null Sun 23 Dec 22:23:05 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 1vlc-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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/1vlc-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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 22:23:15 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/1vlc-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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 321 and 0 Target number of residues in the AU: 321 Target solvent content: 0.6307 Checking the provided sequence file Detected sequence length: 366 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 366 Adjusted target solvent content: 0.58 Input MTZ file: 1vlc-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: 150 Cell parameters: 119.541 119.541 57.022 90.000 90.000 120.000 Input sequence file: 1vlc-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2928 target number of atoms Had to go as low as 0.95 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: 103.526 3.800 Wilson plot Bfac: 66.77 4805 reflections ( 99.67 % complete ) and 0 restraints for refining 3247 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2216 (Rfree = 0.000) for 3247 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.07 Search for helices and strands: 0 residues in 0 chains, 3328 seeds are put forward Round 1: 201 peptides, 34 chains. Longest chain 15 peptides. Score 0.413 Round 2: 236 peptides, 29 chains. Longest chain 20 peptides. Score 0.584 Round 3: 238 peptides, 26 chains. Longest chain 19 peptides. Score 0.624 Round 4: 251 peptides, 26 chains. Longest chain 20 peptides. Score 0.655 Round 5: 251 peptides, 27 chains. Longest chain 28 peptides. Score 0.644 Taking the results from Round 4 Chains 27, Residues 225, Estimated correctness of the model 22.9 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5539 restraints for refining 2648 atoms. 4573 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2972 (Rfree = 0.000) for 2648 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 2: After refmac, R = 0.2339 (Rfree = 0.000) for 2627 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2180 (Rfree = 0.000) for 2622 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2612 (Rfree = 0.000) for 2606 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2420 (Rfree = 0.000) for 2606 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.13 Search for helices and strands: 0 residues in 0 chains, 2719 seeds are put forward Round 1: 228 peptides, 31 chains. Longest chain 18 peptides. Score 0.537 Round 2: 244 peptides, 27 chains. Longest chain 23 peptides. Score 0.627 Round 3: 231 peptides, 28 chains. Longest chain 18 peptides. Score 0.583 Round 4: 232 peptides, 26 chains. Longest chain 31 peptides. Score 0.609 Round 5: 225 peptides, 25 chains. Longest chain 21 peptides. Score 0.603 Taking the results from Round 2 Chains 29, Residues 217, Estimated correctness of the model 11.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5702 restraints for refining 2648 atoms. 4807 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2831 (Rfree = 0.000) for 2648 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 7: After refmac, R = 0.2705 (Rfree = 0.000) for 2645 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 8: After refmac, R = 0.2547 (Rfree = 0.000) for 2637 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.2221 (Rfree = 0.000) for 2630 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2394 (Rfree = 0.000) for 2619 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.12 Search for helices and strands: 0 residues in 0 chains, 2737 seeds are put forward Round 1: 220 peptides, 36 chains. Longest chain 13 peptides. Score 0.447 Round 2: 230 peptides, 27 chains. Longest chain 19 peptides. Score 0.592 Round 3: 231 peptides, 25 chains. Longest chain 29 peptides. Score 0.618 Round 4: 246 peptides, 28 chains. Longest chain 20 peptides. Score 0.621 Round 5: 242 peptides, 25 chains. Longest chain 24 peptides. Score 0.645 Taking the results from Round 5 Chains 27, Residues 217, Estimated correctness of the model 18.7 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5310 restraints for refining 2646 atoms. 4280 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2370 (Rfree = 0.000) for 2646 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 12: After refmac, R = 0.2102 (Rfree = 0.000) for 2625 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2064 (Rfree = 0.000) for 2612 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.2041 (Rfree = 0.000) for 2599 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.1971 (Rfree = 0.000) for 2596 atoms. Found 4 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.11 Search for helices and strands: 0 residues in 0 chains, 2715 seeds are put forward Round 1: 203 peptides, 34 chains. Longest chain 14 peptides. Score 0.419 Round 2: 227 peptides, 29 chains. Longest chain 19 peptides. Score 0.560 Round 3: 237 peptides, 31 chains. Longest chain 18 peptides. Score 0.563 Round 4: 235 peptides, 30 chains. Longest chain 21 peptides. Score 0.569 Round 5: 238 peptides, 30 chains. Longest chain 20 peptides. Score 0.577 Taking the results from Round 5 Chains 31, Residues 208, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5582 restraints for refining 2648 atoms. 4684 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2561 (Rfree = 0.000) for 2648 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 17: After refmac, R = 0.2445 (Rfree = 0.000) for 2634 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 18: After refmac, R = 0.2488 (Rfree = 0.000) for 2624 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2042 (Rfree = 0.000) for 2616 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.2069 (Rfree = 0.000) for 2609 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.17 Search for helices and strands: 0 residues in 0 chains, 2723 seeds are put forward Round 1: 198 peptides, 29 chains. Longest chain 13 peptides. Score 0.474 Round 2: 209 peptides, 27 chains. Longest chain 22 peptides. Score 0.535 Round 3: 213 peptides, 25 chains. Longest chain 25 peptides. Score 0.572 Round 4: 205 peptides, 25 chains. Longest chain 18 peptides. Score 0.549 Round 5: 218 peptides, 22 chains. Longest chain 22 peptides. Score 0.621 Taking the results from Round 5 Chains 22, Residues 196, Estimated correctness of the model 8.