Sun 23 Dec 22:22:59 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 1vp7-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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/1vp7-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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 ============================================================ Sun 23 Dec 22:23:08 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/1vp7-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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 544 and 0 Target number of residues in the AU: 544 Target solvent content: 0.5698 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.6-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.60 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: 207.138 3.600 Wilson plot Bfac: 41.56 8705 reflections ( 99.61 % complete ) and 0 restraints for refining 5317 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3143 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3190 (Rfree = 0.000) for 5317 atoms. Found 34 (34 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 5386 seeds are put forward NCS extension: 0 residues added, 5386 seeds are put forward Round 1: 184 peptides, 39 chains. Longest chain 9 peptides. Score 0.251 Round 2: 257 peptides, 45 chains. Longest chain 10 peptides. Score 0.375 Round 3: 260 peptides, 42 chains. Longest chain 11 peptides. Score 0.413 Round 4: 279 peptides, 43 chains. Longest chain 12 peptides. Score 0.447 Round 5: 288 peptides, 37 chains. Longest chain 30 peptides. Score 0.524 Taking the results from Round 5 Chains 37, Residues 251, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8684 restraints for refining 3885 atoms. 7704 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2924 (Rfree = 0.000) for 3885 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 2: After refmac, R = 0.2880 (Rfree = 0.000) for 3763 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 3: After refmac, R = 0.2832 (Rfree = 0.000) for 3705 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 4: After refmac, R = 0.2607 (Rfree = 0.000) for 3666 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 5: After refmac, R = 0.2441 (Rfree = 0.000) for 3630 atoms. Found 16 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.98 2.86 Search for helices and strands: 0 residues in 0 chains, 3831 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3843 seeds are put forward Round 1: 235 peptides, 41 chains. Longest chain 13 peptides. Score 0.363 Round 2: 283 peptides, 43 chains. Longest chain 13 peptides. Score 0.456 Round 3: 289 peptides, 39 chains. Longest chain 27 peptides. Score 0.507 Round 4: 282 peptides, 39 chains. Longest chain 13 peptides. Score 0.492 Round 5: 291 peptides, 35 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 5 Chains 35, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 7890 restraints for refining 3604 atoms. 6901 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2889 (Rfree = 0.000) for 3604 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 7: After refmac, R = 0.2691 (Rfree = 0.000) for 3570 atoms. Found 21 (23 requested) and removed 22 (11 requested) atoms. Cycle 8: After refmac, R = 0.2668 (Rfree = 0.000) for 3543 atoms. Found 20 (22 requested) and removed 21 (11 requested) atoms. Cycle 9: After refmac, R = 0.2600 (Rfree = 0.000) for 3532 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 10: After refmac, R = 0.2499 (Rfree = 0.000) for 3517 atoms. Found 16 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.04 2.92 Search for helices and strands: 0 residues in 0 chains, 3696 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3723 seeds are put forward Round 1: 262 peptides, 45 chains. Longest chain 13 peptides. Score 0.387 Round 2: 298 peptides, 47 chains. Longest chain 15 peptides. Score 0.450 Round 3: 311 peptides, 46 chains. Longest chain 15 peptides. Score 0.488 Round 4: 331 peptides, 47 chains. Longest chain 17 peptides. Score 0.520 Round 5: 307 peptides, 43 chains. Longest chain 17 peptides. Score 0.507 Taking the results from Round 4 Chains 47, Residues 284, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 7744 restraints for refining 3677 atoms. 