Sun 23 Dec 22:23:05 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 1vr0-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-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/1vr0-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-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 22:23:13 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/1vr0-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-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 462 and 0 Target number of residues in the AU: 462 Target solvent content: 0.6587 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-4.0-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.70 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: 226.759 4.000 Wilson plot Bfac: 83.88 6637 reflections ( 99.51 % complete ) and 0 restraints for refining 6528 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3401 (Rfree = 0.000) for 6528 atoms. Found 31 (31 requested) and removed 75 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.99 Search for helices and strands: 0 residues in 0 chains, 6591 seeds are put forward NCS extension: 0 residues added, 6591 seeds are put forward Round 1: 247 peptides, 47 chains. Longest chain 13 peptides. Score 0.321 Round 2: 318 peptides, 52 chains. Longest chain 19 peptides. Score 0.433 Round 3: 340 peptides, 54 chains. Longest chain 15 peptides. Score 0.460 Round 4: 366 peptides, 51 chains. Longest chain 16 peptides. Score 0.536 Round 5: 379 peptides, 49 chains. Longest chain 18 peptides. Score 0.575 Taking the results from Round 5 Chains 49, Residues 330, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12590 restraints for refining 5353 atoms. 11284 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2760 (Rfree = 0.000) for 5353 atoms. Found 20 (25 requested) and removed 37 (12 requested) atoms. Cycle 2: After refmac, R = 0.2551 (Rfree = 0.000) for 5242 atoms. Found 12 (25 requested) and removed 44 (12 requested) atoms. Cycle 3: After refmac, R = 0.2454 (Rfree = 0.000) for 5170 atoms. Found 21 (24 requested) and removed 36 (12 requested) atoms. Cycle 4: After refmac, R = 0.2372 (Rfree = 0.000) for 5126 atoms. Found 22 (24 requested) and removed 35 (12 requested) atoms. Cycle 5: After refmac, R = 0.2218 (Rfree = 0.000) for 5081 atoms. Found 12 (24 requested) and removed 38 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.95 Search for helices and strands: 0 residues in 0 chains, 5264 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5277 seeds are put forward Round 1: 273 peptides, 54 chains. Longest chain 10 peptides. Score 0.312 Round 2: 329 peptides, 55 chains. Longest chain 12 peptides. Score 0.428 Round 3: 358 peptides, 51 chains. Longest chain 18 peptides. Score 0.521 Round 4: 356 peptides, 53 chains. Longest chain 13 peptides. Score 0.500 Round 5: 377 peptides, 55 chains. Longest chain 15 peptides. Score 0.523 Taking the results from Round 5 Chains 55, Residues 322, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12110 restraints for refining 5186 atoms. 10877 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 5186 atoms. Found 24 (24 requested) and removed 54 (12 requested) atoms. Cycle 7: After refmac, R = 0.2228 (Rfree = 0.000) for 5118 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 8: After refmac, R = 0.2203 (Rfree = 0.000) for 5090 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 9: After refmac, R = 0.2085 (Rfree = 0.000) for 5055 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 10: After refmac, R = 0.2192 (Rfree = 0.000) for 5042 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.95 Search for helices and strands: 0 residues in 0 chains, 5296 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5311 seeds are put forward Round 1: 298 peptides, 57 chains. Longest chain 10 peptides. Score 0.341 Round 2: 355 peptides, 58 chains. Longest chain 13 peptides. Score 0.455 Round 3: 351 peptides, 48 chains. Longest chain 18 peptides. Score 0.533 Round 4: 344 peptides, 50 chains. Longest chain 21 peptides. Score 0.503 Round 5: 346 peptides, 50 chains. Longest chain 15 peptides. Score 0.507 Taking the results from Round 3 Chains 48, Residues 303, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12075 restraints for refining 5222 atoms. 