Mon 24 Dec 07:31:26 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vlm-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:31:31 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/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-parrot-noncs/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 274 and 0 Target number of residues in the AU: 274 Target solvent content: 0.6600 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-4.0-parrot-noncs.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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.70 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 93.922 4.000 Wilson plot Bfac: 84.48 3984 reflections ( 99.60 % complete ) and 0 restraints for refining 3871 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3410 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3196 (Rfree = 0.000) for 3871 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 4.00 Search for helices and strands: 0 residues in 0 chains, 3927 seeds are put forward NCS extension: 0 residues added, 3927 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.260 Round 2: 149 peptides, 23 chains. Longest chain 12 peptides. Score 0.413 Round 3: 186 peptides, 28 chains. Longest chain 13 peptides. Score 0.466 Round 4: 178 peptides, 26 chains. Longest chain 15 peptides. Score 0.469 Round 5: 200 peptides, 27 chains. Longest chain 19 peptides. Score 0.526 Taking the results from Round 5 Chains 27, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7354 restraints for refining 3083 atoms. 6689 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2690 (Rfree = 0.000) for 3083 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 2: After refmac, R = 0.2449 (Rfree = 0.000) for 3029 atoms. Found 5 (14 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2141 (Rfree = 0.000) for 2994 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2053 (Rfree = 0.000) for 2977 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.1999 (Rfree = 0.000) for 2960 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 3069 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3082 seeds are put forward Round 1: 167 peptides, 33 chains. Longest chain 12 peptides. Score 0.315 Round 2: 199 peptides, 33 chains. Longest chain 14 peptides. Score 0.435 Round 3: 186 peptides, 31 chains. Longest chain 11 peptides. Score 0.420 Round 4: 209 peptides, 32 chains. Longest chain 22 peptides. Score 0.484 Round 5: 205 peptides, 32 chains. Longest chain 13 peptides. Score 0.471 Taking the results from Round 4 Chains 32, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7095 restraints for refining 3018 atoms. 6419 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2648 (Rfree = 0.000) for 3018 atoms. Found 12 (14 requested) and removed 26 (7 requested) atoms. Cycle 7: After refmac, R = 0.2473 (Rfree = 0.000) for 2970 atoms. Found 10 (14 requested) and removed 29 (7 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 2921 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2109 (Rfree = 0.000) for 2896 atoms. Found 5 (13 requested) and removed 16 (6 requested) atoms. Cycle 10: After refmac, R = 0.2301 (Rfree = 0.000) for 2871 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 3003 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3032 seeds are put forward Round 1: 162 peptides, 30 chains. Longest chain 9 peptides. Score 0.346 Round 2: 190 peptides, 31 chains. Longest chain 10 peptides. Score 0.434 Round 3: 207 peptides, 31 chains. Longest chain 13 peptides. Score 0.492 Round 4: 205 peptides, 27 chains. Longest chain 12 peptides. Score 0.542 Round 5: 216 peptides, 28 chains. Longest chain 12 peptides. Score 0.561 Taking the results from Round 5 Chains 28, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6782 restraints for refining 2976 atoms. 6058 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2485 (Rfree = 0.000) for 2976 atoms. Found 8 (14 requested) and removed 24 (7 requested) atoms. Cycle 12: After refmac, R = 0.2510 (Rfree = 0.000) for 2921 atoms. Found 10 (14 requested) and removed 27 (7 requested) atoms. Cycle 13: After refmac, R = 0.2262 (Rfree = 0.000) for 2877 atoms. Found 10 (13 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.2258 (Rfree = 0.000) for 2848 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 15: After refmac, R = 0.2369 (Rfree = 0.000) for 2829 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 2925 seeds are put forward NCS extension: 0 residues added, 2925 seeds are put forward Round 1: 175 peptides, 35 chains. Longest chain 11 peptides. Score 0.314 Round 2: 185 peptides, 31 chains. Longest chain 12 peptides. Score 0.416 Round 3: 200 peptides, 32 chains. Longest chain 12 peptides. Score 0.454 Round 4: 204 peptides, 30 chains. Longest chain 14 peptides. Score 0.496 Round 5: 201 peptides, 28 chains. Longest chain 16 peptides. Score 0.515 Taking the results from Round 5 Chains 28, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6864 restraints for refining 2974 atoms. 6200 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2648 (Rfree = 0.000) for 2974 atoms. Found 14 (14 requested) and removed 70 (7 requested) atoms. Cycle 17: After refmac, R = 0.2382 (Rfree = 0.000) for 2863 atoms. Found 12 (13 requested) and removed 31 (6 requested) atoms. Cycle 18: After refmac, R = 0.2290 (Rfree = 0.000) for 2813 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1928 (Rfree = 0.000) for 2783 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1825 (Rfree = 0.000) for 2772 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2855 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2867 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 9 peptides. Score 0.253 Round 2: 164 peptides, 30 chains. Longest chain 10 peptides. Score 0.354 Round 3: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.374 Round 4: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.399 Round 5: 193 peptides, 31 chains. Longest chain 12 peptides. Score 0.445 Taking the results from Round 5 Chains 31, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6279 restraints for refining 2762 atoms. 