 4: 186 peptides, 35 chains. Longest chain 10 peptides. Score 0.304 Round 5: 175 peptides, 31 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 144, 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 1vqs-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6209 reflections ( 99.41 % complete ) and 9698 restraints for refining 4098 atoms. 9153 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2236 (Rfree = 0.000) for 4098 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2272 (Rfree = 0.000) for 4064 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2276 (Rfree = 0.000) for 4039 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2383 (Rfree = 0.000) for 4006 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:31:38 GMT 2018 Job finished. TimeTaking 68.82 Used memory is bytes: 20370136