6655 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2893 (Rfree = 0.000) for 3677 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 12: After refmac, R = 0.2615 (Rfree = 0.000) for 3638 atoms. Found 15 (23 requested) and removed 22 (11 requested) atoms. Cycle 13: After refmac, R = 0.2597 (Rfree = 0.000) for 3615 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. Cycle 14: After refmac, R = 0.2594 (Rfree = 0.000) for 3597 atoms. Found 12 (23 requested) and removed 24 (11 requested) atoms. Cycle 15: After refmac, R = 0.2574 (Rfree = 0.000) for 3575 atoms. Found 11 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 2.89 Search for helices and strands: 0 residues in 0 chains, 3716 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3736 seeds are put forward Round 1: 253 peptides, 44 chains. Longest chain 11 peptides. Score 0.376 Round 2: 300 peptides, 42 chains. Longest chain 16 peptides. Score 0.502 Round 3: 292 peptides, 45 chains. Longest chain 15 peptides. Score 0.456 Round 4: 299 peptides, 42 chains. Longest chain 14 peptides. Score 0.500 Round 5: 284 peptides, 38 chains. Longest chain 22 peptides. Score 0.506 Taking the results from Round 5 Chains 40, Residues 246, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 7968 restraints for refining 3782 atoms. 6925 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2826 (Rfree = 0.000) for 3782 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 17: After refmac, R = 0.2648 (Rfree = 0.000) for 3727 atoms. Found 14 (24 requested) and removed 22 (12 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 3702 atoms. Found 12 (23 requested) and removed 14 (11 requested) atoms. Cycle 19: After refmac, R = 0.2526 (Rfree = 0.000) for 3677 atoms. Found 19 (23 requested) and removed 23 (11 requested) atoms. Cycle 20: After refmac, R = 0.2549 (Rfree = 0.000) for 3663 atoms. Found 11 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.02 2.90 Search for helices and strands: 0 residues in 0 chains, 3803 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3819 seeds are put forward Round 1: 268 peptides, 52 chains. Longest chain 11 peptides. Score 0.328 Round 2: 293 peptides, 48 chains. Longest chain 12 peptides. Score 0.429 Round 3: 285 peptides, 47 chains. Longest chain 16 peptides. Score 0.421 Round 4: 289 peptides, 49 chains. Longest chain 11 peptides. Score 0.410 Round 5: 289 peptides, 44 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 5 Chains 44, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8664 restraints for refining 3915 atoms. 7728 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2893 (Rfree = 0.000) for 3915 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 22: After refmac, R = 0.2566 (Rfree = 0.000) for 3874 atoms. Found 22 (25 requested) and removed 20 (12 requested) atoms. Cycle 23: After refmac, R = 0.2504 (Rfree = 0.000) for 3865 atoms. Found 23 (24 requested) and removed 20 (12 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2411 (Rfree = 0.000) for 3857 atoms. Found 14 (24 requested) and removed 16 (12 requested) atoms. Cycle 25: After refmac, R = 0.2359 (Rfree = 0.000) for 3847 atoms. Found 18 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.97 Search for helices and strands: 0 residues in 0 chains, 4021 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4035 seeds are put forward Round 1: 228 peptides, 44 chains. Longest chain 8 peptides. Score 0.313 Round 2: 264 peptides, 43 chains. Longest chain 14 peptides. Score 0.412 Round 3: 251 peptides, 40 chains. Longest chain 13 peptides. Score 0.413 Round 4: 283 peptides, 43 chains. Longest chain 14 peptides. Score 0.456 Round 5: 273 peptides, 40 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 5 Chains 40, Residues 233, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8960 restraints for refining 4008 atoms. 8068 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2701 (Rfree = 0.000) for 4008 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 27: After refmac, R = 0.2453 (Rfree = 0.000) for 3984 atoms. Found 19 (25 requested) and removed 26 (12 requested) atoms. Cycle 28: After refmac, R = 0.2410 (Rfree = 0.000) for 3962 atoms. Found 18 (25 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.2307 (Rfree = 0.000) for 3954 atoms. Found 16 (25 requested) and removed 19 (12 requested) atoms. Cycle 30: After refmac, R = 0.2263 (Rfree = 0.000) for 3940 atoms. Found 13 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 2.92 Search for helices and strands: 0 residues in 0 chains, 4065 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4082 seeds are put forward Round 1: 203 peptides, 40 chains. Longest chain 10 peptides. Score 0.292 Round 2: 234 peptides, 41 chains. Longest chain 9 peptides. Score 0.361 Round 3: 254 peptides, 44 chains. Longest chain 11 peptides. Score 0.378 Round 4: 250 peptides, 42 chains. Longest chain 11 peptides. Score 0.390 Round 5: 238 peptides, 36 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 5 Chains 38, Residues 202, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9191 restraints for refining 4094 atoms. 