null Mon 24 Dec 07:32:49 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 2nlv-1.3-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nlv-1.3-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nlv-1.3-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-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/2nlv-1.3-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-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 07:32:53 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/2nlv-1.3-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-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 238 and 0 Target number of residues in the AU: 238 Target solvent content: 0.4149 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 224 Adjusted target solvent content: 0.45 Input MTZ file: 2nlv-1.3-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: 4 Cell parameters: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-1.3-parrot-noncs.fasta_lf Building free atoms model in initial map for 1792 target number of atoms Had to go as low as 0.35 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 1 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: 29.104 1.300 Wilson plot Bfac: 9.64 53164 reflections ( 98.78 % complete ) and 0 restraints for refining 1975 atoms. Observations/parameters ratio is 6.73 ------------------------------------------------------ Starting model: R = 0.3614 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3115 (Rfree = 0.000) for 1975 atoms. Found 192 (230 requested) and removed 84 (115 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.35 1.44 Round 1: 186 peptides, 7 chains. Longest chain 57 peptides. Score 0.916 Round 2: 195 peptides, 5 chains. Longest chain 76 peptides. Score 0.940 Round 3: 200 peptides, 6 chains. Longest chain 78 peptides. Score 0.938 Round 4: 203 peptides, 3 chains. Longest chain 98 peptides. Score 0.959 Round 5: 201 peptides, 6 chains. Longest chain 98 peptides. Score 0.939 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2088 restraints for refining 2093 atoms. 384 conditional restraints added. Observations/parameters ratio is 6.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2953 (Rfree = 0.000) for 2093 atoms. Found 140 (244 requested) and removed 26 (122 requested) atoms. Cycle 2: After refmac, R = 0.2784 (Rfree = 0.000) for 2206 atoms. Found 84 (258 requested) and removed 12 (129 requested) atoms. Cycle 3: After refmac, R = 0.2494 (Rfree = 0.000) for 2277 atoms. Found 78 (266 requested) and removed 9 (133 requested) atoms. Cycle 4: After refmac, R = 0.2367 (Rfree = 0.000) for 2337 atoms. Found 67 (274 requested) and removed 8 (137 requested) atoms. Cycle 5: After refmac, R = 0.2258 (Rfree = 0.000) for 2393 atoms. Found 79 (280 requested) and removed 13 (140 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.27 1.36 Round 1: 206 peptides, 4 chains. Longest chain 97 peptides. Score 0.955 Round 2: 205 peptides, 5 chains. Longest chain 97 peptides. Score 0.949 Round 3: 206 peptides, 4 chains. Longest chain 97 peptides. Score 0.955 Round 4: 207 peptides, 4 chains. Longest chain 97 peptides. Score 0.956 Round 5: 207 peptides, 4 chains. Longest chain 97 peptides. Score 0.956 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2303 restraints for refining 2318 atoms. 593 conditional restraints added. Observations/parameters ratio is 5.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2370 (Rfree = 0.000) for 2318 atoms. Found 106 (271 requested) and removed 11 (135 requested) atoms. Cycle 7: After refmac, R = 0.2274 (Rfree = 0.000) for 2411 atoms. Found 97 (282 requested) and removed 8 (141 requested) atoms. Cycle 8: After refmac, R = 0.2210 (Rfree = 0.000) for 2495 atoms. Found 90 (292 requested) and removed 9 (146 requested) atoms. Cycle 9: After refmac, R = 0.2180 (Rfree = 0.000) for 2567 atoms. Found 70 (301 requested) and removed 20 (150 requested) atoms. Cycle 10: After refmac, R = 0.2129 (Rfree = 0.000) for 2612 atoms. Found 67 (306 requested) and removed 8 (153 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.27 1.36 Round 1: 212 peptides, 4 chains. Longest chain 100 peptides. Score 0.959 Round 2: 213 peptides, 4 chains. Longest chain 101 peptides. Score 0.960 Round 3: 212 peptides, 5 chains. Longest chain 101 peptides. Score 0.954 Round 4: 213 peptides, 5 chains. Longest chain 101 peptides. Score 0.954 Round 5: 213 peptides, 5 chains. Longest chain 101 peptides. Score 0.954 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2491 restraints for refining 2471 atoms. 718 conditional restraints added. Observations/parameters ratio is 5.