Sun 23 Dec 23:59:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vlm-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-parrot-mrncs ############### 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 23:59:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-parrot-mrncs/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 287 and 0 Target number of residues in the AU: 287 Target solvent content: 0.6439 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-3.8-parrot-mrncs.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-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 74.33 4626 reflections ( 99.66 % complete ) and 0 restraints for refining 3909 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3152 (Rfree = 0.000) for 3909 atoms. Found 21 (21 requested) and removed 56 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 3928 seeds are put forward NCS extension: 0 residues added, 3928 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 7 peptides. Score 0.244 Round 2: 176 peptides, 32 chains. Longest chain 12 peptides. Score 0.367 Round 3: 203 peptides, 35 chains. Longest chain 12 peptides. Score 0.419 Round 4: 199 peptides, 33 chains. Longest chain 12 peptides. Score 0.435 Round 5: 223 peptides, 34 chains. Longest chain 16 peptides. Score 0.501 Taking the results from Round 5 Chains 34, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7413 restraints for refining 3112 atoms. 6691 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2839 (Rfree = 0.000) for 3112 atoms. Found 16 (17 requested) and removed 27 (8 requested) atoms. Cycle 2: After refmac, R = 0.2350 (Rfree = 0.000) for 3036 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 3: After refmac, R = 0.2419 (Rfree = 0.000) for 2994 atoms. Found 5 (16 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.2440 (Rfree = 0.000) for 2966 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2267 (Rfree = 0.000) for 2948 atoms. Found 4 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.80 Search for helices and strands: 0 residues in 0 chains, 3042 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3062 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 10 peptides. Score 0.293 Round 2: 200 peptides, 30 chains. Longest chain 14 peptides. Score 0.483 Round 3: 210 peptides, 33 chains. Longest chain 14 peptides. Score 0.473 Round 4: 234 peptides, 35 chains. Longest chain 17 peptides. Score 0.522 Round 5: 228 peptides, 34 chains. Longest chain 17 peptides. Score 0.517 Taking the results from Round 4 Chains 35, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6698 restraints for refining 2913 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2477 (Rfree = 0.000) for 2913 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 7: After refmac, R = 0.2239 (Rfree = 0.000) for 2889 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 8: After refmac, R = 0.2392 (Rfree = 0.000) for 2868 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.2256 (Rfree = 0.000) for 2863 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2109 (Rfree = 0.000) for 2855 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2998 seeds are put forward Round 1: 183 peptides, 33 chains. Longest chain 15 peptides. Score 0.377 Round 2: 202 peptides, 29 chains. Longest chain 18 peptides. Score 0.504 Round 3: 219 peptides, 33 chains. Longest chain 18 peptides. Score 0.502 Round 4: 217 peptides, 32 chains. Longest chain 19 peptides. Score 0.510 Round 5: 219 peptides, 32 chains. Longest chain 20 peptides. Score 0.516 Taking the results from Round 5 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6826 restraints for refining 2968 atoms. 6110 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2234 (Rfree = 0.000) for 2968 atoms. Found 16 (16 requested) and removed 64 (8 requested) atoms. Cycle 12: After refmac, R = 0.2061 (Rfree = 0.000) for 2901 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 13: After refmac, R = 0.1682 (Rfree = 0.000) for 2870 atoms. Found 3 (15 requested) and removed 17 (7 requested) atoms. Cycle 14: After refmac, R = 0.1752 (Rfree = 0.000) for 2848 atoms. Found 11 (15 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.2019 (Rfree = 0.000) for 2837 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.76 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2944 seeds are put forward Round 1: 192 peptides, 34 chains. Longest chain 18 peptides. Score 0.395 Round 2: 218 peptides, 31 chains. Longest chain 20 peptides. Score 0.527 Round 3: 214 peptides, 32 chains. Longest chain 27 peptides. Score 0.500 Round 4: 215 peptides, 32 chains. Longest chain 18 peptides. Score 0.503 Round 5: 216 peptides, 33 chains. Longest chain 19 peptides. Score 0.493 Taking the results from Round 2 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6211 restraints for refining 2865 atoms. 5447 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2123 (Rfree = 0.000) for 2865 atoms. Found 13 (15 requested) and removed 13 (7 requested) atoms. Cycle 17: After refmac, R = 0.2074 (Rfree = 0.000) for 2858 atoms. Found 14 (15 requested) and removed 10 (7 requested) atoms. Cycle 18: After refmac, R = 0.1970 (Rfree = 0.000) for 2856 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.1652 (Rfree = 0.000) for 2849 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1582 (Rfree = 0.000) for 2841 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.79 Search for helices and strands: 0 residues in 0 chains, 2953 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2972 seeds are put forward Round 1: 174 peptides, 35 chains. Longest chain 14 peptides. Score 0.310 Round 2: 202 peptides, 33 chains. Longest chain 18 peptides. Score 0.446 Round 3: 208 peptides, 30 chains. Longest chain 19 peptides. Score 0.509 Round 4: 203 peptides, 30 chains. Longest chain 20 peptides. Score 0.493 Round 5: 205 peptides, 32 chains. Longest chain 23 peptides. Score 0.471 Taking the results from Round 3 Chains 31, Residues 178, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6648 restraints for refining 2971 atoms. 