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 1vjz-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.8-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/1vjz-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.8-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 22:22:59 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/1vjz-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.8-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 305 and 0 Target number of residues in the AU: 305 Target solvent content: 0.6100 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.56 Input MTZ file: 1vjz-3.8-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: 96 Cell parameters: 64.677 64.677 202.367 90.000 90.000 90.000 Input sequence file: 1vjz-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 target number of atoms Had to go as low as 0.80 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: 61.607 3.800 Wilson plot Bfac: 56.77 4668 reflections ( 99.89 % complete ) and 0 restraints for refining 3004 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3461 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3621 (Rfree = 0.000) for 3004 atoms. Found 16 (16 requested) and removed 43 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 3039 seeds are put forward Round 1: 146 peptides, 28 chains. Longest chain 12 peptides. Score 0.319 Round 2: 191 peptides, 30 chains. Longest chain 14 peptides. Score 0.459 Round 3: 197 peptides, 32 chains. Longest chain 12 peptides. Score 0.449 Round 4: 194 peptides, 27 chains. Longest chain 18 peptides. Score 0.514 Round 5: 181 peptides, 26 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 4 Chains 27, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5702 restraints for refining 2466 atoms. 5061 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3440 (Rfree = 0.000) for 2466 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 2: After refmac, R = 0.3493 (Rfree = 0.000) for 2419 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 3: After refmac, R = 0.3159 (Rfree = 0.000) for 2349 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 4: After refmac, R = 0.3133 (Rfree = 0.000) for 2317 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 5: After refmac, R = 0.2825 (Rfree = 0.000) for 2293 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.21 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward Round 1: 157 peptides, 31 chains. Longest chain 10 peptides. Score 0.312 Round 2: 194 peptides, 30 chains. Longest chain 13 peptides. Score 0.470 Round 3: 184 peptides, 28 chains. Longest chain 12 peptides. Score 0.465 Round 4: 194 peptides, 27 chains. Longest chain 18 peptides. Score 0.514 Round 5: 185 peptides, 26 chains. Longest chain 22 peptides. Score 0.499 Taking the results from Round 4 Chains 27, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5426 restraints for refining 2452 atoms. 4785 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3314 (Rfree = 0.000) for 2452 atoms. Found 11 (13 requested) and removed 30 (6 requested) atoms. Cycle 7: After refmac, R = 0.3107 (Rfree = 0.000) for 2404 atoms. Found 10 (13 requested) and removed 26 (6 requested) atoms. Cycle 8: After refmac, R = 0.3118 (Rfree = 0.000) for 2359 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 9: After refmac, R = 0.3156 (Rfree = 0.000) for 2319 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 10: After refmac, R = 0.3137 (Rfree = 0.000) for 2283 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 2348 seeds are put forward Round 1: 154 peptides, 26 chains. Longest chain 11 peptides. Score 0.386 Round 2: 170 peptides, 21 chains. Longest chain 27 peptides. Score 0.525 Round 3: 184 peptides, 22 chains. Longest chain 20 peptides. Score 0.555 Round 4: 158 peptides, 21 chains. Longest chain 14 peptides. Score 0.484 Round 5: 179 peptides, 22 chains. Longest chain 19 peptides. Score 0.539 Taking the results from Round 3 Chains 22, Residues 162, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5317 restraints for refining 2442 atoms. 4662 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3255 (Rfree = 0.000) for 2442 atoms. Found 13 (13 requested) and removed 62 (6 requested) atoms. Cycle 12: After refmac, R = 0.3021 (Rfree = 0.000) for 2373 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 13: After refmac, R = 0.2989 (Rfree = 0.000) for 2345 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 14: After refmac, R = 0.3103 (Rfree = 0.000) for 2317 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 15: After refmac, R = 0.3321 (Rfree = 0.000) for 2286 atoms. Found 12 (12 requested) and removed 38 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.43 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward Round 1: 136 peptides, 26 chains. Longest chain 9 peptides. Score 0.313 Round 2: 161 peptides, 24 chains. Longest chain 12 peptides. Score 0.446 Round 3: 172 peptides, 24 chains. Longest chain 16 peptides. Score 0.485 Round 4: 165 peptides, 23 chains. Longest chain 23 peptides. Score 0.477 Round 5: 171 peptides, 24 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 3 Chains 24, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5471 restraints for refining 2436 atoms. 4903 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3328 (Rfree = 0.000) for 2436 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. Cycle 17: After refmac, R = 0.3164 (Rfree = 0.000) for 2398 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. Cycle 18: After refmac, R = 0.3278 (Rfree = 0.000) for 2356 atoms. Found 13 (13 requested) and removed 40 (6 requested) atoms. Cycle 19: After refmac, R = 0.2567 (Rfree = 0.000) for 2305 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 20: After refmac, R = 0.2378 (Rfree = 0.000) for 2293 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2351 seeds are put forward Round 1: 144 peptides, 30 chains. Longest chain 9 peptides. Score 0.275 Round 2: 164 peptides, 25 chains. Longest chain 10 peptides. Score 0.441 Round 3: 164 peptides, 25 chains. Longest chain 14 peptides. Score 0.441 Round 4: 165 peptides, 25 chains. Longest chain 14 peptides. Score 0.445 Round 5: 179 peptides, 27 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 5 Chains 27, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5718 restraints for refining 2467 atoms. 