10911 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2054 (Rfree = 0.000) for 5222 atoms. Found 19 (24 requested) and removed 48 (12 requested) atoms. Cycle 12: After refmac, R = 0.2163 (Rfree = 0.000) for 5162 atoms. Found 20 (24 requested) and removed 32 (12 requested) atoms. Cycle 13: After refmac, R = 0.1933 (Rfree = 0.000) for 5132 atoms. Found 11 (24 requested) and removed 30 (12 requested) atoms. Cycle 14: After refmac, R = 0.1993 (Rfree = 0.000) for 5096 atoms. Found 20 (24 requested) and removed 25 (12 requested) atoms. Cycle 15: After refmac, R = 0.1937 (Rfree = 0.000) for 5085 atoms. Found 17 (24 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 5297 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5316 seeds are put forward Round 1: 281 peptides, 57 chains. Longest chain 11 peptides. Score 0.301 Round 2: 314 peptides, 50 chains. Longest chain 13 peptides. Score 0.442 Round 3: 315 peptides, 50 chains. Longest chain 11 peptides. Score 0.444 Round 4: 317 peptides, 49 chains. Longest chain 18 peptides. Score 0.458 Round 5: 329 peptides, 51 chains. Longest chain 12 peptides. Score 0.464 Taking the results from Round 5 Chains 51, Residues 278, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12667 restraints for refining 5349 atoms. 11583 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2027 (Rfree = 0.000) for 5349 atoms. Found 25 (25 requested) and removed 73 (12 requested) atoms. Cycle 17: After refmac, R = 0.2186 (Rfree = 0.000) for 5268 atoms. Found 25 (25 requested) and removed 47 (12 requested) atoms. Cycle 18: After refmac, R = 0.1952 (Rfree = 0.000) for 5218 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 19: After refmac, R = 0.2026 (Rfree = 0.000) for 5196 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 20: After refmac, R = 0.2025 (Rfree = 0.000) for 5176 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.99 Search for helices and strands: 0 residues in 0 chains, 5363 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5376 seeds are put forward Round 1: 243 peptides, 51 chains. Longest chain 9 peptides. Score 0.269 Round 2: 294 peptides, 50 chains. Longest chain 11 peptides. Score 0.400 Round 3: 299 peptides, 50 chains. Longest chain 11 peptides. Score 0.410 Round 4: 304 peptides, 51 chains. Longest chain 11 peptides. Score 0.412 Round 5: 311 peptides, 51 chains. Longest chain 11 peptides. Score 0.427 Taking the results from Round 5 Chains 51, Residues 260, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12878 restraints for refining 5354 atoms. 11889 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2028 (Rfree = 0.000) for 5354 atoms. Found 25 (25 requested) and removed 49 (12 requested) atoms. Cycle 22: After refmac, R = 0.1964 (Rfree = 0.000) for 5306 atoms. Found 25 (25 requested) and removed 40 (12 requested) atoms. Cycle 23: After refmac, R = 0.1956 (Rfree = 0.000) for 5267 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 24: After refmac, R = 0.1939 (Rfree = 0.000) for 5229 atoms. Found 24 (24 requested) and removed 42 (12 requested) atoms. Cycle 25: After refmac, R = 0.1920 (Rfree = 0.000) for 5199 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.95 Search for helices and strands: 0 residues in 0 chains, 5383 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5395 seeds are put forward Round 1: 213 peptides, 48 chains. Longest chain 7 peptides. Score 0.224 Round 2: 261 peptides, 47 chains. Longest chain 12 peptides. Score 0.354 Round 3: 272 peptides, 48 chains. Longest chain 11 peptides. Score 0.369 Round 4: 270 peptides, 47 chains. Longest chain 19 peptides. Score 0.375 Round 5: 287 peptides, 48 chains. Longest chain 15 peptides. Score 0.403 Taking the results from Round 5 Chains 48, Residues 239, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12603 restraints for refining 5280 atoms. 11695 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1942 (Rfree = 0.000) for 5280 atoms. Found 25 (25 requested) and removed 59 (12 requested) atoms. Cycle 27: After refmac, R = 0.2013 (Rfree = 0.000) for 5225 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 28: After refmac, R = 0.1987 (Rfree = 0.000) for 5200 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 29: After refmac, R = 0.2091 (Rfree = 0.000) for 5173 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 30: After refmac, R = 0.1954 (Rfree = 0.000) for 5157 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.98 Search for helices and strands: 0 residues in 0 chains, 5357 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5374 seeds are put forward Round 1: 191 peptides, 43 chains. Longest chain 7 peptides. Score 0.220 Round 2: 244 peptides, 49 chains. Longest chain 9 peptides. Score 0.293 Round 3: 267 peptides, 51 chains. Longest chain 10 peptides. Score 0.328 Round 4: 243 peptides, 45 chains. Longest chain 10 peptides. Score 0.332 Round 5: 247 peptides, 43 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 5 Chains 43, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12547 restraints for refining 5227 atoms. 