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 1vli-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-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/1vli-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-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 19:28:12 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/1vli-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-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 365 and 0 Target number of residues in the AU: 365 Target solvent content: 0.6660 Checking the provided sequence file Detected sequence length: 385 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 385 Adjusted target solvent content: 0.65 Input MTZ file: 1vli-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: 154 Cell parameters: 70.614 70.614 205.438 90.000 90.000 120.000 Input sequence file: 1vli-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3080 target number of atoms Had to go as low as 1.10 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: 68.479 3.600 Wilson plot Bfac: 89.01 7362 reflections ( 99.69 % complete ) and 0 restraints for refining 3441 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3652 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3250 (Rfree = 0.000) for 3441 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3500 seeds are put forward Round 1: 202 peptides, 33 chains. Longest chain 13 peptides. Score 0.391 Round 2: 233 peptides, 27 chains. Longest chain 19 peptides. Score 0.540 Round 3: 251 peptides, 25 chains. Longest chain 24 peptides. Score 0.600 Round 4: 239 peptides, 26 chains. Longest chain 26 peptides. Score 0.564 Round 5: 247 peptides, 23 chains. Longest chain 37 peptides. Score 0.612 Taking the results from Round 5 Chains 28, Residues 224, Estimated correctness of the model 19.3 % 7 chains (95 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 5086 restraints for refining 2789 atoms. 3857 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2719 (Rfree = 0.000) for 2789 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 2: After refmac, R = 0.2537 (Rfree = 0.000) for 2711 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2416 (Rfree = 0.000) for 2689 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2370 (Rfree = 0.000) for 2676 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2296 (Rfree = 0.000) for 2667 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward Round 1: 230 peptides, 25 chains. Longest chain 24 peptides. Score 0.554 Round 2: 249 peptides, 28 chains. Longest chain 22 peptides. Score 0.566 Round 3: 244 peptides, 22 chains. Longest chain 33 peptides. Score 0.615 Round 4: 252 peptides, 22 chains. Longest chain 38 peptides. Score 0.631 Round 5: 250 peptides, 21 chains. Longest chain 28 peptides. Score 0.637 Taking the results from Round 5 Chains 21, Residues 229, Estimated correctness of the model 28.5 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 5678 restraints for refining 2792 atoms. 4631 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2586 (Rfree = 0.000) for 2792 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 7: After refmac, R = 0.2356 (Rfree = 0.000) for 2758 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.2311 (Rfree = 0.000) for 2736 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2190 (Rfree = 0.000) for 2725 atoms. Found 8 (17 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2182 (Rfree = 0.000) for 2712 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward Round 1: 245 peptides, 32 chains. Longest chain 26 peptides. Score 0.514 Round 2: 246 peptides, 25 chains. Longest chain 29 peptides. Score 0.590 Round 3: 236 peptides, 27 chains. Longest chain 21 peptides. Score 0.547 Round 4: 234 peptides, 26 chains. Longest chain 18 peptides. Score 0.553 Round 5: 230 peptides, 25 chains. Longest chain 26 peptides. Score 0.554 Taking the results from Round 2 Chains 26, Residues 221, Estimated correctness of the model 10.7 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 5815 restraints for refining 2790 atoms. 4812 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2380 (Rfree = 0.000) for 2790 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.2614 (Rfree = 0.000) for 2772 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2261 (Rfree = 0.000) for 2764 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2217 (Rfree = 0.000) for 2762 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2276 (Rfree = 0.000) for 2756 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 2.87 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward Round 1: 217 peptides, 28 chains. Longest chain 15 peptides. Score 0.490 Round 2: 251 peptides, 26 chains. Longest chain 23 peptides. Score 0.590 Round 3: 254 peptides, 25 chains. Longest chain 38 peptides. Score 0.606 Round 4: 246 peptides, 23 chains. Longest chain 47 peptides. Score 0.610 Round 5: 236 peptides, 21 chains. Longest chain 38 peptides. Score 0.609 Taking the results from Round 4 Chains 27, Residues 223, Estimated correctness of the model 18.5 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 5560 restraints for refining 2791 atoms. 4458 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2690 (Rfree = 0.000) for 2791 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 17: After refmac, R = 0.2414 (Rfree = 0.000) for 2761 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2333 (Rfree = 0.000) for 2754 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2273 (Rfree = 0.000) for 2742 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2162 (Rfree = 0.000) for 2731 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 2843 seeds are put forward Round 1: 219 peptides, 28 chains. Longest chain 17 peptides. Score 0.495 Round 2: 235 peptides, 27 chains. Longest chain 21 peptides. Score 0.544 Round 3: 244 peptides, 22 chains. Longest chain 36 peptides. Score 0.615 Round 4: 260 peptides, 24 chains. Longest chain 28 peptides. Score 0.628 Round 5: 256 peptides, 25 chains. Longest chain 30 peptides. Score 0.610 Taking the results from Round 4 Chains 26, Residues 236, Estimated correctness of the model 25.3 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 5506 restraints for refining 2792 atoms. 