5137 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3203 (Rfree = 0.000) for 2467 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 22: After refmac, R = 0.3090 (Rfree = 0.000) for 2427 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 23: After refmac, R = 0.2930 (Rfree = 0.000) for 2399 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 24: After refmac, R = 0.2912 (Rfree = 0.000) for 2387 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 25: After refmac, R = 0.2978 (Rfree = 0.000) for 2364 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2430 seeds are put forward Round 1: 147 peptides, 28 chains. Longest chain 8 peptides. Score 0.324 Round 2: 183 peptides, 30 chains. Longest chain 17 peptides. Score 0.430 Round 3: 174 peptides, 26 chains. Longest chain 19 peptides. Score 0.461 Round 4: 176 peptides, 27 chains. Longest chain 15 peptides. Score 0.452 Round 5: 160 peptides, 24 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 3 Chains 26, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5644 restraints for refining 2467 atoms. 5078 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3025 (Rfree = 0.000) for 2467 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. Cycle 27: After refmac, R = 0.2863 (Rfree = 0.000) for 2416 atoms. Found 7 (13 requested) and removed 25 (6 requested) atoms. Cycle 28: After refmac, R = 0.2780 (Rfree = 0.000) for 2383 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2699 (Rfree = 0.000) for 2373 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 30: After refmac, R = 0.2651 (Rfree = 0.000) for 2362 atoms. Found 9 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 2405 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 12 peptides. Score 0.345 Round 2: 181 peptides, 27 chains. Longest chain 16 peptides. Score 0.470 Round 3: 171 peptides, 21 chains. Longest chain 19 peptides. Score 0.528 Round 4: 175 peptides, 26 chains. Longest chain 13 peptides. Score 0.465 Round 5: 182 peptides, 23 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 5 Chains 23, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5529 restraints for refining 2466 atoms. 4916 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2990 (Rfree = 0.000) for 2466 atoms. Found 8 (13 requested) and removed 29 (6 requested) atoms. Cycle 32: After refmac, R = 0.2857 (Rfree = 0.000) for 2412 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 33: After refmac, R = 0.2761 (Rfree = 0.000) for 2398 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 34: After refmac, R = 0.2679 (Rfree = 0.000) for 2384 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.2592 (Rfree = 0.000) for 2381 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2432 seeds are put forward Round 1: 141 peptides, 28 chains. Longest chain 11 peptides. Score 0.298 Round 2: 167 peptides, 26 chains. Longest chain 13 peptides. Score 0.436 Round 3: 154 peptides, 26 chains. Longest chain 12 peptides. Score 0.386 Round 4: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.437 Round 5: 173 peptides, 27 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 5 Chains 27, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5508 restraints for refining 2467 atoms. 4951 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2890 (Rfree = 0.000) for 2467 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 37: After refmac, R = 0.2767 (Rfree = 0.000) for 2441 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.2284 (Rfree = 0.000) for 2426 atoms. Found 11 (13 requested) and removed 15 (6 requested) atoms. Cycle 39: After refmac, R = 0.2182 (Rfree = 0.000) for 2413 atoms. Found 10 (13 requested) and removed 16 (6 requested) atoms. Cycle 40: After refmac, R = 0.1997 (Rfree = 0.000) for 2406 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 2473 seeds are put forward Round 1: 140 peptides, 28 chains. Longest chain 8 peptides. Score 0.294 Round 2: 149 peptides, 27 chains. Longest chain 9 peptides. Score 0.349 Round 3: 151 peptides, 26 chains. Longest chain 11 peptides. Score 0.375 Round 4: 152 peptides, 27 chains. Longest chain 16 peptides. Score 0.361 Round 5: 160 peptides, 26 chains. Longest chain 24 peptides. Score 0.410 Taking the results from Round 5 Chains 27, Residues 134, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.89 % complete ) and 5555 restraints for refining 2467 atoms. 4972 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2649 (Rfree = 0.000) for 2467 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 42: After refmac, R = 0.2618 (Rfree = 0.000) for 2441 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 43: After refmac, R = 0.2510 (Rfree = 0.000) for 2426 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 44: After refmac, R = 0.2536 (Rfree = 0.000) for 2411 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.2512 (Rfree = 0.000) for 2401 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2464 seeds are put forward Round 1: 140 peptides, 27 chains. Longest chain 13 peptides. Score 0.312 Round 2: 146 peptides, 23 chains. Longest chain 14 peptides. Score 0.407 Round 3: 153 peptides, 26 chains. Longest chain 16 peptides. Score 0.383 Round 4: 140 peptides, 23 chains. Longest chain 10 peptides. Score 0.383 Round 5: 148 peptides, 23 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 125, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vjz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4668 reflections ( 99.89 % complete ) and 5676 restraints for refining 2467 atoms. 5187 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2890 (Rfree = 0.000) for 2467 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2886 (Rfree = 0.000) for 2442 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2885 (Rfree = 0.000) for 2424 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3092 (Rfree = 0.000) for 2399 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 47.03