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 1vpb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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/1vpb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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/1vpb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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 412 and 0 Target number of residues in the AU: 412 Target solvent content: 0.6326 Checking the provided sequence file Detected sequence length: 451 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 451 Adjusted target solvent content: 0.60 Input MTZ file: 1vpb-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: 20 Cell parameters: 74.004 155.044 105.800 90.000 90.000 90.000 Input sequence file: 1vpb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3608 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 Loops will be built when appropriate and at the last cycle Resolution range: 77.522 3.600 Wilson plot Bfac: 67.50 7281 reflections ( 99.02 % complete ) and 0 restraints for refining 3987 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3095 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2697 (Rfree = 0.000) for 3987 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.94 Search for helices and strands: 0 residues in 0 chains, 4057 seeds are put forward Round 1: 263 peptides, 46 chains. Longest chain 15 peptides. Score 0.398 Round 2: 293 peptides, 36 chains. Longest chain 27 peptides. Score 0.574 Round 3: 309 peptides, 34 chains. Longest chain 24 peptides. Score 0.624 Round 4: 328 peptides, 34 chains. Longest chain 24 peptides. Score 0.658 Round 5: 313 peptides, 37 chains. Longest chain 19 peptides. Score 0.605 Taking the results from Round 4 Chains 35, Residues 294, Estimated correctness of the model 35.9 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6782 restraints for refining 3270 atoms. 5577 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2541 (Rfree = 0.000) for 3270 atoms. Found 18 (20 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.2415 (Rfree = 0.000) for 3215 atoms. Found 12 (20 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.2348 (Rfree = 0.000) for 3199 atoms. Found 8 (20 requested) and removed 14 (10 requested) atoms. Cycle 4: After refmac, R = 0.2453 (Rfree = 0.000) for 3184 atoms. Found 4 (20 requested) and removed 15 (10 requested) atoms. Cycle 5: After refmac, R = 0.2463 (Rfree = 0.000) for 3166 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.94 Search for helices and strands: 0 residues in 0 chains, 3269 seeds are put forward Round 1: 275 peptides, 38 chains. Longest chain 16 peptides. Score 0.514 Round 2: 303 peptides, 31 chains. Longest chain 23 peptides. Score 0.639 Round 3: 302 peptides, 35 chains. Longest chain 31 peptides. Score 0.601 Round 4: 318 peptides, 33 chains. Longest chain 31 peptides. Score 0.649 Round 5: 314 peptides, 33 chains. Longest chain 28 peptides. Score 0.642 Taking the results from Round 4 Chains 36, Residues 285, Estimated correctness of the model 32.8 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6891 restraints for refining 3271 atoms. 5711 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2638 (Rfree = 0.000) for 3271 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. Cycle 7: After refmac, R = 0.2493 (Rfree = 0.000) for 3265 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.2633 (Rfree = 0.000) for 3255 atoms. Found 3 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2460 (Rfree = 0.000) for 3242 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2567 (Rfree = 0.000) for 3232 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 2.93 Search for helices and strands: 0 residues in 0 chains, 3320 seeds are put forward Round 1: 283 peptides, 41 chains. Longest chain 17 peptides. Score 0.502 Round 2: 301 peptides, 34 chains. Longest chain 27 peptides. Score 0.608 Round 3: 296 peptides, 33 chains. Longest chain 23 peptides. Score 0.608 Round 4: 293 peptides, 32 chains. Longest chain 23 peptides. Score 0.611 Round 5: 305 peptides, 33 chains. Longest chain 24 peptides. Score 0.625 Taking the results from Round 5 Chains 38, Residues 272, Estimated correctness of the model 24.2 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6697 restraints for refining 3271 atoms. 5490 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2619 (Rfree = 0.000) for 3271 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 12: After refmac, R = 0.2471 (Rfree = 0.000) for 3243 atoms. Found 5 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.2509 (Rfree = 0.000) for 3229 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.2526 (Rfree = 0.000) for 3216 atoms. Found 1 (20 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2736 (Rfree = 0.000) for 3200 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 2.98 Search for helices and strands: 0 residues in 0 chains, 3293 seeds are put forward Round 1: 266 peptides, 42 chains. Longest chain 14 peptides. Score 0.450 Round 2: 305 peptides, 41 chains. Longest chain 23 peptides. Score 0.551 Round 3: 300 peptides, 34 chains. Longest chain 28 peptides. Score 0.607 Round 4: 289 peptides, 41 chains. Longest chain 16 peptides. Score 0.516 Round 5: 295 peptides, 32 chains. Longest chain 27 peptides. Score 0.615 Taking the results from Round 5 Chains 38, Residues 263, Estimated correctness of the model 20.4 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6813 restraints for refining 3271 atoms. 5658 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2638 (Rfree = 0.000) for 3271 atoms. Found 13 (20 requested) and removed 20 (10 requested) atoms. Cycle 17: After refmac, R = 0.2491 (Rfree = 0.000) for 3247 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.2479 (Rfree = 0.000) for 3231 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. Cycle 19: After refmac, R = 0.2299 (Rfree = 0.000) for 3219 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.2312 (Rfree = 0.000) for 3211 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 2.94 Search for helices and strands: 0 residues in 0 chains, 3303 seeds are put forward Round 1: 281 peptides, 44 chains. Longest chain 18 peptides. Score 0.466 Round 2: 302 peptides, 40 chains. Longest chain 28 peptides. Score 0.554 Round 3: 293 peptides, 45 chains. Longest chain 20 peptides. Score 0.484 Round 4: 296 peptides, 39 chains. Longest chain 21 peptides. Score 0.551 Round 5: 304 peptides, 34 chains. Longest chain 26 peptides. Score 0.614 Taking the results from Round 5 Chains 36, Residues 270, Estimated correctness of the model 20.