null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nlv-1.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-1.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nlv-1.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-parrot-hancs/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-hancs.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-hancs.fasta_lf Building free atoms model in initial map for 1792 target number of atoms Had to go as low as 0.45 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 1978 atoms. Observations/parameters ratio is 6.72 ------------------------------------------------------ Starting model: R = 0.3715 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3257 (Rfree = 0.000) for 1978 atoms. Found 204 (231 requested) and removed 63 (115 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.39 1.49 Round 1: 190 peptides, 9 chains. Longest chain 51 peptides. Score 0.905 Round 2: 201 peptides, 5 chains. Longest chain 94 peptides. Score 0.946 Round 3: 206 peptides, 5 chains. Longest chain 97 peptides. Score 0.949 Round 4: 209 peptides, 5 chains. Longest chain 100 peptides. Score 0.952 Round 5: 209 peptides, 5 chains. Longest chain 100 peptides. Score 0.952 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 2154 restraints for refining 2131 atoms. 438 conditional restraints added. Observations/parameters ratio is 6.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3062 (Rfree = 0.000) for 2131 atoms. Found 140 (249 requested) and removed 30 (124 requested) atoms. Cycle 2: After refmac, R = 0.2891 (Rfree = 0.000) for 2240 atoms. Found 83 (262 requested) and removed 15 (131 requested) atoms. Cycle 3: After refmac, R = 0.2573 (Rfree = 0.000) for 2304 atoms. Found 78 (269 requested) and removed 16 (134 requested) atoms. Cycle 4: After refmac, R = 0.2424 (Rfree = 0.000) for 2362 atoms. Found 74 (276 requested) and removed 11 (138 requested) atoms. Cycle 5: After refmac, R = 0.2326 (Rfree = 0.000) for 2422 atoms. Found 74 (283 requested) and removed 6 (141 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.27 1.36 Round 1: 211 peptides, 4 chains. Longest chain 100 peptides. Score 0.958 Round 2: 211 peptides, 5 chains. Longest chain 101 peptides. Score 0.953 Round 3: 212 peptides, 4 chains. Longest chain 101 peptides. Score 0.959 Round 4: 212 peptides, 4 chains. Longest chain 101 peptides. Score 0.959 Round 5: 212 peptides, 4 chains. Longest chain 101 peptides. Score 0.959 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 2319 restraints for refining 2359 atoms. 564 conditional restraints added. Observations/parameters ratio is 5.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2405 (Rfree = 0.000) for 2359 atoms. Found 115 (275 requested) and removed 16 (137 requested) atoms. Cycle 7: After refmac, R = 0.2325 (Rfree = 0.000) for 2456 atoms. Found 73 (287 requested) and removed 11 (143 requested) atoms. Cycle 8: After refmac, R = 0.2241 (Rfree = 0.000) for 2512 atoms. Found 49 (294 requested) and removed 10 (147 requested) atoms. Cycle 9: After refmac, R = 0.2199 (Rfree = 0.000) for 2541 atoms. Found 60 (298 requested) and removed 14 (149 requested) atoms. Cycle 10: After refmac, R = 0.2152 (Rfree = 0.000) for 2583 atoms. Found 63 (302 requested) and removed 13 (151 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.27 1.36 Round 1: 212 peptides, 4 chains. Longest chain 101 peptides. Score 0.959 Round 2: 212 peptides, 4 chains. Longest chain 101 peptides. Score 0.959 Round 3: 212 peptides, 5 chains. Longest chain 102 peptides. Score 0.954 Round 4: 212 peptides, 5 chains. Longest chain 102 peptides. Score 0.954 Round 5: 213 peptides, 4 chains. Longest chain 102 peptides. Score 0.960 Taking the results from Round 5 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 2404 restraints for refining 2413 atoms. 641 conditional restraints added. Observations/parameters ratio is 5.