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2276 (Rfree = 0.000) for 2471 atoms. Found 118 (288 requested) and removed 24 (144 requested) atoms. Cycle 12: After refmac, R = 0.2229 (Rfree = 0.000) for 2560 atoms. Found 82 (299 requested) and removed 8 (149 requested) atoms. Cycle 13: After refmac, R = 0.2166 (Rfree = 0.000) for 2627 atoms. Found 64 (308 requested) and removed 14 (154 requested) atoms. Cycle 14: After refmac, R = 0.2119 (Rfree = 0.000) for 2669 atoms. Found 70 (313 requested) and removed 10 (156 requested) atoms. Cycle 15: After refmac, R = 0.2087 (Rfree = 0.000) for 2723 atoms. Found 65 (319 requested) and removed 23 (159 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.27 1.36 Round 1: 213 peptides, 4 chains. Longest chain 101 peptides. Score 0.960 Round 2: 214 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 3: 211 peptides, 6 chains. Longest chain 83 peptides. Score 0.947 Round 4: 214 peptides, 4 chains. Longest chain 83 peptides. Score 0.960 Round 5: 210 peptides, 5 chains. Longest chain 79 peptides. Score 0.952 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2507 restraints for refining 2506 atoms. 721 conditional restraints added. Observations/parameters ratio is 5.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2287 (Rfree = 0.000) for 2506 atoms. Found 141 (293 requested) and removed 31 (146 requested) atoms. Cycle 17: After refmac, R = 0.2247 (Rfree = 0.000) for 2612 atoms. Found 85 (305 requested) and removed 11 (152 requested) atoms. Cycle 18: After refmac, R = 0.2172 (Rfree = 0.000) for 2678 atoms. Found 80 (314 requested) and removed 13 (157 requested) atoms. Cycle 19: After refmac, R = 0.2130 (Rfree = 0.000) for 2734 atoms. Found 71 (320 requested) and removed 19 (160 requested) atoms. Cycle 20: After refmac, R = 0.2094 (Rfree = 0.000) for 2775 atoms. Found 67 (325 requested) and removed 17 (162 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.27 1.36 Round 1: 211 peptides, 4 chains. Longest chain 83 peptides. Score 0.958 Round 2: 212 peptides, 3 chains. Longest chain 107 peptides. Score 0.964 Round 3: 209 peptides, 5 chains. Longest chain 101 peptides. Score 0.952 Round 4: 211 peptides, 4 chains. Longest chain 83 peptides. Score 0.958 Round 5: 211 peptides, 4 chains. Longest chain 83 peptides. Score 0.958 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2604 restraints for refining 2553 atoms. 823 conditional restraints added. Observations/parameters ratio is 5.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2270 (Rfree = 0.000) for 2553 atoms. Found 155 (298 requested) and removed 23 (149 requested) atoms. Cycle 22: After refmac, R = 0.2223 (Rfree = 0.000) for 2682 atoms. Found 68 (313 requested) and removed 13 (156 requested) atoms. Cycle 23: After refmac, R = 0.2142 (Rfree = 0.000) for 2726 atoms. Found 76 (320 requested) and removed 7 (160 requested) atoms. Cycle 24: After refmac, R = 0.2116 (Rfree = 0.000) for 2782 atoms. Found 83 (326 requested) and removed 15 (163 requested) atoms. Cycle 25: After refmac, R = 0.2073 (Rfree = 0.000) for 2838 atoms. Found 75 (333 requested) and removed 18 (166 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.27 1.36 Round 1: 215 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 2: 215 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 3: 214 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 4: 213 peptides, 5 chains. Longest chain 79 peptides. Score 0.954 Round 5: 212 peptides, 4 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2685 restraints for refining 2598 atoms. 883 conditional restraints added. Observations/parameters ratio is 5.12 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 2598 atoms. Found 150 (303 requested) and removed 27 (151 requested) atoms. Cycle 27: After refmac, R = 0.2240 (Rfree = 0.000) for 2717 atoms. Found 82 (318 requested) and removed 8 (159 requested) atoms. Cycle 28: After refmac, R = 0.2169 (Rfree = 0.000) for 2778 atoms. Found 72 (326 requested) and removed 15 (163 requested) atoms. Cycle 29: After refmac, R = 0.2117 (Rfree = 0.000) for 2818 atoms. Found 67 (331 requested) and removed 21 (165 requested) atoms. Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 2851 atoms. Found 68 (334 requested) and removed 12 (167 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.27 1.36 Round 1: 213 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Round 2: 213 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Round 3: 208 peptides, 6 chains. Longest chain 79 peptides. Score 0.945 Round 4: 209 peptides, 5 chains. Longest chain 100 peptides. Score 0.952 Round 5: 210 peptides, 4 chains. Longest chain 100 peptides. Score 0.958 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2782 restraints for refining 2611 atoms. 