Mon 24 Dec 00:51:27 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o3l-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o3l-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-3.4-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 00:51:32 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-3.4-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 147 and 0 Target number of residues in the AU: 147 Target solvent content: 0.6375 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 70.34 3275 reflections ( 99.79 % complete ) and 0 restraints for refining 1508 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3524 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2891 (Rfree = 0.000) for 1508 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 1544 seeds are put forward NCS extension: 0 residues added, 1544 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.355 Round 2: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.459 Round 3: 103 peptides, 15 chains. Longest chain 20 peptides. Score 0.502 Round 4: 98 peptides, 13 chains. Longest chain 24 peptides. Score 0.527 Round 5: 103 peptides, 14 chains. Longest chain 15 peptides. Score 0.530 Taking the results from Round 5 Chains 14, Residues 89, Estimated correctness of the model 4.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2727 restraints for refining 1235 atoms. 2385 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2691 (Rfree = 0.000) for 1235 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.2734 (Rfree = 0.000) for 1203 atoms. Found 7 (9 requested) and removed 13 (4 requested) atoms. Cycle 3: After refmac, R = 0.2544 (Rfree = 0.000) for 1182 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2580 (Rfree = 0.000) for 1169 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2244 (Rfree = 0.000) for 1161 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.95 Search for helices and strands: 0 residues in 0 chains, 1215 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1231 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 14 peptides. Score 0.381 Round 2: 103 peptides, 16 chains. Longest chain 11 peptides. Score 0.473 Round 3: 106 peptides, 15 chains. Longest chain 16 peptides. Score 0.521 Round 4: 112 peptides, 12 chains. Longest chain 27 peptides. Score 0.633 Round 5: 112 peptides, 11 chains. Longest chain 28 peptides. Score 0.656 Taking the results from Round 5 Chains 12, Residues 101, Estimated correctness of the model 45.9 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2325 restraints for refining 1235 atoms. 1811 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2491 (Rfree = 0.000) for 1235 atoms. Found 5 (9 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2466 (Rfree = 0.000) for 1217 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 1202 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2261 (Rfree = 0.000) for 1199 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2768 (Rfree = 0.000) for 1198 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 2.93 Search for helices and strands: 0 residues in 0 chains, 1273 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1290 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 13 peptides. Score 0.381 Round 2: 99 peptides, 15 chains. Longest chain 18 peptides. Score 0.475 Round 3: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.441 Round 4: 98 peptides, 14 chains. Longest chain 14 peptides. Score 0.498 Round 5: 109 peptides, 16 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 5 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2726 restraints for refining 1236 atoms. 2370 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3074 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2501 (Rfree = 0.000) for 1229 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2438 (Rfree = 0.000) for 1226 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2471 (Rfree = 0.000) for 1224 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 15: After refmac, R = 0.2256 (Rfree = 0.000) for 1214 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.00 Search for helices and strands: 0 residues in 0 chains, 1276 seeds are put forward NCS extension: 0 residues added, 1276 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 13 peptides. Score 0.408 Round 2: 109 peptides, 15 chains. Longest chain 16 peptides. Score 0.539 Round 3: 106 peptides, 14 chains. Longest chain 14 peptides. Score 0.548 Round 4: 110 peptides, 11 chains. Longest chain 22 peptides. Score 0.646 Round 5: 102 peptides, 12 chains. Longest chain 15 peptides. Score 0.578 Taking the results from Round 4 Chains 11, Residues 99, Estimated correctness of the model 43.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2636 restraints for refining 1236 atoms. 2251 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2541 (Rfree = 0.000) for 1236 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.2584 (Rfree = 0.000) for 1226 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2441 (Rfree = 0.000) for 1225 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2301 (Rfree = 0.000) for 1217 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2351 (Rfree = 0.000) for 1218 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 1296 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1303 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.314 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.391 Round 3: 90 peptides, 13 chains. Longest chain 11 peptides. Score 0.474 Round 4: 93 peptides, 13 chains. Longest chain 12 peptides. Score 0.495 Round 5: 94 peptides, 13 chains. Longest chain 13 peptides. Score 0.501 Taking the results from Round 5 Chains 13, Residues 81, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2698 restraints for refining 1236 atoms. 