11774 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2058 (Rfree = 0.000) for 5227 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 32: After refmac, R = 0.2046 (Rfree = 0.000) for 5192 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 33: After refmac, R = 0.1881 (Rfree = 0.000) for 5176 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 34: After refmac, R = 0.1787 (Rfree = 0.000) for 5151 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 35: After refmac, R = 0.1822 (Rfree = 0.000) for 5138 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.97 Search for helices and strands: 0 residues in 0 chains, 5345 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5360 seeds are put forward Round 1: 179 peptides, 40 chains. Longest chain 7 peptides. Score 0.222 Round 2: 231 peptides, 46 chains. Longest chain 10 peptides. Score 0.292 Round 3: 251 peptides, 51 chains. Longest chain 10 peptides. Score 0.289 Round 4: 247 peptides, 45 chains. Longest chain 10 peptides. Score 0.341 Round 5: 258 peptides, 47 chains. Longest chain 14 peptides. Score 0.347 Taking the results from Round 5 Chains 47, Residues 211, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12439 restraints for refining 5225 atoms. 11580 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2040 (Rfree = 0.000) for 5225 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 37: After refmac, R = 0.1960 (Rfree = 0.000) for 5183 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 38: After refmac, R = 0.2053 (Rfree = 0.000) for 5153 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 39: After refmac, R = 0.2060 (Rfree = 0.000) for 5122 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 40: After refmac, R = 0.2077 (Rfree = 0.000) for 5109 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.89 Search for helices and strands: 0 residues in 0 chains, 5308 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5320 seeds are put forward Round 1: 195 peptides, 44 chains. Longest chain 6 peptides. Score 0.220 Round 2: 236 peptides, 47 chains. Longest chain 13 peptides. Score 0.294 Round 3: 238 peptides, 45 chains. Longest chain 13 peptides. Score 0.320 Round 4: 231 peptides, 45 chains. Longest chain 13 peptides. Score 0.303 Round 5: 235 peptides, 46 chains. Longest chain 9 peptides. Score 0.302 Taking the results from Round 3 Chains 45, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 11931 restraints for refining 5086 atoms. 11204 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1997 (Rfree = 0.000) for 5086 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 42: After refmac, R = 0.2005 (Rfree = 0.000) for 5053 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 5035 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 44: After refmac, R = 0.1739 (Rfree = 0.000) for 5016 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 45: After refmac, R = 0.1791 (Rfree = 0.000) for 5001 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.93 Search for helices and strands: 0 residues in 0 chains, 5168 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5185 seeds are put forward Round 1: 173 peptides, 40 chains. Longest chain 6 peptides. Score 0.205 Round 2: 207 peptides, 41 chains. Longest chain 8 peptides. Score 0.285 Round 3: 199 peptides, 40 chains. Longest chain 8 peptides. Score 0.275 Round 4: 213 peptides, 39 chains. Longest chain 9 peptides. Score 0.322 Round 5: 218 peptides, 40 chains. Longest chain 8 peptides. Score 0.323 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 178, 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 1vr0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6637 reflections ( 99.51 % complete ) and 11734 restraints for refining 5000 atoms. 11062 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2021 (Rfree = 0.000) for 5000 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2118 (Rfree = 0.000) for 4976 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1815 (Rfree = 0.000) for 4944 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1829 (Rfree = 0.000) for 4919 atoms. TimeTaking 75.32