null Mon 24 Dec 07:33:55 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-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 07:33:59 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 74.33 4626 reflections ( 99.66 % complete ) and 0 restraints for refining 3867 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3278 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3231 (Rfree = 0.000) for 3867 atoms. Found 20 (21 requested) and removed 28 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 3906 seeds are put forward NCS extension: 0 residues added, 3906 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 12 peptides. Score 0.271 Round 2: 166 peptides, 32 chains. Longest chain 10 peptides. Score 0.328 Round 3: 205 peptides, 37 chains. Longest chain 13 peptides. Score 0.395 Round 4: 234 peptides, 30 chains. Longest chain 20 peptides. Score 0.587 Round 5: 232 peptides, 35 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 4 Chains 34, Residues 204, Estimated correctness of the model 0.0 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6746 restraints for refining 3135 atoms. 5808 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2997 (Rfree = 0.000) for 3135 atoms. Found 16 (17 requested) and removed 33 (8 requested) atoms. Cycle 2: After refmac, R = 0.2795 (Rfree = 0.000) for 3030 atoms. Found 13 (17 requested) and removed 25 (8 requested) atoms. Cycle 3: After refmac, R = 0.2654 (Rfree = 0.000) for 2984 atoms. Found 12 (16 requested) and removed 20 (8 requested) atoms. Cycle 4: After refmac, R = 0.2193 (Rfree = 0.000) for 2948 atoms. Found 9 (16 requested) and removed 26 (8 requested) atoms. Cycle 5: After refmac, R = 0.2494 (Rfree = 0.000) for 2913 atoms. Found 9 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 3017 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3036 seeds are put forward Round 1: 178 peptides, 34 chains. Longest chain 12 peptides. Score 0.342 Round 2: 211 peptides, 34 chains. Longest chain 13 peptides. Score 0.462 Round 3: 209 peptides, 34 chains. Longest chain 12 peptides. Score 0.455 Round 4: 210 peptides, 31 chains. Longest chain 15 peptides. Score 0.502 Round 5: 223 peptides, 34 chains. Longest chain 18 peptides. Score 0.501 Taking the results from Round 4 Chains 31, Residues 179, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6753 restraints for refining 2930 atoms. 6042 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2258 (Rfree = 0.000) for 2930 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 7: After refmac, R = 0.2058 (Rfree = 0.000) for 2900 atoms. Found 10 (16 requested) and removed 29 (8 requested) atoms. Cycle 8: After refmac, R = 0.1840 (Rfree = 0.000) for 2868 atoms. Found 8 (15 requested) and removed 18 (7 requested) atoms. Cycle 9: After refmac, R = 0.1781 (Rfree = 0.000) for 2850 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.1799 (Rfree = 0.000) for 2836 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2953 seeds are put forward Round 1: 192 peptides, 38 chains. Longest chain 11 peptides. Score 0.331 Round 2: 205 peptides, 37 chains. Longest chain 11 peptides. Score 0.395 Round 3: 228 peptides, 38 chains. Longest chain 13 peptides. Score 0.461 Round 4: 232 peptides, 40 chains. Longest chain 10 peptides. Score 0.445 Round 5: 215 peptides, 33 chains. Longest chain 13 peptides. Score 0.489 Taking the results from Round 5 Chains 33, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7119 restraints for refining 3075 atoms. 6424 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2414 (Rfree = 0.000) for 3075 atoms. Found 12 (16 requested) and removed 53 (8 requested) atoms. Cycle 12: After refmac, R = 0.2157 (Rfree = 0.000) for 3012 atoms. Found 16 (16 requested) and removed 42 (8 requested) atoms. Cycle 13: After refmac, R = 0.2114 (Rfree = 0.000) for 2963 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1771 (Rfree = 0.000) for 2956 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1801 (Rfree = 0.000) for 2938 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 3042 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3056 seeds are put forward Round 1: 176 peptides, 37 chains. Longest chain 10 peptides. Score 0.285 Round 2: 212 peptides, 38 chains. Longest chain 13 peptides. Score 0.405 Round 3: 213 peptides, 35 chains. Longest chain 15 peptides. Score 0.454 Round 4: 220 peptides, 36 chains. Longest chain 13 peptides. Score 0.463 Round 5: 198 peptides, 31 chains. Longest chain 14 peptides. Score 0.462 Taking the results from Round 4 Chains 36, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6727 restraints for refining 3005 atoms. 6027 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2339 (Rfree = 0.000) for 3005 atoms. Found 15 (16 requested) and removed 22 (8 requested) atoms. Cycle 17: After refmac, R = 0.2227 (Rfree = 0.000) for 2981 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.2208 (Rfree = 0.000) for 2962 atoms. Found 8 (16 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.2199 (Rfree = 0.000) for 2942 atoms. Found 14 (16 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2247 (Rfree = 0.000) for 2920 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 3026 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3044 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.311 Round 2: 202 peptides, 34 chains. Longest chain 14 peptides. Score 0.431 Round 3: 178 peptides, 29 chains. Longest chain 14 peptides. Score 0.422 Round 4: 200 peptides, 34 chains. Longest chain 14 peptides. Score 0.423 Round 5: 200 peptides, 30 chains. Longest chain 15 peptides. Score 0.483 Taking the results from Round 5 Chains 30, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6774 restraints for refining 3006 atoms. 