2354 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2478 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2354 (Rfree = 0.000) for 1228 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 1221 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2201 (Rfree = 0.000) for 1212 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2115 (Rfree = 0.000) for 1207 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.98 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1283 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.373 Round 2: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.432 Round 3: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.482 Round 4: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.495 Round 5: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 4 Chains 15, Residues 87, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2646 restraints for refining 1236 atoms. 2293 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2439 (Rfree = 0.000) for 1236 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.2053 (Rfree = 0.000) for 1225 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2012 (Rfree = 0.000) for 1217 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2295 (Rfree = 0.000) for 1214 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.1963 (Rfree = 0.000) for 1213 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 1280 seeds are put forward NCS extension: 0 residues added, 1280 seeds are put forward Round 1: 90 peptides, 15 chains. Longest chain 13 peptides. Score 0.413 Round 2: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.448 Round 3: 86 peptides, 12 chains. Longest chain 12 peptides. Score 0.478 Round 4: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.448 Round 5: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 3 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2613 restraints for refining 1236 atoms. 2304 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2818 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 32: After refmac, R = 0.2383 (Rfree = 0.000) for 1229 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.2408 (Rfree = 0.000) for 1215 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.1913 (Rfree = 0.000) for 1212 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2383 (Rfree = 0.000) for 1208 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 2.92 Search for helices and strands: 0 residues in 0 chains, 1265 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1276 seeds are put forward Round 1: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.381 Round 2: 76 peptides, 11 chains. Longest chain 10 peptides. Score 0.439 Round 3: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.418 Round 4: 79 peptides, 11 chains. Longest chain 14 peptides. Score 0.461 Round 5: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 4 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2687 restraints for refining 1236 atoms. 2426 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2619 (Rfree = 0.000) for 1236 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 37: After refmac, R = 0.2183 (Rfree = 0.000) for 1225 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2085 (Rfree = 0.000) for 1216 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1943 (Rfree = 0.000) for 1212 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1831 (Rfree = 0.000) for 1211 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 1273 seeds are put forward NCS extension: 0 residues added, 1273 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.320 Round 2: 85 peptides, 13 chains. Longest chain 15 peptides. Score 0.440 Round 3: 88 peptides, 13 chains. Longest chain 16 peptides. Score 0.461 Round 4: 93 peptides, 14 chains. Longest chain 18 peptides. Score 0.465 Round 5: 89 peptides, 14 chains. Longest chain 12 peptides. Score 0.437 Taking the results from Round 4 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3275 reflections ( 99.79 % complete ) and 2572 restraints for refining 1200 atoms. 2270 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2012 (Rfree = 0.000) for 1200 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.1885 (Rfree = 0.000) for 1197 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 1192 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 1188 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1927 (Rfree = 0.000) for 1185 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 1243 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1262 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.363 Round 2: 89 peptides, 14 chains. Longest chain 11 peptides. Score 0.437 Round 3: 97 peptides, 14 chains. Longest chain 22 peptides. Score 0.491 Round 4: 92 peptides, 14 chains. Longest chain 22 peptides. Score 0.458 Round 5: 91 peptides, 12 chains. Longest chain 22 peptides. Score 0.511 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 79, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2o3l-3_warpNtrace.pdb as input Building loops using Loopy2018 12 chains (79 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3275 reflections ( 99.79 % complete ) and 2536 restraints for refining 1236 atoms. 2215 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2140 (Rfree = 0.000) for 1236 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1934 (Rfree = 0.000) for 1227 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1943 (Rfree = 0.000) for 1220 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1863 (Rfree = 0.000) for 1216 atoms. TimeTaking 24.92