null Mon 24 Dec 00:54:44 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 2nlv-1.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-1.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-1.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-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/2nlv-1.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-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 00:54:48 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/2nlv-1.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-1.3-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 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-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: 4 Cell parameters: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-1.3-parrot-mrncs.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 1981 atoms. Observations/parameters ratio is 6.71 ------------------------------------------------------ Starting model: R = 0.3728 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3181 (Rfree = 0.000) for 1981 atoms. Found 173 (231 requested) and removed 107 (115 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.37 1.46 Round 1: 188 peptides, 7 chains. Longest chain 81 peptides. Score 0.919 Round 2: 197 peptides, 5 chains. Longest chain 78 peptides. Score 0.942 Round 3: 201 peptides, 5 chains. Longest chain 80 peptides. Score 0.946 Round 4: 204 peptides, 4 chains. Longest chain 84 peptides. Score 0.954 Round 5: 205 peptides, 4 chains. Longest chain 98 peptides. Score 0.954 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 2081 restraints for refining 2113 atoms. 376 conditional restraints added. Observations/parameters ratio is 6.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3026 (Rfree = 0.000) for 2113 atoms. Found 135 (247 requested) and removed 35 (123 requested) atoms. Cycle 2: After refmac, R = 0.2865 (Rfree = 0.000) for 2213 atoms. Found 80 (258 requested) and removed 16 (129 requested) atoms. Cycle 3: After refmac, R = 0.2566 (Rfree = 0.000) for 2275 atoms. Found 83 (266 requested) and removed 10 (133 requested) atoms. Cycle 4: After refmac, R = 0.2415 (Rfree = 0.000) for 2342 atoms. Found 80 (274 requested) and removed 10 (137 requested) atoms. Cycle 5: After refmac, R = 0.2319 (Rfree = 0.000) for 2405 atoms. Found 70 (282 requested) and removed 12 (141 requested) atoms. ------------------------------------------------------ Building Cycle 2 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 106 peptides. Score 0.959 Round 3: 211 peptides, 5 chains. Longest chain 106 peptides. Score 0.953 Round 4: 212 peptides, 4 chains. Longest chain 106 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 2250 restraints for refining 2335 atoms. 495 conditional restraints added. Observations/parameters ratio is 5.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2389 (Rfree = 0.000) for 2335 atoms. Found 113 (273 requested) and removed 15 (136 requested) atoms. Cycle 7: After refmac, R = 0.2306 (Rfree = 0.000) for 2430 atoms. Found 81 (284 requested) and removed 8 (142 requested) atoms. Cycle 8: After refmac, R = 0.2229 (Rfree = 0.000) for 2497 atoms. Found 60 (292 requested) and removed 11 (146 requested) atoms. Cycle 9: After refmac, R = 0.2172 (Rfree = 0.000) for 2534 atoms. Found 78 (297 requested) and removed 15 (148 requested) atoms. Cycle 10: After refmac, R = 0.2147 (Rfree = 0.000) for 2589 atoms. Found 74 (303 requested) and removed 10 (151 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.27 1.36 Round 1: 210 peptides, 4 chains. Longest chain 101 peptides. Score 0.958 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: 213 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 5: 210 peptides, 4 chains. Longest chain 104 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 2363 restraints for refining 2438 atoms. 567 conditional restraints added. Observations/parameters ratio is 5.