Sun 23 Dec 22:23:02 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-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/1vlo-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-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 22:23:12 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/1vlo-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-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 248 and 0 Target number of residues in the AU: 248 Target solvent content: 0.6192 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-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: 19 Cell parameters: 46.529 64.578 117.291 90.000 90.000 90.000 Input sequence file: 1vlo-3.6-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 3.600 Wilson plot Bfac: 60.79 4308 reflections ( 97.51 % complete ) and 0 restraints for refining 3370 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3383 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3179 (Rfree = 0.000) for 3370 atoms. Found 21 (21 requested) and removed 53 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 3408 seeds are put forward Round 1: 130 peptides, 26 chains. Longest chain 9 peptides. Score 0.305 Round 2: 147 peptides, 28 chains. Longest chain 11 peptides. Score 0.346 Round 3: 168 peptides, 30 chains. Longest chain 16 peptides. Score 0.404 Round 4: 162 peptides, 27 chains. Longest chain 11 peptides. Score 0.434 Round 5: 175 peptides, 28 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 5 Chains 28, Residues 147, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6432 restraints for refining 2761 atoms. 5842 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2526 (Rfree = 0.000) for 2761 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 2: After refmac, R = 0.2404 (Rfree = 0.000) for 2723 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 3: After refmac, R = 0.2474 (Rfree = 0.000) for 2697 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.2308 (Rfree = 0.000) for 2683 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.2351 (Rfree = 0.000) for 2676 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 2767 seeds are put forward Round 1: 131 peptides, 29 chains. Longest chain 7 peptides. Score 0.247 Round 2: 157 peptides, 30 chains. Longest chain 9 peptides. Score 0.354 Round 3: 165 peptides, 29 chains. Longest chain 15 peptides. Score 0.410 Round 4: 169 peptides, 28 chains. Longest chain 13 peptides. Score 0.446 Round 5: 166 peptides, 27 chains. Longest chain 11 peptides. Score 0.451 Taking the results from Round 5 Chains 28, Residues 139, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 5893 restraints for refining 2661 atoms. 5270 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2144 (Rfree = 0.000) for 2661 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.2038 (Rfree = 0.000) for 2634 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.1972 (Rfree = 0.000) for 2623 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.1968 (Rfree = 0.000) for 2609 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2012 (Rfree = 0.000) for 2604 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 2706 seeds are put forward Round 1: 132 peptides, 30 chains. Longest chain 9 peptides. Score 0.231 Round 2: 161 peptides, 29 chains. Longest chain 13 peptides. Score 0.392 Round 3: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.368 Round 4: 166 peptides, 29 chains. Longest chain 12 peptides. Score 0.414 Round 5: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 5 Chains 30, Residues 146, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6025 restraints for refining 2668 atoms. 5441 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2105 (Rfree = 0.000) for 2668 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 12: After refmac, R = 0.1990 (Rfree = 0.000) for 2650 atoms. Found 16 (17 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.1902 (Rfree = 0.000) for 2634 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.1907 (Rfree = 0.000) for 2625 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.1477 (Rfree = 0.000) for 2618 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 9 peptides. Score 0.288 Round 2: 172 peptides, 30 chains. Longest chain 13 peptides. Score 0.422 Round 3: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.410 Round 4: 170 peptides, 29 chains. Longest chain 10 peptides. Score 0.432 Round 5: 177 peptides, 30 chains. Longest chain 10 peptides. Score 0.443 Taking the results from Round 5 Chains 30, Residues 147, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6398 restraints for refining 2744 atoms. 5830 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2140 (Rfree = 0.000) for 2744 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 17: After refmac, R = 0.1948 (Rfree = 0.000) for 2727 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 18: After refmac, R = 0.1896 (Rfree = 0.000) for 2718 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.1901 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.1503 (Rfree = 0.000) for 2709 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 2791 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 7 peptides. Score 0.258 Round 2: 156 peptides, 30 chains. Longest chain 12 peptides. Score 0.349 Round 3: 162 peptides, 28 chains. Longest chain 13 peptides. Score 0.415 Round 4: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.400 Round 5: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 3 Chains 28, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6528 restraints for refining 2763 atoms. 