6124 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2281 (Rfree = 0.000) for 3006 atoms. Found 15 (16 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.2260 (Rfree = 0.000) for 2986 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 23: After refmac, R = 0.2174 (Rfree = 0.000) for 2979 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 2963 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. Cycle 25: After refmac, R = 0.1695 (Rfree = 0.000) for 2951 atoms. Found 0 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 3022 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3049 seeds are put forward Round 1: 156 peptides, 30 chains. Longest chain 13 peptides. Score 0.322 Round 2: 184 peptides, 30 chains. Longest chain 14 peptides. Score 0.428 Round 3: 194 peptides, 30 chains. Longest chain 15 peptides. Score 0.463 Round 4: 183 peptides, 28 chains. Longest chain 11 peptides. Score 0.455 Round 5: 192 peptides, 28 chains. Longest chain 16 peptides. Score 0.486 Taking the results from Round 5 Chains 28, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6768 restraints for refining 3014 atoms. 6140 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2166 (Rfree = 0.000) for 3014 atoms. Found 10 (16 requested) and removed 26 (8 requested) atoms. Cycle 27: After refmac, R = 0.2175 (Rfree = 0.000) for 2980 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 2966 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.1661 (Rfree = 0.000) for 2956 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1534 (Rfree = 0.000) for 2945 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 3030 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3054 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 8 peptides. Score 0.263 Round 2: 176 peptides, 34 chains. Longest chain 8 peptides. Score 0.334 Round 3: 175 peptides, 30 chains. Longest chain 13 peptides. Score 0.395 Round 4: 178 peptides, 29 chains. Longest chain 13 peptides. Score 0.422 Round 5: 179 peptides, 26 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 26, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6809 restraints for refining 2992 atoms. 6223 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2036 (Rfree = 0.000) for 2992 atoms. Found 10 (16 requested) and removed 26 (8 requested) atoms. Cycle 32: After refmac, R = 0.1974 (Rfree = 0.000) for 2968 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 33: After refmac, R = 0.1812 (Rfree = 0.000) for 2958 atoms. Found 7 (16 requested) and removed 17 (8 requested) atoms. Cycle 34: After refmac, R = 0.1715 (Rfree = 0.000) for 2943 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.1612 (Rfree = 0.000) for 2936 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.64 Search for helices and strands: 0 residues in 0 chains, 3017 seeds are put forward NCS extension: 0 residues added, 3017 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 9 peptides. Score 0.249 Round 2: 155 peptides, 30 chains. Longest chain 11 peptides. Score 0.318 Round 3: 162 peptides, 30 chains. Longest chain 11 peptides. Score 0.346 Round 4: 166 peptides, 29 chains. Longest chain 12 peptides. Score 0.378 Round 5: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Chains 27, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7168 restraints for refining 3102 atoms. 6647 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2032 (Rfree = 0.000) for 3102 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 37: After refmac, R = 0.1697 (Rfree = 0.000) for 3076 atoms. Found 7 (17 requested) and removed 17 (8 requested) atoms. Cycle 38: After refmac, R = 0.1395 (Rfree = 0.000) for 3053 atoms. Found 3 (16 requested) and removed 14 (8 requested) atoms. Cycle 39: After refmac, R = 0.1337 (Rfree = 0.000) for 3032 atoms. Found 4 (16 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.1299 (Rfree = 0.000) for 3024 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.68 Search for helices and strands: 0 residues in 0 chains, 3076 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3097 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 10 peptides. Score 0.245 Round 2: 158 peptides, 30 chains. Longest chain 12 peptides. Score 0.330 Round 3: 159 peptides, 26 chains. Longest chain 12 peptides. Score 0.401 Round 4: 154 peptides, 28 chains. Longest chain 12 peptides. Score 0.348 Round 5: 157 peptides, 26 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 3 Chains 26, Residues 133, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6905 restraints for refining 3042 atoms. 6379 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1772 (Rfree = 0.000) for 3042 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.1576 (Rfree = 0.000) for 3025 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.1366 (Rfree = 0.000) for 3023 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.1447 (Rfree = 0.000) for 3012 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.1310 (Rfree = 0.000) for 3003 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.70 Search for helices and strands: 0 residues in 0 chains, 3051 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3063 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 8 peptides. Score 0.236 Round 2: 143 peptides, 28 chains. Longest chain 10 peptides. Score 0.304 Round 3: 147 peptides, 29 chains. Longest chain 9 peptides. Score 0.303 Round 4: 162 peptides, 30 chains. Longest chain 11 peptides. Score 0.346 Round 5: 155 peptides, 27 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 128, 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 7105 restraints for refining 3089 atoms. 6620 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1828 (Rfree = 0.000) for 3089 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1864 (Rfree = 0.000) for 3075 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1702 (Rfree = 0.000) for 3063 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1417 (Rfree = 0.000) for 3052 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:10:07 GMT 2018 Job finished. TimeTaking 36.22 Used memory is bytes: 2746064