4390 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2811 (Rfree = 0.000) for 2792 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 22: After refmac, R = 0.2303 (Rfree = 0.000) for 2749 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2504 (Rfree = 0.000) for 2713 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.2194 (Rfree = 0.000) for 2701 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.2192 (Rfree = 0.000) for 2688 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward Round 1: 209 peptides, 29 chains. Longest chain 17 peptides. Score 0.458 Round 2: 238 peptides, 25 chains. Longest chain 23 peptides. Score 0.572 Round 3: 223 peptides, 26 chains. Longest chain 21 peptides. Score 0.527 Round 4: 231 peptides, 24 chains. Longest chain 22 peptides. Score 0.567 Round 5: 231 peptides, 29 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 2 Chains 28, Residues 213, Estimated correctness of the model 3.4 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 5766 restraints for refining 2790 atoms. 4747 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2339 (Rfree = 0.000) for 2790 atoms. Found 14 (17 requested) and removed 12 (8 requested) atoms. Cycle 27: After refmac, R = 0.2207 (Rfree = 0.000) for 2767 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2179 (Rfree = 0.000) for 2751 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.2127 (Rfree = 0.000) for 2744 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2147 (Rfree = 0.000) for 2734 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 2.90 Search for helices and strands: 0 residues in 0 chains, 2824 seeds are put forward Round 1: 211 peptides, 32 chains. Longest chain 20 peptides. Score 0.428 Round 2: 231 peptides, 29 chains. Longest chain 29 peptides. Score 0.513 Round 3: 238 peptides, 25 chains. Longest chain 20 peptides. Score 0.572 Round 4: 231 peptides, 26 chains. Longest chain 30 peptides. Score 0.546 Round 5: 230 peptides, 21 chains. Longest chain 28 peptides. Score 0.597 Taking the results from Round 5 Chains 21, Residues 209, Estimated correctness of the model 13.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 6076 restraints for refining 2791 atoms. 5209 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2607 (Rfree = 0.000) for 2791 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.2476 (Rfree = 0.000) for 2768 atoms. Found 16 (17 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.2430 (Rfree = 0.000) for 2763 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.2418 (Rfree = 0.000) for 2761 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2369 (Rfree = 0.000) for 2758 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 2.87 Search for helices and strands: 0 residues in 0 chains, 2838 seeds are put forward Round 1: 206 peptides, 29 chains. Longest chain 19 peptides. Score 0.450 Round 2: 232 peptides, 27 chains. Longest chain 21 peptides. Score 0.537 Round 3: 247 peptides, 24 chains. Longest chain 29 peptides. Score 0.602 Round 4: 247 peptides, 23 chains. Longest chain 31 peptides. Score 0.612 Round 5: 243 peptides, 25 chains. Longest chain 27 peptides. Score 0.583 Taking the results from Round 4 Chains 23, Residues 224, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 6092 restraints for refining 2791 atoms. 5219 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2655 (Rfree = 0.000) for 2791 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.2402 (Rfree = 0.000) for 2783 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2377 (Rfree = 0.000) for 2784 atoms. Found 15 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2247 (Rfree = 0.000) for 2780 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.2344 (Rfree = 0.000) for 2769 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 2907 seeds are put forward Round 1: 207 peptides, 28 chains. Longest chain 24 peptides. Score 0.465 Round 2: 219 peptides, 28 chains. Longest chain 25 peptides. Score 0.495 Round 3: 224 peptides, 24 chains. Longest chain 26 peptides. Score 0.552 Round 4: 225 peptides, 24 chains. Longest chain 27 peptides. Score 0.554 Round 5: 233 peptides, 25 chains. Longest chain 19 peptides. Score 0.561 Taking the results from Round 5 Chains 26, Residues 208, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7362 reflections ( 99.69 % complete ) and 6051 restraints for refining 2792 atoms. 5190 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2402 (Rfree = 0.000) for 2792 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2359 (Rfree = 0.000) for 2779 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2417 (Rfree = 0.000) for 2772 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2401 (Rfree = 0.000) for 2767 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2389 (Rfree = 0.000) for 2760 atoms. Found 16 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 2.85 Search for helices and strands: 0 residues in 0 chains, 2872 seeds are put forward Round 1: 200 peptides, 33 chains. Longest chain 16 peptides. Score 0.385 Round 2: 223 peptides, 26 chains. Longest chain 24 peptides. Score 0.527 Round 3: 218 peptides, 27 chains. Longest chain 20 peptides. Score 0.504 Round 4: 223 peptides, 26 chains. Longest chain 24 peptides. Score 0.527 Round 5: 221 peptides, 27 chains. Longest chain 23 peptides. Score 0.511 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 197, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 1vli-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 14 A and 27 A 28 chains (204 residues) following loop building 2 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7362 reflections ( 99.69 % complete ) and 5901 restraints for refining 2791 atoms. 4972 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2467 (Rfree = 0.000) for 2791 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2491 (Rfree = 0.000) for 2762 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2527 (Rfree = 0.000) for 2739 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2501 (Rfree = 0.000) for 2714 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:39:18 GMT 2018 Job finished. TimeTaking 71.35 Used memory is bytes: 6839456