null Mon 24 Dec 00:16:47 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlm-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-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 ============================================================ Mon 24 Dec 00:16:52 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlm-4.0-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 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-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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.75 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 3855 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3355 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 3855 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 3924 seeds are put forward NCS extension: 0 residues added, 3924 seeds are put forward Round 1: 133 peptides, 26 chains. Longest chain 9 peptides. Score 0.298 Round 2: 172 peptides, 30 chains. Longest chain 9 peptides. Score 0.384 Round 3: 188 peptides, 31 chains. Longest chain 12 peptides. Score 0.427 Round 4: 203 peptides, 32 chains. Longest chain 10 peptides. Score 0.464 Round 5: 217 peptides, 32 chains. Longest chain 12 peptides. Score 0.510 Taking the results from Round 5 Chains 32, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7497 restraints for refining 3160 atoms. 6789 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2578 (Rfree = 0.000) for 3160 atoms. Found 6 (15 requested) and removed 34 (7 requested) atoms. Cycle 2: After refmac, R = 0.2244 (Rfree = 0.000) for 3084 atoms. Found 5 (14 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2367 (Rfree = 0.000) for 3051 atoms. Found 7 (14 requested) and removed 22 (7 requested) atoms. Cycle 4: After refmac, R = 0.2294 (Rfree = 0.000) for 3016 atoms. Found 7 (14 requested) and removed 19 (7 requested) atoms. Cycle 5: After refmac, R = 0.2301 (Rfree = 0.000) for 2994 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 0 residues added, 3109 seeds are put forward Round 1: 173 peptides, 36 chains. Longest chain 11 peptides. Score 0.289 Round 2: 199 peptides, 32 chains. Longest chain 13 peptides. Score 0.450 Round 3: 199 peptides, 30 chains. Longest chain 12 peptides. Score 0.480 Round 4: 212 peptides, 32 chains. Longest chain 16 peptides. Score 0.494 Round 5: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.467 Taking the results from Round 4 Chains 32, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7175 restraints for refining 3040 atoms. 6487 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2529 (Rfree = 0.000) for 3040 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 7: After refmac, R = 0.2326 (Rfree = 0.000) for 2976 atoms. Found 9 (14 requested) and removed 25 (7 requested) atoms. Cycle 8: After refmac, R = 0.2217 (Rfree = 0.000) for 2930 atoms. Found 8 (14 requested) and removed 39 (7 requested) atoms. Cycle 9: After refmac, R = 0.2194 (Rfree = 0.000) for 2877 atoms. Found 9 (13 requested) and removed 15 (6 requested) atoms. Cycle 10: After refmac, R = 0.2127 (Rfree = 0.000) for 2859 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2971 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2989 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 7 peptides. Score 0.271 Round 2: 185 peptides, 32 chains. Longest chain 14 peptides. Score 0.400 Round 3: 200 peptides, 35 chains. Longest chain 13 peptides. Score 0.408 Round 4: 201 peptides, 33 chains. Longest chain 17 peptides. Score 0.442 Round 5: 198 peptides, 30 chains. Longest chain 17 peptides. Score 0.477 Taking the results from Round 5 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6947 restraints for refining 2939 atoms. 6305 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2468 (Rfree = 0.000) for 2939 atoms. Found 10 (13 requested) and removed 25 (6 requested) atoms. Cycle 12: After refmac, R = 0.2149 (Rfree = 0.000) for 2879 atoms. Found 11 (13 requested) and removed 23 (6 requested) atoms. Cycle 13: After refmac, R = 0.2004 (Rfree = 0.000) for 2849 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2006 (Rfree = 0.000) for 2830 atoms. Found 8 (13 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.1935 (Rfree = 0.000) for 2817 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2904 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2922 seeds are put forward Round 1: 157 peptides, 32 chains. Longest chain 10 peptides. Score 0.292 Round 2: 176 peptides, 32 chains. Longest chain 12 peptides. Score 0.367 Round 3: 186 peptides, 30 chains. Longest chain 15 peptides. Score 0.435 Round 4: 181 peptides, 30 chains. Longest chain 13 peptides. Score 0.417 Round 5: 179 peptides, 27 chains. Longest chain 16 peptides. Score 0.457 Taking the results from Round 5 Chains 27, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6618 restraints for refining 2879 atoms. 6037 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2141 (Rfree = 0.000) for 2879 atoms. Found 5 (13 requested) and removed 19 (6 requested) atoms. Cycle 17: After refmac, R = 0.1830 (Rfree = 0.000) for 2843 atoms. Found 1 (13 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.1797 (Rfree = 0.000) for 2822 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1872 (Rfree = 0.000) for 2814 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.1848 (Rfree = 0.000) for 2806 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2907 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2926 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 7 peptides. Score 0.263 Round 2: 195 peptides, 35 chains. Longest chain 19 peptides. Score 0.390 Round 3: 186 peptides, 31 chains. Longest chain 15 peptides. Score 0.420 Round 4: 189 peptides, 31 chains. Longest chain 16 peptides. Score 0.430 Round 5: 195 peptides, 34 chains. Longest chain 12 peptides. Score 0.406 Taking the results from Round 4 Chains 33, Residues 158, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6690 restraints for refining 2920 atoms. 