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2282 (Rfree = 0.000) for 2413 atoms. Found 141 (282 requested) and removed 14 (141 requested) atoms. Cycle 12: After refmac, R = 0.2272 (Rfree = 0.000) for 2535 atoms. Found 73 (297 requested) and removed 14 (148 requested) atoms. Cycle 13: After refmac, R = 0.2193 (Rfree = 0.000) for 2586 atoms. Found 79 (303 requested) and removed 16 (151 requested) atoms. Cycle 14: After refmac, R = 0.2155 (Rfree = 0.000) for 2640 atoms. Found 64 (309 requested) and removed 14 (154 requested) atoms. Cycle 15: After refmac, R = 0.2123 (Rfree = 0.000) for 2680 atoms. Found 75 (314 requested) and removed 13 (157 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.27 1.36 Round 1: 214 peptides, 4 chains. Longest chain 102 peptides. Score 0.960 Round 2: 214 peptides, 4 chains. Longest chain 102 peptides. Score 0.960 Round 3: 213 peptides, 5 chains. Longest chain 102 peptides. Score 0.954 Round 4: 209 peptides, 6 chains. Longest chain 77 peptides. Score 0.946 Round 5: 214 peptides, 4 chains. Longest chain 102 peptides. Score 0.960 Taking the results from Round 5 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 2463 restraints for refining 2485 atoms. 693 conditional restraints added. Observations/parameters ratio is 5.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2430 (Rfree = 0.000) for 2485 atoms. Found 144 (290 requested) and removed 23 (145 requested) atoms. Cycle 17: After refmac, R = 0.2328 (Rfree = 0.000) for 2601 atoms. Found 95 (304 requested) and removed 8 (152 requested) atoms. Cycle 18: After refmac, R = 0.2250 (Rfree = 0.000) for 2677 atoms. Found 75 (314 requested) and removed 14 (157 requested) atoms. Cycle 19: After refmac, R = 0.2194 (Rfree = 0.000) for 2730 atoms. Found 71 (320 requested) and removed 12 (160 requested) atoms. Cycle 20: After refmac, R = 0.2142 (Rfree = 0.000) for 2776 atoms. Found 68 (326 requested) and removed 18 (163 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.27 1.36 Round 1: 213 peptides, 4 chains. Longest chain 101 peptides. Score 0.960 Round 2: 212 peptides, 5 chains. Longest chain 101 peptides. Score 0.954 Round 3: 213 peptides, 4 chains. Longest chain 101 peptides. Score 0.960 Round 4: 213 peptides, 4 chains. Longest chain 101 peptides. Score 0.960 Round 5: 211 peptides, 6 chains. Longest chain 80 peptides. Score 0.947 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 2658 restraints for refining 2562 atoms. 897 conditional restraints added. Observations/parameters ratio is 5.19 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2285 (Rfree = 0.000) for 2562 atoms. Found 139 (299 requested) and removed 27 (149 requested) atoms. Cycle 22: After refmac, R = 0.2262 (Rfree = 0.000) for 2670 atoms. Found 84 (312 requested) and removed 10 (156 requested) atoms. Cycle 23: After refmac, R = 0.2198 (Rfree = 0.000) for 2734 atoms. Found 61 (320 requested) and removed 11 (160 requested) atoms. Cycle 24: After refmac, R = 0.2129 (Rfree = 0.000) for 2779 atoms. Found 70 (325 requested) and removed 11 (162 requested) atoms. Cycle 25: After refmac, R = 0.2123 (Rfree = 0.000) for 2826 atoms. Found 69 (331 requested) and removed 14 (165 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.28 1.37 Round 1: 213 peptides, 4 chains. Longest chain 101 peptides. Score 0.960 Round 2: 213 peptides, 5 chains. Longest chain 102 peptides. Score 0.954 Round 3: 214 peptides, 4 chains. Longest chain 102 peptides. Score 0.960 Round 4: 214 peptides, 5 chains. Longest chain 84 peptides. Score 0.955 Round 5: 214 peptides, 4 chains. Longest chain 102 peptides. Score 0.960 Taking the results from Round 5 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 2644 restraints for refining 2591 atoms. 862 conditional restraints added. Observations/parameters ratio is 5.13 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2304 (Rfree = 0.000) for 2591 atoms. Found 153 (302 requested) and removed 28 (151 requested) atoms. Cycle 27: After refmac, R = 0.2264 (Rfree = 0.000) for 2710 atoms. Found 91 (317 requested) and removed 10 (158 requested) atoms. Cycle 28: After refmac, R = 0.2217 (Rfree = 0.000) for 2782 atoms. Found 76 (326 requested) and removed 13 (163 requested) atoms. Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 2827 atoms. Found 74 (332 requested) and removed 17 (166 requested) atoms. Cycle 30: After refmac, R = 0.2128 (Rfree = 0.000) for 2868 atoms. Found 78 (337 requested) and removed 20 (168 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.27 1.36 Round 1: 213 peptides, 3 chains. Longest chain 106 peptides. Score 0.965 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, 4 chains. Longest chain 106 peptides. Score 0.959 Round 5: 212 peptides, 5 chains. Longest chain 79 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 2710 restraints for refining 2625 atoms. 