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2313 (Rfree = 0.000) for 2438 atoms. Found 116 (285 requested) and removed 27 (142 requested) atoms. Cycle 12: After refmac, R = 0.2246 (Rfree = 0.000) for 2521 atoms. Found 84 (295 requested) and removed 9 (147 requested) atoms. Cycle 13: After refmac, R = 0.2180 (Rfree = 0.000) for 2589 atoms. Found 71 (303 requested) and removed 7 (151 requested) atoms. Cycle 14: After refmac, R = 0.2129 (Rfree = 0.000) for 2644 atoms. Found 78 (310 requested) and removed 11 (155 requested) atoms. Cycle 15: After refmac, R = 0.2118 (Rfree = 0.000) for 2698 atoms. Found 71 (317 requested) and removed 18 (158 requested) atoms. ------------------------------------------------------ Building Cycle 4 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: 213 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 5: 210 peptides, 3 chains. Longest chain 107 peptides. Score 0.963 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 2503 restraints for refining 2519 atoms. 707 conditional restraints added. Observations/parameters ratio is 5.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2272 (Rfree = 0.000) for 2519 atoms. Found 145 (294 requested) and removed 28 (147 requested) atoms. Cycle 17: After refmac, R = 0.2239 (Rfree = 0.000) for 2630 atoms. Found 79 (308 requested) and removed 13 (154 requested) atoms. Cycle 18: After refmac, R = 0.2160 (Rfree = 0.000) for 2687 atoms. Found 60 (315 requested) and removed 17 (157 requested) atoms. Cycle 19: After refmac, R = 0.2108 (Rfree = 0.000) for 2724 atoms. Found 56 (319 requested) and removed 19 (159 requested) atoms. Cycle 20: After refmac, R = 0.2088 (Rfree = 0.000) for 2750 atoms. Found 67 (322 requested) and removed 13 (161 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.27 1.36 Round 1: 212 peptides, 4 chains. Longest chain 81 peptides. Score 0.959 Round 2: 213 peptides, 5 chains. Longest chain 80 peptides. Score 0.954 Round 3: 213 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 4: 214 peptides, 4 chains. Longest chain 83 peptides. Score 0.960 Round 5: 215 peptides, 4 chains. Longest chain 107 peptides. Score 0.961 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 2629 restraints for refining 2550 atoms. 840 conditional restraints added. Observations/parameters ratio is 5.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2299 (Rfree = 0.000) for 2550 atoms. Found 152 (298 requested) and removed 33 (149 requested) atoms. Cycle 22: After refmac, R = 0.2264 (Rfree = 0.000) for 2661 atoms. Found 82 (312 requested) and removed 13 (156 requested) atoms. Cycle 23: After refmac, R = 0.2180 (Rfree = 0.000) for 2720 atoms. Found 71 (319 requested) and removed 10 (159 requested) atoms. Cycle 24: After refmac, R = 0.2134 (Rfree = 0.000) for 2766 atoms. Found 69 (325 requested) and removed 15 (162 requested) atoms. Cycle 25: After refmac, R = 0.2103 (Rfree = 0.000) for 2802 atoms. Found 73 (329 requested) and removed 15 (164 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.27 1.36 Round 1: 216 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 2: 216 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 3: 215 peptides, 4 chains. Longest chain 107 peptides. Score 0.961 Round 4: 215 peptides, 4 chains. Longest chain 107 peptides. Score 0.961 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 2581 restraints for refining 2580 atoms. 771 conditional restraints added. Observations/parameters ratio is 5.15 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2259 (Rfree = 0.000) for 2580 atoms. Found 152 (301 requested) and removed 27 (150 requested) atoms. Cycle 27: After refmac, R = 0.2231 (Rfree = 0.000) for 2697 atoms. Found 73 (316 requested) and removed 11 (158 requested) atoms. Cycle 28: After refmac, R = 0.2148 (Rfree = 0.000) for 2749 atoms. Found 60 (322 requested) and removed 13 (161 requested) atoms. Cycle 29: After refmac, R = 0.2117 (Rfree = 0.000) for 2783 atoms. Found 66 (326 requested) and removed 11 (163 requested) atoms. Cycle 30: After refmac, R = 0.2084 (Rfree = 0.000) for 2823 atoms. Found 68 (331 requested) and removed 21 (165 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.28 1.37 Round 1: 216 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 2: 215 peptides, 4 chains. Longest chain 107 peptides. Score 0.961 Round 3: 216 peptides, 4 chains. Longest chain 107 peptides. Score 0.961 Round 4: 216 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 5: 215 peptides, 4 chains. Longest chain 83 peptides. Score 0.961 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 2665 restraints for refining 2582 atoms. 