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5959 restraints for refining 2648 atoms. 5197 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2596 (Rfree = 0.000) for 2648 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.2600 (Rfree = 0.000) for 2632 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.1999 (Rfree = 0.000) for 2624 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.2037 (Rfree = 0.000) for 2611 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.1840 (Rfree = 0.000) for 2605 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.11 Search for helices and strands: 0 residues in 0 chains, 2695 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 13 peptides. Score 0.375 Round 2: 207 peptides, 29 chains. Longest chain 18 peptides. Score 0.502 Round 3: 209 peptides, 29 chains. Longest chain 17 peptides. Score 0.508 Round 4: 218 peptides, 29 chains. Longest chain 19 peptides. Score 0.534 Round 5: 218 peptides, 24 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 5 Chains 26, Residues 194, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5734 restraints for refining 2648 atoms. 4912 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2488 (Rfree = 0.000) for 2648 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2197 (Rfree = 0.000) for 2636 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.2072 (Rfree = 0.000) for 2625 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1962 (Rfree = 0.000) for 2615 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1868 (Rfree = 0.000) for 2609 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.13 Search for helices and strands: 0 residues in 0 chains, 2709 seeds are put forward Round 1: 161 peptides, 28 chains. Longest chain 13 peptides. Score 0.364 Round 2: 176 peptides, 27 chains. Longest chain 14 peptides. Score 0.432 Round 3: 202 peptides, 27 chains. Longest chain 15 peptides. Score 0.514 Round 4: 205 peptides, 27 chains. Longest chain 21 peptides. Score 0.523 Round 5: 203 peptides, 30 chains. Longest chain 19 peptides. Score 0.476 Taking the results from Round 4 Chains 29, Residues 178, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5917 restraints for refining 2648 atoms. 5194 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2134 (Rfree = 0.000) for 2648 atoms. Found 12 (14 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.1883 (Rfree = 0.000) for 2644 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1786 (Rfree = 0.000) for 2639 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.1770 (Rfree = 0.000) for 2631 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1750 (Rfree = 0.000) for 2620 atoms. Found 9 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.11 Search for helices and strands: 0 residues in 0 chains, 2730 seeds are put forward Round 1: 174 peptides, 33 chains. Longest chain 16 peptides. Score 0.333 Round 2: 204 peptides, 32 chains. Longest chain 15 peptides. Score 0.451 Round 3: 198 peptides, 30 chains. Longest chain 20 peptides. Score 0.460 Round 4: 204 peptides, 30 chains. Longest chain 21 peptides. Score 0.479 Round 5: 209 peptides, 30 chains. Longest chain 27 peptides. Score 0.495 Taking the results from Round 5 Chains 30, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 6007 restraints for refining 2648 atoms. 5321 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2292 (Rfree = 0.000) for 2648 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.2011 (Rfree = 0.000) for 2634 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.1965 (Rfree = 0.000) for 2625 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.1878 (Rfree = 0.000) for 2618 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1791 (Rfree = 0.000) for 2614 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.08 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward Round 1: 157 peptides, 29 chains. Longest chain 13 peptides. Score 0.334 Round 2: 189 peptides, 29 chains. Longest chain 18 peptides. Score 0.445 Round 3: 197 peptides, 31 chains. Longest chain 15 peptides. Score 0.443 Round 4: 204 peptides, 30 chains. Longest chain 15 peptides. Score 0.479 Round 5: 213 peptides, 30 chains. Longest chain 23 peptides. Score 0.507 Taking the results from Round 5 Chains 30, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4805 reflections ( 99.67 % complete ) and 5946 restraints for refining 2648 atoms. 5244 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2203 (Rfree = 0.000) for 2648 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.2051 (Rfree = 0.000) for 2636 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.1901 (Rfree = 0.000) for 2628 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1832 (Rfree = 0.000) for 2619 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1786 (Rfree = 0.000) for 2610 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.12 Search for helices and strands: 0 residues in 0 chains, 2684 seeds are put forward Round 1: 169 peptides, 32 chains. Longest chain 10 peptides. Score 0.330 Round 2: 170 peptides, 29 chains. Longest chain 14 peptides. Score 0.381 Round 3: 191 peptides, 30 chains. Longest chain 17 peptides. Score 0.438 Round 4: 181 peptides, 29 chains. Longest chain 13 peptides. Score 0.419 Round 5: 179 peptides, 30 chains. Longest chain 18 peptides. Score 0.397 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 161, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vlc-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (161 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4805 reflections ( 99.67 % complete ) and 6085 restraints for refining 2648 atoms. 5440 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2297 (Rfree = 0.000) for 2648 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2282 (Rfree = 0.000) for 2628 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2199 (Rfree = 0.000) for 2612 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1849 (Rfree = 0.000) for 2603 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:19:56 GMT 2018 Job finished. TimeTaking 56.86 Used memory is bytes: 15818200