Sun 23 Dec 23:48:51 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 2o3l-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o3l-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o3l-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-3.8-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/2o3l-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-3.8-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 ============================================================ Sun 23 Dec 23:48:56 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/2o3l-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-3.8-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6572 Checking the provided sequence file Detected sequence length: 85 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 170 Adjusted target solvent content: 0.58 Input MTZ file: 2o3l-3.8-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: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1360 target number of atoms Had to go as low as 0.90 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: 52.947 3.801 Wilson plot Bfac: 82.65 2367 reflections ( 99.71 % complete ) and 0 restraints for refining 1499 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3656 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3435 (Rfree = 0.000) for 1499 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.20 Search for helices and strands: 0 residues in 0 chains, 1541 seeds are put forward NCS extension: 0 residues added, 1541 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.293 Round 2: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.408 Round 3: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.441 Round 4: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.418 Round 5: 83 peptides, 12 chains. Longest chain 12 peptides. Score 0.457 Taking the results from Round 5 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2686 restraints for refining 1177 atoms. 2384 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3156 (Rfree = 0.000) for 1177 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 2: After refmac, R = 0.2726 (Rfree = 0.000) for 1153 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2685 (Rfree = 0.000) for 1140 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2681 (Rfree = 0.000) for 1135 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2633 (Rfree = 0.000) for 1126 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.17 Search for helices and strands: 0 residues in 0 chains, 1194 seeds are put forward NCS extension: 1 residues added (5 deleted due to clashes), 1195 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 11 peptides. Score 0.304 Round 2: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.430 Round 3: 92 peptides, 14 chains. Longest chain 17 peptides. Score 0.458 Round 4: 92 peptides, 12 chains. Longest chain 15 peptides. Score 0.517 Round 5: 85 peptides, 12 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 4 Chains 12, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2330 restraints for refining 1090 atoms. 2022 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2896 (Rfree = 0.000) for 1090 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 7: After refmac, R = 0.2588 (Rfree = 0.000) for 1075 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2635 (Rfree = 0.000) for 1068 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2398 (Rfree = 0.000) for 1059 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2456 (Rfree = 0.000) for 1057 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.22 Search for helices and strands: 0 residues in 0 chains, 1131 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1153 seeds are put forward Round 1: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.420 Round 2: 86 peptides, 12 chains. Longest chain 14 peptides. Score 0.478 Round 3: 89 peptides, 13 chains. Longest chain 15 peptides. Score 0.468 Round 4: 93 peptides, 15 chains. Longest chain 16 peptides. Score 0.434 Round 5: 89 peptides, 13 chains. Longest chain 18 peptides. Score 0.468 Taking the results from Round 2 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2380 restraints for refining 1152 atoms. 2047 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2539 (Rfree = 0.000) for 1152 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.2315 (Rfree = 0.000) for 1140 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2231 (Rfree = 0.000) for 1135 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2205 (Rfree = 0.000) for 1131 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2255 (Rfree = 0.000) for 1126 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 1183 seeds are put forward NCS extension: 0 residues added, 1183 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.291 Round 2: 79 peptides, 11 chains. Longest chain 15 peptides. Score 0.461 Round 3: 88 peptides, 15 chains. Longest chain 15 peptides. Score 0.398 Round 4: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.387 Round 5: 88 peptides, 14 chains. Longest chain 10 peptides. Score 0.430 Taking the results from Round 2 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2599 restraints for refining 1137 atoms. 2338 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 1137 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 17: After refmac, R = 0.2635 (Rfree = 0.000) for 1132 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2673 (Rfree = 0.000) for 1125 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2617 (Rfree = 0.000) for 1116 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2540 (Rfree = 0.000) for 1113 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 1155 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1170 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 12 peptides. Score 0.342 Round 2: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.312 Round 3: 86 peptides, 14 chains. Longest chain 10 peptides. Score 0.415 Round 4: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.361 Round 5: 81 peptides, 13 chains. Longest chain 9 peptides. Score 0.411 Taking the results from Round 3 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2757 restraints for refining 1187 atoms. 2483 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2700 (Rfree = 0.000) for 1187 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2610 (Rfree = 0.000) for 1175 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2582 (Rfree = 0.000) for 1165 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2651 (Rfree = 0.000) for 1162 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2499 (Rfree = 0.000) for 1159 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 1213 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 1218 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.304 Round 2: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.329 Round 3: 82 peptides, 14 chains. Longest chain 12 peptides. Score 0.386 Round 4: 83 peptides, 12 chains. Longest chain 21 peptides. Score 0.457 Round 5: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.358 Taking the results from Round 4 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2696 restraints for refining 1229 atoms. 2387 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2792 (Rfree = 0.000) for 1229 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. Cycle 27: After refmac, R = 0.2683 (Rfree = 0.000) for 1207 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2539 (Rfree = 0.000) for 1202 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2542 (Rfree = 0.000) for 1192 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2505 (Rfree = 0.000) for 1188 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 1242 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 1246 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.306 Round 2: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.396 Round 3: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.429 Round 4: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.404 Round 5: 85 peptides, 12 chains. Longest chain 13 peptides. Score 0.471 Taking the results from Round 5 Chains 12, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2796 restraints for refining 1230 atoms. 2516 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2771 (Rfree = 0.000) for 1230 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2702 (Rfree = 0.000) for 1225 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2617 (Rfree = 0.000) for 1220 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2522 (Rfree = 0.000) for 1216 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2500 (Rfree = 0.000) for 1214 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 1265 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 1269 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.326 Round 2: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.353 Round 3: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.384 Round 4: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.387 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 5 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2828 restraints for refining 1230 atoms. 2573 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2755 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2431 (Rfree = 0.000) for 1224 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2442 (Rfree = 0.000) for 1215 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2362 (Rfree = 0.000) for 1207 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2357 (Rfree = 0.000) for 1206 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.30 Search for helices and strands: 0 residues in 0 chains, 1253 seeds are put forward NCS extension: 0 residues added, 1253 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.214 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.332 Round 4: 57 peptides, 10 chains. Longest chain 12 peptides. Score 0.326 Round 5: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.318 Taking the results from Round 3 Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2896 restraints for refining 1224 atoms. 2703 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2586 (Rfree = 0.000) for 1224 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.2448 (Rfree = 0.000) for 1215 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2363 (Rfree = 0.000) for 1213 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2294 (Rfree = 0.000) for 1212 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2230 (Rfree = 0.000) for 1208 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.32 Search for helices and strands: 0 residues in 0 chains, 1260 seeds are put forward NCS extension: 0 residues added, 1260 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.243 Round 2: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.320 Round 3: 63 peptides, 11 chains. Longest chain 13 peptides. Score 0.340 Round 4: 61 peptides, 10 chains. Longest chain 15 peptides. Score 0.359 Round 5: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 51, 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 2o3l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2367 reflections ( 99.71 % complete ) and 2770 restraints for refining 1201 atoms. 2576 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2781 (Rfree = 0.000) for 1201 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3027 (Rfree = 0.000) for 1189 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3105 (Rfree = 0.000) for 1180 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2916 (Rfree = 0.000) for 1172 atoms. TimeTaking 23.52