6055 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2252 (Rfree = 0.000) for 2920 atoms. Found 9 (13 requested) and removed 26 (6 requested) atoms. Cycle 22: After refmac, R = 0.2096 (Rfree = 0.000) for 2894 atoms. Found 4 (13 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.2056 (Rfree = 0.000) for 2877 atoms. Found 1 (13 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.1872 (Rfree = 0.000) for 2855 atoms. Found 3 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1762 (Rfree = 0.000) for 2847 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2945 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2958 seeds are put forward Round 1: 165 peptides, 33 chains. Longest chain 12 peptides. Score 0.307 Round 2: 196 peptides, 34 chains. Longest chain 14 peptides. Score 0.409 Round 3: 198 peptides, 33 chains. Longest chain 15 peptides. Score 0.432 Round 4: 213 peptides, 34 chains. Longest chain 15 peptides. Score 0.468 Round 5: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.441 Taking the results from Round 4 Chains 34, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 6868 restraints for refining 3030 atoms. 6186 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2206 (Rfree = 0.000) for 3030 atoms. Found 8 (14 requested) and removed 19 (7 requested) atoms. Cycle 27: After refmac, R = 0.2614 (Rfree = 0.000) for 3005 atoms. Found 10 (14 requested) and removed 15 (7 requested) atoms. Cycle 28: After refmac, R = 0.2764 (Rfree = 0.000) for 2996 atoms. Found 3 (14 requested) and removed 17 (7 requested) atoms. Cycle 29: After refmac, R = 0.2692 (Rfree = 0.000) for 2982 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2569 (Rfree = 0.000) for 2973 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.92 Search for helices and strands: 0 residues in 0 chains, 3068 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3086 seeds are put forward Round 1: 141 peptides, 28 chains. Longest chain 11 peptides. Score 0.296 Round 2: 162 peptides, 27 chains. Longest chain 11 peptides. Score 0.396 Round 3: 161 peptides, 24 chains. Longest chain 14 peptides. Score 0.440 Round 4: 179 peptides, 24 chains. Longest chain 14 peptides. Score 0.502 Round 5: 167 peptides, 25 chains. Longest chain 13 peptides. Score 0.446 Taking the results from Round 4 Chains 24, Residues 155, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7333 restraints for refining 3096 atoms. 6702 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2145 (Rfree = 0.000) for 3096 atoms. Found 5 (14 requested) and removed 17 (7 requested) atoms. Cycle 32: After refmac, R = 0.1984 (Rfree = 0.000) for 3075 atoms. Found 4 (14 requested) and removed 17 (7 requested) atoms. Cycle 33: After refmac, R = 0.2071 (Rfree = 0.000) for 3058 atoms. Found 10 (14 requested) and removed 20 (7 requested) atoms. Cycle 34: After refmac, R = 0.1879 (Rfree = 0.000) for 3042 atoms. Found 9 (14 requested) and removed 15 (7 requested) atoms. Cycle 35: After refmac, R = 0.1816 (Rfree = 0.000) for 3033 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.88 Search for helices and strands: 0 residues in 0 chains, 3118 seeds are put forward NCS extension: 0 residues added, 3118 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 8 peptides. Score 0.247 Round 2: 162 peptides, 30 chains. Longest chain 10 peptides. Score 0.346 Round 3: 161 peptides, 27 chains. Longest chain 11 peptides. Score 0.392 Round 4: 148 peptides, 25 chains. Longest chain 11 peptides. Score 0.375 Round 5: 147 peptides, 21 chains. Longest chain 17 peptides. Score 0.439 Taking the results from Round 5 Chains 21, Residues 126, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7573 restraints for refining 3163 atoms. 7026 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1991 (Rfree = 0.000) for 3163 atoms. Found 6 (15 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.2023 (Rfree = 0.000) for 3134 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.2016 (Rfree = 0.000) for 3111 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.1995 (Rfree = 0.000) for 3084 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1780 (Rfree = 0.000) for 3073 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 3133 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3149 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 8 peptides. Score 0.236 Round 2: 136 peptides, 28 chains. Longest chain 8 peptides. Score 0.275 Round 3: 132 peptides, 26 chains. Longest chain 9 peptides. Score 0.293 Round 4: 136 peptides, 26 chains. Longest chain 9 peptides. Score 0.310 Round 5: 144 peptides, 27 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 5 Chains 27, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3984 reflections ( 99.60 % complete ) and 7442 restraints for refining 3077 atoms. 7001 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1966 (Rfree = 0.000) for 3077 atoms. Found 8 (14 requested) and removed 21 (7 requested) atoms. Cycle 42: After refmac, R = 0.2025 (Rfree = 0.000) for 3049 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 3031 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1896 (Rfree = 0.000) for 3021 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1457 (Rfree = 0.000) for 3012 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 3098 seeds are put forward NCS extension: 0 residues added, 3098 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 6 peptides. Score 0.210 Round 2: 112 peptides, 22 chains. Longest chain 10 peptides. Score 0.281 Round 3: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.301 Round 4: 120 peptides, 24 chains. Longest chain 8 peptides. Score 0.278 Round 5: 124 peptides, 24 chains. Longest chain 8 peptides. Score 0.296 Taking the results from Round 3 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 7353 restraints for refining 3003 atoms. 7021 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1827 (Rfree = 0.000) for 3003 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1936 (Rfree = 0.000) for 2985 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1876 (Rfree = 0.000) for 2973 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1726 (Rfree = 0.000) for 2960 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:56:26 GMT 2018 Job finished. TimeTaking 39.65 Used memory is bytes: 7876096