5662 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2475 (Rfree = 0.000) for 2762 atoms. Found 13 (13 requested) and removed 51 (6 requested) atoms. Cycle 22: After refmac, R = 0.2173 (Rfree = 0.000) for 2713 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 23: After refmac, R = 0.1806 (Rfree = 0.000) for 2685 atoms. Found 6 (12 requested) and removed 15 (6 requested) atoms. Cycle 24: After refmac, R = 0.1907 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 25: After refmac, R = 0.1995 (Rfree = 0.000) for 2667 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2763 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2775 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 7 peptides. Score 0.253 Round 2: 166 peptides, 31 chains. Longest chain 11 peptides. Score 0.345 Round 3: 176 peptides, 29 chains. Longest chain 12 peptides. Score 0.415 Round 4: 160 peptides, 28 chains. Longest chain 11 peptides. Score 0.371 Round 5: 174 peptides, 30 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 3 Chains 29, Residues 147, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6276 restraints for refining 2790 atoms. 5702 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2036 (Rfree = 0.000) for 2790 atoms. Found 8 (13 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.1913 (Rfree = 0.000) for 2770 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 2759 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.1771 (Rfree = 0.000) for 2748 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1401 (Rfree = 0.000) for 2741 atoms. Found 2 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 2848 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2863 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 6 peptides. Score 0.228 Round 2: 154 peptides, 29 chains. Longest chain 9 peptides. Score 0.331 Round 3: 158 peptides, 27 chains. Longest chain 13 peptides. Score 0.380 Round 4: 162 peptides, 26 chains. Longest chain 13 peptides. Score 0.412 Round 5: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 5 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3984 reflections ( 99.60 % complete ) and 6879 restraints for refining 2939 atoms. 6342 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1958 (Rfree = 0.000) for 2939 atoms. Found 11 (13 requested) and removed 18 (6 requested) atoms. Cycle 32: After refmac, R = 0.2141 (Rfree = 0.000) for 2918 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 33: After refmac, R = 0.2117 (Rfree = 0.000) for 2899 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 34: After refmac, R = 0.2215 (Rfree = 0.000) for 2868 atoms. Found 13 (13 requested) and removed 36 (6 requested) atoms. Cycle 35: After refmac, R = 0.2167 (Rfree = 0.000) for 2835 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2921 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2941 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 7 peptides. Score 0.234 Round 2: 143 peptides, 29 chains. Longest chain 10 peptides. Score 0.286 Round 3: 153 peptides, 29 chains. Longest chain 10 peptides. Score 0.327 Round 4: 140 peptides, 27 chains. Longest chain 11 peptides. Score 0.309 Round 5: 151 peptides, 29 chains. Longest chain 10 peptides. Score 0.319 Taking the results from Round 3 Chains 29, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6537 restraints for refining 2824 atoms. 6070 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2202 (Rfree = 0.000) for 2824 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 37: After refmac, R = 0.2156 (Rfree = 0.000) for 2806 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.1554 (Rfree = 0.000) for 2790 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1444 (Rfree = 0.000) for 2773 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1367 (Rfree = 0.000) for 2765 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2861 seeds are put forward Round 1: 137 peptides, 31 chains. Longest chain 8 peptides. Score 0.225 Round 2: 165 peptides, 33 chains. Longest chain 9 peptides. Score 0.307 Round 3: 167 peptides, 32 chains. Longest chain 16 peptides. Score 0.332 Round 4: 156 peptides, 31 chains. Longest chain 9 peptides. Score 0.305 Round 5: 162 peptides, 30 chains. Longest chain 8 peptides. Score 0.346 Taking the results from Round 5 Chains 30, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3984 reflections ( 99.60 % complete ) and 6723 restraints for refining 2862 atoms. 6225 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1902 (Rfree = 0.000) for 2862 atoms. Found 8 (13 requested) and removed 76 (6 requested) atoms. Cycle 42: After refmac, R = 0.1997 (Rfree = 0.000) for 2783 atoms. Found 13 (13 requested) and removed 44 (6 requested) atoms. Cycle 43: After refmac, R = 0.2115 (Rfree = 0.000) for 2746 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 44: After refmac, R = 0.1585 (Rfree = 0.000) for 2720 atoms. Found 2 (12 requested) and removed 15 (6 requested) atoms. Cycle 45: After refmac, R = 0.1811 (Rfree = 0.000) for 2701 atoms. Found 6 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 2762 seeds are put forward NCS extension: 0 residues added, 2762 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 8 peptides. Score 0.218 Round 2: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.248 Round 3: 96 peptides, 19 chains. Longest chain 12 peptides. Score 0.267 Round 4: 108 peptides, 20 chains. Longest chain 9 peptides. Score 0.301 Round 5: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.290 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vlm-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3984 reflections ( 99.60 % complete ) and 6524 restraints for refining 2759 atoms. 6192 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2279 (Rfree = 0.000) for 2759 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2034 (Rfree = 0.000) for 2747 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1857 (Rfree = 0.000) for 2734 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2066 (Rfree = 0.000) for 2728 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 34.28