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 1vlo-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-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/1vlo-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-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 ============================================================ Tue 25 Dec 19:28:07 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/1vlo-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-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 229 and 0 Target number of residues in the AU: 229 Target solvent content: 0.6483 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 381 Adjusted target solvent content: 0.41 Input MTZ file: 1vlo-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: 19 Cell parameters: 46.529 64.578 117.291 90.000 90.000 90.000 Input sequence file: 1vlo-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3048 target number of atoms Had to go as low as 0.65 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: 43.415 4.001 Wilson plot Bfac: 76.29 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3169 reflections ( 97.15 % complete ) and 0 restraints for refining 3372 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3542 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3241 (Rfree = 0.000) for 3372 atoms. Found 12 (16 requested) and removed 51 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 3391 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.231 Round 2: 128 peptides, 25 chains. Longest chain 11 peptides. Score 0.316 Round 3: 136 peptides, 25 chains. Longest chain 13 peptides. Score 0.355 Round 4: 142 peptides, 26 chains. Longest chain 9 peptides. Score 0.363 Round 5: 139 peptides, 26 chains. Longest chain 14 peptides. Score 0.349 Taking the results from Round 4 Chains 26, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 6861 restraints for refining 2752 atoms. 6423 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2622 (Rfree = 0.000) for 2752 atoms. Found 11 (13 requested) and removed 25 (6 requested) atoms. Cycle 2: After refmac, R = 0.2540 (Rfree = 0.000) for 2698 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 3: After refmac, R = 0.1911 (Rfree = 0.000) for 2662 atoms. Found 4 (12 requested) and removed 13 (6 requested) atoms. Cycle 4: After refmac, R = 0.1769 (Rfree = 0.000) for 2634 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.2702 (Rfree = 0.000) for 2614 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 2695 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 9 peptides. Score 0.266 Round 2: 136 peptides, 26 chains. Longest chain 13 peptides. Score 0.334 Round 3: 139 peptides, 25 chains. Longest chain 9 peptides. Score 0.369 Round 4: 136 peptides, 25 chains. Longest chain 9 peptides. Score 0.355 Round 5: 148 peptides, 25 chains. Longest chain 15 peptides. Score 0.410 Taking the results from Round 5 Chains 25, Residues 123, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 6094 restraints for refining 2574 atoms. 5610 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2303 (Rfree = 0.000) for 2574 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 7: After refmac, R = 0.2199 (Rfree = 0.000) for 2539 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 8: After refmac, R = 0.2325 (Rfree = 0.000) for 2514 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 9: After refmac, R = 0.2122 (Rfree = 0.000) for 2501 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 10: After refmac, R = 0.2144 (Rfree = 0.000) for 2490 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 4.08 Search for helices and strands: 0 residues in 0 chains, 2592 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 8 peptides. Score 0.250 Round 2: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.358 Round 3: 141 peptides, 27 chains. Longest chain 10 peptides. Score 0.338 Round 4: 148 peptides, 28 chains. Longest chain 11 peptides. Score 0.351 Round 5: 156 peptides, 28 chains. Longest chain 14 peptides. Score 0.388 Taking the results from Round 5 Chains 28, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 6073 restraints for refining 2602 atoms. 5589 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2338 (Rfree = 0.000) for 2602 atoms. Found 12 (12 requested) and removed 41 (6 requested) atoms. Cycle 12: After refmac, R = 0.2247 (Rfree = 0.000) for 2556 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 13: After refmac, R = 0.1939 (Rfree = 0.000) for 2534 atoms. Found 9 (12 requested) and removed 16 (6 requested) atoms. Cycle 14: After refmac, R = 0.1998 (Rfree = 0.000) for 2509 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 15: After refmac, R = 0.2206 (Rfree = 0.000) for 2496 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 2619 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 8 peptides. Score 0.282 Round 2: 145 peptides, 25 chains. Longest chain 13 peptides. Score 0.397 Round 3: 145 peptides, 24 chains. Longest chain 15 peptides. Score 0.416 Round 4: 139 peptides, 25 chains. Longest chain 9 peptides. Score 0.369 Round 5: 161 peptides, 23 chains. Longest chain 19 peptides. Score 0.503 Taking the results from Round 5 Chains 24, Residues 138, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 5806 restraints for refining 2617 atoms. 5207 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1856 (Rfree = 0.000) for 2617 atoms. Found 4 (12 requested) and removed 32 (6 requested) atoms. Cycle 17: After refmac, R = 0.2032 (Rfree = 0.000) for 2567 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 18: After refmac, R = 0.1848 (Rfree = 0.000) for 2553 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 19: After refmac, R = 0.1382 (Rfree = 0.000) for 2553 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 20: After refmac, R = 0.1406 (Rfree = 0.000) for 2545 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 13 peptides. Score 0.345 Round 2: 154 peptides, 25 chains. Longest chain 19 peptides. Score 0.437 Round 3: 157 peptides, 28 chains. Longest chain 10 peptides. Score 0.393 Round 4: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.385 Round 5: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 5 Chains 23, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 6340 restraints for refining 2676 atoms. 