6020 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1940 (Rfree = 0.000) for 2763 atoms. Found 7 (17 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.1941 (Rfree = 0.000) for 2738 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.1929 (Rfree = 0.000) for 2737 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.1883 (Rfree = 0.000) for 2737 atoms. Found 16 (17 requested) and removed 15 (8 requested) atoms. Cycle 25: After refmac, R = 0.1513 (Rfree = 0.000) for 2736 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 2824 seeds are put forward Round 1: 130 peptides, 28 chains. Longest chain 8 peptides. Score 0.263 Round 2: 148 peptides, 26 chains. Longest chain 9 peptides. Score 0.391 Round 3: 149 peptides, 25 chains. Longest chain 13 peptides. Score 0.415 Round 4: 148 peptides, 24 chains. Longest chain 17 peptides. Score 0.430 Round 5: 163 peptides, 25 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Chains 25, Residues 138, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6288 restraints for refining 2755 atoms. 5736 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2050 (Rfree = 0.000) for 2755 atoms. Found 15 (17 requested) and removed 24 (8 requested) atoms. Cycle 27: After refmac, R = 0.1834 (Rfree = 0.000) for 2739 atoms. Found 9 (17 requested) and removed 14 (8 requested) atoms. Cycle 28: After refmac, R = 0.1850 (Rfree = 0.000) for 2732 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.1798 (Rfree = 0.000) for 2729 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 30: After refmac, R = 0.1551 (Rfree = 0.000) for 2723 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward Round 1: 125 peptides, 26 chains. Longest chain 12 peptides. Score 0.280 Round 2: 148 peptides, 26 chains. Longest chain 15 peptides. Score 0.391 Round 3: 146 peptides, 24 chains. Longest chain 15 peptides. Score 0.421 Round 4: 136 peptides, 23 chains. Longest chain 14 peptides. Score 0.395 Round 5: 143 peptides, 25 chains. Longest chain 17 peptides. Score 0.388 Taking the results from Round 3 Chains 25, Residues 122, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6269 restraints for refining 2762 atoms. 5753 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1919 (Rfree = 0.000) for 2762 atoms. Found 14 (17 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.1891 (Rfree = 0.000) for 2752 atoms. Found 13 (17 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.1912 (Rfree = 0.000) for 2750 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1665 (Rfree = 0.000) for 2752 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.1668 (Rfree = 0.000) for 2754 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 2842 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 11 peptides. Score 0.291 Round 2: 147 peptides, 29 chains. Longest chain 10 peptides. Score 0.326 Round 3: 149 peptides, 25 chains. Longest chain 13 peptides. Score 0.415 Round 4: 152 peptides, 24 chains. Longest chain 15 peptides. Score 0.447 Round 5: 146 peptides, 24 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 4 Chains 26, Residues 128, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6216 restraints for refining 2762 atoms. 5646 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2055 (Rfree = 0.000) for 2762 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2125 (Rfree = 0.000) for 2757 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 38: After refmac, R = 0.2152 (Rfree = 0.000) for 2753 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 39: After refmac, R = 0.2046 (Rfree = 0.000) for 2743 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.2059 (Rfree = 0.000) for 2745 atoms. Found 15 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 2814 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 10 peptides. Score 0.252 Round 2: 111 peptides, 20 chains. Longest chain 13 peptides. Score 0.338 Round 3: 108 peptides, 18 chains. Longest chain 15 peptides. Score 0.366 Round 4: 119 peptides, 18 chains. Longest chain 11 peptides. Score 0.419 Round 5: 123 peptides, 18 chains. Longest chain 17 peptides. Score 0.437 Taking the results from Round 5 Chains 19, Residues 105, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4308 reflections ( 97.51 % complete ) and 6301 restraints for refining 2763 atoms. 5828 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 2763 atoms. Found 12 (17 requested) and removed 20 (8 requested) atoms. Cycle 42: After refmac, R = 0.1796 (Rfree = 0.000) for 2744 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.1971 (Rfree = 0.000) for 2734 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 44: After refmac, R = 0.1969 (Rfree = 0.000) for 2729 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 45: After refmac, R = 0.1842 (Rfree = 0.000) for 2731 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 2798 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.252 Round 2: 114 peptides, 19 chains. Longest chain 17 peptides. Score 0.374 Round 3: 119 peptides, 21 chains. Longest chain 17 peptides. Score 0.356 Round 4: 125 peptides, 23 chains. Longest chain 14 peptides. Score 0.343 Round 5: 117 peptides, 20 chains. Longest chain 14 peptides. Score 0.367 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 95, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vlo-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (95 residues) following loop building 4 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4308 reflections ( 97.51 % complete ) and 6354 restraints for refining 2763 atoms. 5935 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1871 (Rfree = 0.000) for 2763 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1811 (Rfree = 0.000) for 2742 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1737 (Rfree = 0.000) for 2732 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1642 (Rfree = 0.000) for 2719 atoms. TimeTaking 48.02