993 conditional restraints added. Observations/parameters ratio is 5.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2263 (Rfree = 0.000) for 2611 atoms. Found 158 (305 requested) and removed 18 (152 requested) atoms. Cycle 32: After refmac, R = 0.2238 (Rfree = 0.000) for 2749 atoms. Found 75 (321 requested) and removed 11 (160 requested) atoms. Cycle 33: After refmac, R = 0.2159 (Rfree = 0.000) for 2803 atoms. Found 70 (328 requested) and removed 6 (164 requested) atoms. Cycle 34: After refmac, R = 0.2136 (Rfree = 0.000) for 2857 atoms. Found 74 (335 requested) and removed 23 (167 requested) atoms. Cycle 35: After refmac, R = 0.2086 (Rfree = 0.000) for 2902 atoms. Found 70 (340 requested) and removed 16 (170 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.27 1.36 Round 1: 212 peptides, 3 chains. Longest chain 107 peptides. Score 0.964 Round 2: 214 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Round 3: 213 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 4: 212 peptides, 5 chains. Longest chain 79 peptides. Score 0.954 Round 5: 211 peptides, 5 chains. Longest chain 83 peptides. Score 0.953 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2875 restraints for refining 2649 atoms. 1079 conditional restraints added. Observations/parameters ratio is 5.02 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2271 (Rfree = 0.000) for 2649 atoms. Found 150 (309 requested) and removed 33 (154 requested) atoms. Cycle 37: After refmac, R = 0.2257 (Rfree = 0.000) for 2762 atoms. Found 88 (323 requested) and removed 10 (161 requested) atoms. Cycle 38: After refmac, R = 0.2186 (Rfree = 0.000) for 2834 atoms. Found 77 (332 requested) and removed 12 (166 requested) atoms. Cycle 39: After refmac, R = 0.2123 (Rfree = 0.000) for 2894 atoms. Found 63 (339 requested) and removed 7 (169 requested) atoms. Cycle 40: After refmac, R = 0.2084 (Rfree = 0.000) for 2939 atoms. Found 59 (344 requested) and removed 13 (172 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.27 1.36 Round 1: 212 peptides, 3 chains. Longest chain 107 peptides. Score 0.964 Round 2: 215 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 3: 212 peptides, 5 chains. Longest chain 101 peptides. Score 0.954 Round 4: 212 peptides, 5 chains. Longest chain 101 peptides. Score 0.954 Round 5: 209 peptides, 6 chains. Longest chain 77 peptides. Score 0.946 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 53164 reflections ( 98.78 % complete ) and 2815 restraints for refining 2658 atoms. 1013 conditional restraints added. Observations/parameters ratio is 5.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2458 (Rfree = 0.000) for 2658 atoms. Found 181 (310 requested) and removed 26 (155 requested) atoms. Cycle 42: After refmac, R = 0.2337 (Rfree = 0.000) for 2809 atoms. Found 102 (328 requested) and removed 10 (164 requested) atoms. Cycle 43: After refmac, R = 0.2241 (Rfree = 0.000) for 2889 atoms. Found 75 (339 requested) and removed 14 (169 requested) atoms. Cycle 44: After refmac, R = 0.2181 (Rfree = 0.000) for 2938 atoms. Found 74 (344 requested) and removed 14 (172 requested) atoms. Cycle 45: After refmac, R = 0.2136 (Rfree = 0.000) for 2989 atoms. Found 82 (350 requested) and removed 17 (175 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.27 1.36 Round 1: 210 peptides, 4 chains. Longest chain 81 peptides. Score 0.958 Round 2: 213 peptides, 4 chains. Longest chain 83 peptides. Score 0.960 Round 3: 212 peptides, 5 chains. Longest chain 75 peptides. Score 0.954 Round 4: 211 peptides, 7 chains. Longest chain 75 peptides. Score 0.941 Round 5: 212 peptides, 5 chains. Longest chain 76 peptides. Score 0.954 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 100.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nlv-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 53164 reflections ( 98.78 % complete ) and 2959 restraints for refining 2744 atoms. 1180 conditional restraints added. Observations/parameters ratio is 4.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2288 (Rfree = 0.000) for 2744 atoms. Found 0 (320 requested) and removed 2 (160 requested) atoms. Cycle 47: After refmac, R = 0.2168 (Rfree = 0.000) for 2737 atoms. Found 0 (314 requested) and removed 4 (160 requested) atoms. Cycle 48: After refmac, R = 0.2107 (Rfree = 0.000) for 2727 atoms. Found 0 (306 requested) and removed 1 (159 requested) atoms. Cycle 49: After refmac, R = 0.2071 (Rfree = 0.000) for 2721 atoms. Found 0 (299 requested) and removed 0 (159 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:06:45 GMT 2018 Job finished. TimeTaking 33.94 Used memory is bytes: 14656064