null Sun 23 Dec 22:22:46 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 2osd-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2osd-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-3.4-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/2osd-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-3.4-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 ============================================================ Sun 23 Dec 22:22:55 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/2osd-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-3.4-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 113 and 0 Target number of residues in the AU: 113 Target solvent content: 0.6697 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 163 Adjusted target solvent content: 0.52 Input MTZ file: 2osd-3.4-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: 96 Cell parameters: 55.786 55.786 118.990 90.000 90.000 90.000 Input sequence file: 2osd-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1304 target number of atoms Had to go as low as 0.65 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.510 3.400 Wilson plot Bfac: 90.84 2883 reflections ( 99.79 % complete ) and 0 restraints for refining 1448 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3595 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3524 (Rfree = 0.000) for 1448 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1467 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 11 peptides. Score 0.359 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.418 Round 3: 78 peptides, 10 chains. Longest chain 14 peptides. Score 0.525 Round 4: 82 peptides, 10 chains. Longest chain 18 peptides. Score 0.554 Round 5: 87 peptides, 10 chains. Longest chain 13 peptides. Score 0.589 Taking the results from Round 5 Chains 10, Residues 77, Estimated correctness of the model 25.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2736 restraints for refining 1186 atoms. 2438 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3164 (Rfree = 0.000) for 1186 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 2: After refmac, R = 0.2971 (Rfree = 0.000) for 1165 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.3117 (Rfree = 0.000) for 1151 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2554 (Rfree = 0.000) for 1143 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2441 (Rfree = 0.000) for 1138 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 1181 seeds are put forward Round 1: 78 peptides, 13 chains. Longest chain 9 peptides. Score 0.418 Round 2: 87 peptides, 10 chains. Longest chain 19 peptides. Score 0.589 Round 3: 98 peptides, 13 chains. Longest chain 20 peptides. Score 0.571 Round 4: 84 peptides, 7 chains. Longest chain 18 peptides. Score 0.659 Round 5: 89 peptides, 7 chains. Longest chain 32 peptides. Score 0.688 Taking the results from Round 5 Chains 9, Residues 82, Estimated correctness of the model 54.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2481 restraints for refining 1141 atoms. 2134 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2782 (Rfree = 0.000) for 1141 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2794 (Rfree = 0.000) for 1127 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2833 (Rfree = 0.000) for 1123 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2546 (Rfree = 0.000) for 1119 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2594 (Rfree = 0.000) for 1111 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1142 seeds are put forward Round 1: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.407 Round 2: 88 peptides, 11 chains. Longest chain 19 peptides. Score 0.564 Round 3: 91 peptides, 9 chains. Longest chain 27 peptides. Score 0.644 Round 4: 86 peptides, 10 chains. Longest chain 16 peptides. Score 0.582 Round 5: 88 peptides, 12 chains. Longest chain 22 peptides. Score 0.532 Taking the results from Round 3 Chains 9, Residues 82, Estimated correctness of the model 42.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2351 restraints for refining 1108 atoms. 2032 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2581 (Rfree = 0.000) for 1108 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2391 (Rfree = 0.000) for 1097 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.2326 (Rfree = 0.000) for 1090 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2201 (Rfree = 0.000) for 1082 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2433 (Rfree = 0.000) for 1079 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 1120 seeds are put forward Round 1: 80 peptides, 11 chains. Longest chain 20 peptides. Score 0.506 Round 2: 84 peptides, 10 chains. Longest chain 17 peptides. Score 0.568 Round 3: 97 peptides, 12 chains. Longest chain 21 peptides. Score 0.594 Round 4: 96 peptides, 10 chains. Longest chain 26 peptides. Score 0.646 Round 5: 93 peptides, 12 chains. Longest chain 23 peptides. Score 0.567 Taking the results from Round 4 Chains 10, Residues 86, Estimated correctness of the model 43.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2528 restraints for refining 1183 atoms. 2194 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2670 (Rfree = 0.000) for 1183 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2778 (Rfree = 0.000) for 1175 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2340 (Rfree = 0.000) for 1165 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2260 (Rfree = 0.000) for 1164 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2075 (Rfree = 0.000) for 1161 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 1194 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.378 Round 2: 89 peptides, 14 chains. Longest chain 19 peptides. Score 0.472 Round 3: 83 peptides, 12 chains. Longest chain 14 peptides. Score 0.494 Round 4: 84 peptides, 11 chains. Longest chain 17 peptides. Score 0.535 Round 5: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.443 Taking the results from Round 4 Chains 11, Residues 73, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2770 restraints for refining 1186 atoms. 