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6816 restraints for refining 3270 atoms. 5696 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2552 (Rfree = 0.000) for 3270 atoms. Found 16 (20 requested) and removed 26 (10 requested) atoms. Cycle 22: After refmac, R = 0.2534 (Rfree = 0.000) for 3247 atoms. Found 7 (20 requested) and removed 18 (10 requested) atoms. Cycle 23: After refmac, R = 0.2412 (Rfree = 0.000) for 3230 atoms. Found 14 (20 requested) and removed 20 (10 requested) atoms. Cycle 24: After refmac, R = 0.2390 (Rfree = 0.000) for 3216 atoms. Found 17 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.2223 (Rfree = 0.000) for 3215 atoms. Found 13 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.93 Search for helices and strands: 0 residues in 0 chains, 3316 seeds are put forward Round 1: 264 peptides, 46 chains. Longest chain 17 peptides. Score 0.401 Round 2: 289 peptides, 39 chains. Longest chain 22 peptides. Score 0.536 Round 3: 278 peptides, 36 chains. Longest chain 19 peptides. Score 0.541 Round 4: 284 peptides, 33 chains. Longest chain 22 peptides. Score 0.584 Round 5: 289 peptides, 34 chains. Longest chain 22 peptides. Score 0.584 Taking the results from Round 5 Chains 35, Residues 255, Estimated correctness of the model 8.3 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6897 restraints for refining 3271 atoms. 5806 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2445 (Rfree = 0.000) for 3271 atoms. Found 15 (20 requested) and removed 17 (10 requested) atoms. Cycle 27: After refmac, R = 0.2235 (Rfree = 0.000) for 3247 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.2263 (Rfree = 0.000) for 3239 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.2081 (Rfree = 0.000) for 3229 atoms. Found 8 (20 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.2111 (Rfree = 0.000) for 3222 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 2.94 Search for helices and strands: 0 residues in 0 chains, 3347 seeds are put forward Round 1: 266 peptides, 40 chains. Longest chain 22 peptides. Score 0.472 Round 2: 288 peptides, 39 chains. Longest chain 19 peptides. Score 0.534 Round 3: 298 peptides, 35 chains. Longest chain 28 peptides. Score 0.593 Round 4: 299 peptides, 36 chains. Longest chain 22 peptides. Score 0.586 Round 5: 306 peptides, 34 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 5 Chains 35, Residues 272, Estimated correctness of the model 21.6 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6728 restraints for refining 3271 atoms. 5550 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 3271 atoms. Found 16 (20 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.2446 (Rfree = 0.000) for 3254 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.2496 (Rfree = 0.000) for 3243 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.2307 (Rfree = 0.000) for 3235 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.2415 (Rfree = 0.000) for 3231 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.94 Search for helices and strands: 0 residues in 0 chains, 3317 seeds are put forward Round 1: 242 peptides, 38 chains. Longest chain 19 peptides. Score 0.434 Round 2: 288 peptides, 38 chains. Longest chain 20 peptides. Score 0.544 Round 3: 286 peptides, 36 chains. Longest chain 18 peptides. Score 0.559 Round 4: 262 peptides, 32 chains. Longest chain 23 peptides. Score 0.546 Round 5: 287 peptides, 35 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 5 Chains 35, Residues 252, Estimated correctness of the model 3.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 7163 restraints for refining 3271 atoms. 6143 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2500 (Rfree = 0.000) for 3271 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.2250 (Rfree = 0.000) for 3265 atoms. Found 7 (21 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.2214 (Rfree = 0.000) for 3254 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2143 (Rfree = 0.000) for 3242 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2117 (Rfree = 0.000) for 3237 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 2.95 Search for helices and strands: 0 residues in 0 chains, 3330 seeds are put forward Round 1: 234 peptides, 38 chains. Longest chain 11 peptides. Score 0.413 Round 2: 262 peptides, 33 chains. Longest chain 21 peptides. Score 0.536 Round 3: 255 peptides, 35 chains. Longest chain 19 peptides. Score 0.499 Round 4: 269 peptides, 37 chains. Longest chain 13 peptides. Score 0.511 Round 5: 266 peptides, 38 chains. Longest chain 19 peptides. Score 0.493 Taking the results from Round 2 Chains 34, Residues 229, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7281 reflections ( 99.02 % complete ) and 6966 restraints for refining 3270 atoms. 5991 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2332 (Rfree = 0.000) for 3270 atoms. Found 16 (20 requested) and removed 14 (10 requested) atoms. Cycle 42: After refmac, R = 0.2182 (Rfree = 0.000) for 3263 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.2131 (Rfree = 0.000) for 3255 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 44: After refmac, R = 0.2014 (Rfree = 0.000) for 3248 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 3240 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 2.96 Search for helices and strands: 0 residues in 0 chains, 3329 seeds are put forward Round 1: 220 peptides, 41 chains. Longest chain 11 peptides. Score 0.340 Round 2: 251 peptides, 39 chains. Longest chain 14 peptides. Score 0.446 Round 3: 238 peptides, 36 chains. Longest chain 16 peptides. Score 0.447 Round 4: 252 peptides, 36 chains. Longest chain 17 peptides. Score 0.481 Round 5: 250 peptides, 39 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 216, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vpb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7281 reflections ( 99.02 % complete ) and 7326 restraints for refining 3271 atoms. 6472 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2408 (Rfree = 0.000) for 3271 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2425 (Rfree = 0.000) for 3244 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2304 (Rfree = 0.000) for 3229 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2247 (Rfree = 0.000) for 3210 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:29:28 GMT 2018 Job finished. TimeTaking 61.52 Used memory is bytes: 864568