5871 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2245 (Rfree = 0.000) for 2676 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 22: After refmac, R = 0.2094 (Rfree = 0.000) for 2639 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 23: After refmac, R = 0.2076 (Rfree = 0.000) for 2612 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 24: After refmac, R = 0.2035 (Rfree = 0.000) for 2593 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 25: After refmac, R = 0.2110 (Rfree = 0.000) for 2580 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 2686 seeds are put forward Round 1: 109 peptides, 25 chains. Longest chain 6 peptides. Score 0.217 Round 2: 129 peptides, 26 chains. Longest chain 12 peptides. Score 0.300 Round 3: 132 peptides, 27 chains. Longest chain 7 peptides. Score 0.294 Round 4: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.325 Round 5: 131 peptides, 22 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 22, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 6335 restraints for refining 2627 atoms. 5921 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2242 (Rfree = 0.000) for 2627 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. Cycle 27: After refmac, R = 0.2089 (Rfree = 0.000) for 2594 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 28: After refmac, R = 0.2069 (Rfree = 0.000) for 2576 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 29: After refmac, R = 0.1806 (Rfree = 0.000) for 2561 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 30: After refmac, R = 0.1241 (Rfree = 0.000) for 2552 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 2624 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 6 peptides. Score 0.207 Round 2: 107 peptides, 22 chains. Longest chain 9 peptides. Score 0.273 Round 3: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.326 Round 4: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.309 Round 5: 105 peptides, 21 chains. Longest chain 7 peptides. Score 0.285 Taking the results from Round 3 Chains 21, Residues 92, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 5994 restraints for refining 2588 atoms. 5614 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1992 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 32: After refmac, R = 0.1976 (Rfree = 0.000) for 2565 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 33: After refmac, R = 0.2012 (Rfree = 0.000) for 2558 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 34: After refmac, R = 0.1920 (Rfree = 0.000) for 2554 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.1814 (Rfree = 0.000) for 2550 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 4.08 Search for helices and strands: 0 residues in 0 chains, 2630 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 6 peptides. Score 0.207 Round 2: 120 peptides, 24 chains. Longest chain 7 peptides. Score 0.297 Round 3: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.291 Round 4: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.325 Round 5: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 4 Chains 22, Residues 95, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 6094 restraints for refining 2653 atoms. 5706 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2151 (Rfree = 0.000) for 2653 atoms. Found 10 (12 requested) and removed 32 (6 requested) atoms. Cycle 37: After refmac, R = 0.2264 (Rfree = 0.000) for 2620 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 38: After refmac, R = 0.1875 (Rfree = 0.000) for 2596 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 39: After refmac, R = 0.2237 (Rfree = 0.000) for 2582 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 40: After refmac, R = 0.1943 (Rfree = 0.000) for 2570 atoms. Found 9 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 4.10 Search for helices and strands: 0 residues in 0 chains, 2630 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 7 peptides. Score 0.195 Round 2: 66 peptides, 14 chains. Longest chain 8 peptides. Score 0.233 Round 3: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.305 Round 4: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.305 Round 5: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.311 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3169 reflections ( 97.15 % complete ) and 5894 restraints for refining 2505 atoms. 5685 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2166 (Rfree = 0.000) for 2505 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 42: After refmac, R = 0.2245 (Rfree = 0.000) for 2487 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 43: After refmac, R = 0.1980 (Rfree = 0.000) for 2474 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 44: After refmac, R = 0.2177 (Rfree = 0.000) for 2465 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 45: After refmac, R = 0.1770 (Rfree = 0.000) for 2456 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 4.08 Search for helices and strands: 0 residues in 0 chains, 2522 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.218 Round 2: 64 peptides, 14 chains. Longest chain 9 peptides. Score 0.220 Round 3: 63 peptides, 13 chains. Longest chain 9 peptides. Score 0.240 Round 4: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.231 Round 5: 77 peptides, 16 chains. Longest chain 9 peptides. Score 0.248 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 61, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vlo-4_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (61 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3169 reflections ( 97.15 % complete ) and 5135 restraints for refining 2306 atoms. 4891 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2220 (Rfree = 0.000) for 2306 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2157 (Rfree = 0.000) for 2292 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2002 (Rfree = 0.000) for 2280 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1960 (Rfree = 0.000) for 2272 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:15:51 GMT 2018 Job finished. TimeTaking 47.92 Used memory is bytes: 16461304