855 conditional restraints added. Observations/parameters ratio is 5.15 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2267 (Rfree = 0.000) for 2582 atoms. Found 152 (301 requested) and removed 26 (150 requested) atoms. Cycle 32: After refmac, R = 0.2241 (Rfree = 0.000) for 2701 atoms. Found 78 (316 requested) and removed 12 (158 requested) atoms. Cycle 33: After refmac, R = 0.2193 (Rfree = 0.000) for 2756 atoms. Found 59 (323 requested) and removed 8 (161 requested) atoms. Cycle 34: After refmac, R = 0.2122 (Rfree = 0.000) for 2791 atoms. Found 73 (328 requested) and removed 12 (164 requested) atoms. Cycle 35: After refmac, R = 0.2101 (Rfree = 0.000) for 2843 atoms. Found 71 (333 requested) and removed 18 (166 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.27 1.36 Round 1: 213 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Round 2: 214 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 3: 214 peptides, 3 chains. Longest chain 107 peptides. Score 0.965 Round 4: 215 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 5: 215 peptides, 4 chains. Longest chain 108 peptides. Score 0.961 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 2768 restraints for refining 2616 atoms. 966 conditional restraints added. Observations/parameters ratio is 5.08 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2277 (Rfree = 0.000) for 2616 atoms. Found 159 (305 requested) and removed 26 (152 requested) atoms. Cycle 37: After refmac, R = 0.2243 (Rfree = 0.000) for 2744 atoms. Found 77 (321 requested) and removed 15 (160 requested) atoms. Cycle 38: After refmac, R = 0.2167 (Rfree = 0.000) for 2790 atoms. Found 73 (328 requested) and removed 14 (164 requested) atoms. Cycle 39: After refmac, R = 0.2156 (Rfree = 0.000) for 2832 atoms. Found 73 (333 requested) and removed 17 (166 requested) atoms. Cycle 40: After refmac, R = 0.2113 (Rfree = 0.000) for 2880 atoms. Found 65 (337 requested) and removed 11 (168 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.27 1.36 Round 1: 215 peptides, 3 chains. Longest chain 107 peptides. Score 0.966 Round 2: 214 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 3: 214 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 Round 4: 214 peptides, 4 chains. Longest chain 84 peptides. Score 0.960 Round 5: 212 peptides, 5 chains. Longest chain 79 peptides. Score 0.954 Taking the results from Round 1 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 2670 atoms. 1073 conditional restraints added. Observations/parameters ratio is 4.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2255 (Rfree = 0.000) for 2670 atoms. Found 156 (312 requested) and removed 20 (156 requested) atoms. Cycle 42: After refmac, R = 0.2230 (Rfree = 0.000) for 2797 atoms. Found 82 (328 requested) and removed 22 (164 requested) atoms. Cycle 43: After refmac, R = 0.2189 (Rfree = 0.000) for 2848 atoms. Found 79 (334 requested) and removed 11 (167 requested) atoms. Cycle 44: After refmac, R = 0.2145 (Rfree = 0.000) for 2903 atoms. Found 71 (340 requested) and removed 12 (170 requested) atoms. Cycle 45: After refmac, R = 0.2122 (Rfree = 0.000) for 2948 atoms. Found 71 (346 requested) and removed 14 (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: 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: 214 peptides, 4 chains. Longest chain 84 peptides. Score 0.960 Round 5: 213 peptides, 4 chains. Longest chain 107 peptides. Score 0.960 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 2928 restraints for refining 2700 atoms. 1126 conditional restraints added. Observations/parameters ratio is 4.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2279 (Rfree = 0.000) for 2700 atoms. Found 0 (315 requested) and removed 1 (157 requested) atoms. Cycle 47: After refmac, R = 0.2147 (Rfree = 0.000) for 2695 atoms. Found 0 (309 requested) and removed 1 (157 requested) atoms. Cycle 48: After refmac, R = 0.2084 (Rfree = 0.000) for 2689 atoms. Found 0 (302 requested) and removed 1 (157 requested) atoms. Cycle 49: After refmac, R = 0.2047 (Rfree = 0.000) for 2682 atoms. Found 0 (295 requested) and removed 2 (157 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:27:13 GMT 2018 Job finished. TimeTaking 32.48 Used memory is bytes: 2561944