8371 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2615 (Rfree = 0.000) for 4094 atoms. Found 24 (26 requested) and removed 47 (13 requested) atoms. Cycle 32: After refmac, R = 0.2409 (Rfree = 0.000) for 4051 atoms. Found 17 (26 requested) and removed 25 (13 requested) atoms. Cycle 33: After refmac, R = 0.2328 (Rfree = 0.000) for 4033 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2266 (Rfree = 0.000) for 4018 atoms. Found 11 (25 requested) and removed 31 (12 requested) atoms. Cycle 35: After refmac, R = 0.2233 (Rfree = 0.000) for 3994 atoms. Found 9 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 2.90 Search for helices and strands: 0 residues in 0 chains, 4134 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4151 seeds are put forward Round 1: 209 peptides, 40 chains. Longest chain 9 peptides. Score 0.308 Round 2: 239 peptides, 41 chains. Longest chain 13 peptides. Score 0.373 Round 3: 226 peptides, 40 chains. Longest chain 13 peptides. Score 0.352 Round 4: 242 peptides, 38 chains. Longest chain 15 peptides. Score 0.412 Round 5: 235 peptides, 37 chains. Longest chain 21 peptides. Score 0.406 Taking the results from Round 4 Chains 38, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9039 restraints for refining 4002 atoms. 8261 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2622 (Rfree = 0.000) for 4002 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 37: After refmac, R = 0.2500 (Rfree = 0.000) for 3984 atoms. Found 21 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.2402 (Rfree = 0.000) for 3977 atoms. Found 13 (25 requested) and removed 18 (12 requested) atoms. Cycle 39: After refmac, R = 0.2344 (Rfree = 0.000) for 3965 atoms. Found 16 (25 requested) and removed 25 (12 requested) atoms. Cycle 40: After refmac, R = 0.2294 (Rfree = 0.000) for 3950 atoms. Found 14 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 4139 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4154 seeds are put forward Round 1: 206 peptides, 44 chains. Longest chain 12 peptides. Score 0.254 Round 2: 237 peptides, 43 chains. Longest chain 11 peptides. Score 0.347 Round 3: 248 peptides, 42 chains. Longest chain 12 peptides. Score 0.385 Round 4: 249 peptides, 43 chains. Longest chain 12 peptides. Score 0.377 Round 5: 266 peptides, 42 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 5 Chains 42, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9131 restraints for refining 4048 atoms. 8277 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2736 (Rfree = 0.000) for 4048 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 42: After refmac, R = 0.2585 (Rfree = 0.000) for 4031 atoms. Found 16 (25 requested) and removed 24 (12 requested) atoms. Cycle 43: After refmac, R = 0.2613 (Rfree = 0.000) for 4015 atoms. Found 13 (25 requested) and removed 23 (12 requested) atoms. Cycle 44: After refmac, R = 0.2475 (Rfree = 0.000) for 3997 atoms. Found 20 (25 requested) and removed 22 (12 requested) atoms. Cycle 45: After refmac, R = 0.2378 (Rfree = 0.000) for 3990 atoms. Found 7 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 4161 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 4194 seeds are put forward Round 1: 183 peptides, 37 chains. Longest chain 11 peptides. Score 0.272 Round 2: 197 peptides, 34 chains. Longest chain 13 peptides. Score 0.345 Round 3: 204 peptides, 33 chains. Longest chain 15 peptides. Score 0.374 Round 4: 218 peptides, 36 chains. Longest chain 17 peptides. Score 0.376 Round 5: 217 peptides, 35 chains. Longest chain 17 peptides. Score 0.384 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 182, 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 1vp7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8705 reflections ( 99.61 % complete ) and 9425 restraints for refining 4073 atoms. 8732 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2577 (Rfree = 0.000) for 4073 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2539 (Rfree = 0.000) for 4051 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2422 (Rfree = 0.000) for 4035 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2375 (Rfree = 0.000) for 4018 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 78.32