2489 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2255 (Rfree = 0.000) for 1186 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2251 (Rfree = 0.000) for 1183 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2295 (Rfree = 0.000) for 1183 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2264 (Rfree = 0.000) for 1182 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.3091 (Rfree = 0.000) for 1178 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 1219 seeds are put forward Round 1: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.416 Round 2: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.458 Round 3: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.416 Round 4: 70 peptides, 10 chains. Longest chain 11 peptides. Score 0.462 Round 5: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.482 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2662 restraints for refining 1186 atoms. 2409 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2589 (Rfree = 0.000) for 1186 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2281 (Rfree = 0.000) for 1177 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2512 (Rfree = 0.000) for 1171 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2151 (Rfree = 0.000) for 1166 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2119 (Rfree = 0.000) for 1160 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 1197 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 10 peptides. Score 0.298 Round 2: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.365 Round 3: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.377 Round 4: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.359 Round 5: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 3 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2780 restraints for refining 1162 atoms. 2564 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2498 (Rfree = 0.000) for 1162 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2428 (Rfree = 0.000) for 1159 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2855 (Rfree = 0.000) for 1157 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2439 (Rfree = 0.000) for 1154 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2952 (Rfree = 0.000) for 1156 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.41 Search for helices and strands: 0 residues in 0 chains, 1202 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.249 Round 2: 79 peptides, 14 chains. Longest chain 11 peptides. Score 0.389 Round 3: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.446 Round 4: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.404 Round 5: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.368 Taking the results from Round 3 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2509 restraints for refining 1142 atoms. 2261 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2944 (Rfree = 0.000) for 1142 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 37: After refmac, R = 0.3118 (Rfree = 0.000) for 1129 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2404 (Rfree = 0.000) for 1117 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2273 (Rfree = 0.000) for 1110 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2622 (Rfree = 0.000) for 1109 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 1157 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.321 Round 2: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.395 Round 3: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.419 Round 4: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.389 Round 5: 67 peptides, 10 chains. Longest chain 9 peptides. Score 0.436 Taking the results from Round 5 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2883 reflections ( 99.79 % complete ) and 2654 restraints for refining 1165 atoms. 2436 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2994 (Rfree = 0.000) for 1165 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.2822 (Rfree = 0.000) for 1153 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2417 (Rfree = 0.000) for 1152 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2914 (Rfree = 0.000) for 1151 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2759 (Rfree = 0.000) for 1145 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 1193 seeds are put forward Round 1: 37 peptides, 7 chains. Longest chain 9 peptides. Score 0.277 Round 2: 51 peptides, 8 chains. Longest chain 15 peptides. Score 0.374 Round 3: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.324 Round 4: 57 peptides, 10 chains. Longest chain 16 peptides. Score 0.346 Round 5: 58 peptides, 9 chains. Longest chain 16 peptides. Score 0.397 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 49, 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 2osd-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2883 reflections ( 99.79 % complete ) and 2506 restraints for refining 1123 atoms. 2319 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2648 (Rfree = 0.000) for 1123 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2342 (Rfree = 0.000) for 1110 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1970 (Rfree = 0.000) for 1102 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1824 (Rfree = 0.000) for 1097 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:18 GMT 2018 Job finished. TimeTaking 26.53 Used memory is bytes: 12366456