5925 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2145 (Rfree = 0.000) for 2971 atoms. Found 12 (16 requested) and removed 17 (8 requested) atoms. Cycle 22: After refmac, R = 0.2191 (Rfree = 0.000) for 2955 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 23: After refmac, R = 0.1764 (Rfree = 0.000) for 2938 atoms. Found 3 (16 requested) and removed 21 (8 requested) atoms. Cycle 24: After refmac, R = 0.1682 (Rfree = 0.000) for 2918 atoms. Found 1 (16 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1699 (Rfree = 0.000) for 2908 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2995 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3006 seeds are put forward Round 1: 174 peptides, 34 chains. Longest chain 13 peptides. Score 0.326 Round 2: 183 peptides, 32 chains. Longest chain 14 peptides. Score 0.393 Round 3: 188 peptides, 32 chains. Longest chain 15 peptides. Score 0.411 Round 4: 192 peptides, 32 chains. Longest chain 16 peptides. Score 0.426 Round 5: 192 peptides, 29 chains. Longest chain 17 peptides. Score 0.471 Taking the results from Round 5 Chains 29, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7237 restraints for refining 3120 atoms. 6614 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2216 (Rfree = 0.000) for 3120 atoms. Found 15 (17 requested) and removed 24 (8 requested) atoms. Cycle 27: After refmac, R = 0.2258 (Rfree = 0.000) for 3088 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 28: After refmac, R = 0.2242 (Rfree = 0.000) for 3061 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 29: After refmac, R = 0.2166 (Rfree = 0.000) for 3045 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 30: After refmac, R = 0.2081 (Rfree = 0.000) for 3027 atoms. Found 12 (16 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 3115 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3140 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 9 peptides. Score 0.235 Round 2: 147 peptides, 29 chains. Longest chain 10 peptides. Score 0.303 Round 3: 158 peptides, 30 chains. Longest chain 10 peptides. Score 0.330 Round 4: 181 peptides, 34 chains. Longest chain 9 peptides. Score 0.353 Round 5: 172 peptides, 31 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 5 Chains 31, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7149 restraints for refining 3006 atoms. 6616 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2267 (Rfree = 0.000) for 3006 atoms. Found 16 (16 requested) and removed 67 (8 requested) atoms. Cycle 32: After refmac, R = 0.1980 (Rfree = 0.000) for 2936 atoms. Found 11 (16 requested) and removed 33 (8 requested) atoms. Cycle 33: After refmac, R = 0.1873 (Rfree = 0.000) for 2905 atoms. Found 4 (16 requested) and removed 18 (8 requested) atoms. Cycle 34: After refmac, R = 0.1831 (Rfree = 0.000) for 2882 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 2870 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 0 residues added, 2959 seeds are put forward Round 1: 132 peptides, 28 chains. Longest chain 8 peptides. Score 0.257 Round 2: 190 peptides, 33 chains. Longest chain 15 peptides. Score 0.403 Round 3: 183 peptides, 32 chains. Longest chain 11 peptides. Score 0.393 Round 4: 182 peptides, 31 chains. Longest chain 13 peptides. Score 0.405 Round 5: 180 peptides, 28 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 5 Chains 28, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6844 restraints for refining 2979 atoms. 6264 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2159 (Rfree = 0.000) for 2979 atoms. Found 14 (16 requested) and removed 15 (8 requested) atoms. Cycle 37: After refmac, R = 0.1821 (Rfree = 0.000) for 2962 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.1761 (Rfree = 0.000) for 2951 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.1768 (Rfree = 0.000) for 2944 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1766 (Rfree = 0.000) for 2935 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 3001 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3020 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 9 peptides. Score 0.289 Round 2: 174 peptides, 30 chains. Longest chain 15 peptides. Score 0.392 Round 3: 176 peptides, 33 chains. Longest chain 10 peptides. Score 0.351 Round 4: 165 peptides, 29 chains. Longest chain 10 peptides. Score 0.374 Round 5: 168 peptides, 31 chains. Longest chain 8 peptides. Score 0.353 Taking the results from Round 2 Chains 30, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6762 restraints for refining 2944 atoms. 6216 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2217 (Rfree = 0.000) for 2944 atoms. Found 16 (16 requested) and removed 56 (8 requested) atoms. Cycle 42: After refmac, R = 0.1983 (Rfree = 0.000) for 2895 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 43: After refmac, R = 0.1900 (Rfree = 0.000) for 2868 atoms. Found 14 (15 requested) and removed 20 (7 requested) atoms. Cycle 44: After refmac, R = 0.1739 (Rfree = 0.000) for 2862 atoms. Found 5 (15 requested) and removed 16 (7 requested) atoms. Cycle 45: After refmac, R = 0.1739 (Rfree = 0.000) for 2847 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2933 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 9 peptides. Score 0.255 Round 2: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.302 Round 3: 134 peptides, 22 chains. Longest chain 12 peptides. Score 0.372 Round 4: 135 peptides, 25 chains. Longest chain 8 peptides. Score 0.324 Round 5: 139 peptides, 26 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 112, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4626 reflections ( 99.66 % complete ) and 6747 restraints for refining 2881 atoms. 6321 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1972 (Rfree = 0.000) for 2881 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1859 (Rfree = 0.000) for 2866 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1883 (Rfree = 0.000) for 2853 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1831 (Rfree = 0.000) for 2843 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 38.97