914 conditional restraints added. Observations/parameters ratio is 5.06 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2298 (Rfree = 0.000) for 2625 atoms. Found 136 (306 requested) and removed 38 (153 requested) atoms. Cycle 32: After refmac, R = 0.2264 (Rfree = 0.000) for 2715 atoms. Found 95 (318 requested) and removed 18 (159 requested) atoms. Cycle 33: After refmac, R = 0.2208 (Rfree = 0.000) for 2783 atoms. Found 75 (326 requested) and removed 12 (163 requested) atoms. Cycle 34: After refmac, R = 0.2175 (Rfree = 0.000) for 2834 atoms. Found 69 (332 requested) and removed 19 (166 requested) atoms. Cycle 35: After refmac, R = 0.2127 (Rfree = 0.000) for 2873 atoms. Found 79 (337 requested) and removed 11 (168 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.27 1.36 Round 1: 209 peptides, 4 chains. Longest chain 81 peptides. Score 0.957 Round 2: 210 peptides, 5 chains. Longest chain 80 peptides. Score 0.952 Round 3: 211 peptides, 4 chains. Longest chain 83 peptides. Score 0.958 Round 4: 211 peptides, 4 chains. Longest chain 83 peptides. Score 0.958 Round 5: 210 peptides, 5 chains. Longest chain 80 peptides. Score 0.952 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 2900 restraints for refining 2651 atoms. 1132 conditional restraints added. Observations/parameters ratio is 5.01 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2283 (Rfree = 0.000) for 2651 atoms. Found 157 (310 requested) and removed 33 (155 requested) atoms. Cycle 37: After refmac, R = 0.2236 (Rfree = 0.000) for 2769 atoms. Found 87 (324 requested) and removed 14 (162 requested) atoms. Cycle 38: After refmac, R = 0.2180 (Rfree = 0.000) for 2835 atoms. Found 76 (332 requested) and removed 14 (166 requested) atoms. Cycle 39: After refmac, R = 0.2127 (Rfree = 0.000) for 2891 atoms. Found 82 (338 requested) and removed 21 (169 requested) atoms. Cycle 40: After refmac, R = 0.2132 (Rfree = 0.000) for 2928 atoms. Found 70 (345 requested) and removed 14 (172 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.28 1.37 Round 1: 210 peptides, 4 chains. Longest chain 82 peptides. Score 0.958 Round 2: 209 peptides, 5 chains. Longest chain 80 peptides. Score 0.952 Round 3: 210 peptides, 5 chains. Longest chain 80 peptides. Score 0.952 Round 4: 210 peptides, 5 chains. Longest chain 80 peptides. Score 0.952 Round 5: 211 peptides, 4 chains. Longest chain 83 peptides. Score 0.958 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 2977 restraints for refining 2680 atoms. 1209 conditional restraints added. Observations/parameters ratio is 4.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2293 (Rfree = 0.000) for 2680 atoms. Found 149 (313 requested) and removed 28 (156 requested) atoms. Cycle 42: After refmac, R = 0.2255 (Rfree = 0.000) for 2797 atoms. Found 93 (327 requested) and removed 17 (163 requested) atoms. Cycle 43: After refmac, R = 0.2194 (Rfree = 0.000) for 2864 atoms. Found 87 (335 requested) and removed 18 (167 requested) atoms. Cycle 44: After refmac, R = 0.2132 (Rfree = 0.000) for 2926 atoms. Found 68 (342 requested) and removed 22 (171 requested) atoms. Cycle 45: After refmac, R = 0.2095 (Rfree = 0.000) for 2963 atoms. Found 78 (347 requested) and removed 16 (173 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.27 1.36 Round 1: 212 peptides, 3 chains. Longest chain 107 peptides. Score 0.964 Round 2: 212 peptides, 4 chains. Longest chain 83 peptides. Score 0.959 Round 3: 211 peptides, 4 chains. Longest chain 107 peptides. Score 0.958 Round 4: 213 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Round 5: 214 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Taking the results from Round 5 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 2909 restraints for refining 2691 atoms. 1113 conditional restraints added. Observations/parameters ratio is 4.94 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2465 (Rfree = 0.000) for 2691 atoms. Found 0 (314 requested) and removed 2 (157 requested) atoms. Cycle 47: After refmac, R = 0.2243 (Rfree = 0.000) for 2687 atoms. Found 0 (308 requested) and removed 0 (157 requested) atoms. Cycle 48: After refmac, R = 0.2146 (Rfree = 0.000) for 2681 atoms. Found 0 (308 requested) and removed 0 (157 requested) atoms. Cycle 49: After refmac, R = 0.2096 (Rfree = 0.000) for 2675 atoms. Found 0 (307 requested) and removed 1 (156 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:19:37 GMT 2018 Job finished. TimeTaking 51.68 Used memory is bytes: 19826288