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 2o3l-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.8-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/2o3l-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.8-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 19:28:07 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/2o3l-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.8-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 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-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: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-3.8-parrot-hancs.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 1497 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3679 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3171 (Rfree = 0.000) for 1497 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.20 Search for helices and strands: 0 residues in 0 chains, 1538 seeds are put forward NCS extension: 0 residues added, 1538 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.306 Round 2: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.418 Round 3: 85 peptides, 12 chains. Longest chain 12 peptides. Score 0.471 Round 4: 82 peptides, 11 chains. Longest chain 16 peptides. Score 0.481 Round 5: 81 peptides, 12 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 4 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2932 restraints for refining 1230 atoms. 2659 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3078 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.3277 (Rfree = 0.000) for 1200 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 3: After refmac, R = 0.2872 (Rfree = 0.000) for 1188 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2895 (Rfree = 0.000) for 1180 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2648 (Rfree = 0.000) for 1170 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.22 Search for helices and strands: 0 residues in 0 chains, 1256 seeds are put forward NCS extension: 0 residues added, 1256 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.363 Round 2: 84 peptides, 12 chains. Longest chain 14 peptides. Score 0.464 Round 3: 92 peptides, 13 chains. Longest chain 20 peptides. Score 0.488 Round 4: 101 peptides, 12 chains. Longest chain 14 peptides. Score 0.572 Round 5: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 4 Chains 13, Residues 89, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2555 restraints for refining 1230 atoms. 2160 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2740 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.2575 (Rfree = 0.000) for 1209 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.2545 (Rfree = 0.000) for 1198 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.2245 (Rfree = 0.000) for 1191 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2242 (Rfree = 0.000) for 1184 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.26 Search for helices and strands: 0 residues in 0 chains, 1259 seeds are put forward NCS extension: 0 residues added, 1259 seeds are put forward Round 1: 77 peptides, 13 chains. Longest chain 11 peptides. Score 0.381 Round 2: 90 peptides, 13 chains. Longest chain 12 peptides. Score 0.474 Round 3: 91 peptides, 12 chains. Longest chain 15 peptides. Score 0.511 Round 4: 84 peptides, 12 chains. Longest chain 16 peptides. Score 0.464 Round 5: 94 peptides, 12 chains. Longest chain 15 peptides. Score 0.530 Taking the results from Round 5 Chains 12, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2711 restraints for refining 1230 atoms. 2395 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2645 (Rfree = 0.000) for 1230 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 12: After refmac, R = 0.2289 (Rfree = 0.000) for 1218 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2246 (Rfree = 0.000) for 1213 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2431 (Rfree = 0.000) for 1204 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2479 (Rfree = 0.000) for 1199 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.24 Search for helices and strands: 0 residues in 0 chains, 1256 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1275 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.294 Round 2: 99 peptides, 15 chains. Longest chain 12 peptides. Score 0.475 Round 3: 92 peptides, 12 chains. Longest chain 14 peptides. Score 0.517 Round 4: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.430 Round 5: 89 peptides, 11 chains. Longest chain 14 peptides. Score 0.527 Taking the results from Round 5 Chains 11, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2846 restraints for refining 1230 atoms. 2545 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2673 (Rfree = 0.000) for 1230 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 1223 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2390 (Rfree = 0.000) for 1218 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2195 (Rfree = 0.000) for 1214 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2298 (Rfree = 0.000) for 1210 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.21 Search for helices and strands: 0 residues in 0 chains, 1296 seeds are put forward NCS extension: 0 residues added, 1296 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 14 peptides. Score 0.368 Round 2: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.469 Round 3: 81 peptides, 11 chains. Longest chain 11 peptides. Score 0.475 Round 4: 81 peptides, 10 chains. Longest chain 17 peptides. Score 0.505 Round 5: 90 peptides, 13 chains. Longest chain 11 peptides. Score 0.474 Taking the results from Round 4 Chains 10, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2367 reflections ( 99.71 % complete ) and 2800 restraints for refining 1230 atoms. 2526 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2845 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2426 (Rfree = 0.000) for 1215 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2316 (Rfree = 0.000) for 1203 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2280 (Rfree = 0.000) for 1201 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2254 (Rfree = 0.000) for 1199 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.24 Search for helices and strands: 0 residues in 0 chains, 1255 seeds are put forward NCS extension: 0 residues added, 1255 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 12 peptides. Score 0.332 Round 2: 89 peptides, 14 chains. Longest chain 15 peptides. Score 0.437 Round 3: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.461 Round 4: 89 peptides, 12 chains. Longest chain 17 peptides. Score 0.498 Round 5: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 4 Chains 12, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2676 restraints for refining 1229 atoms. 2380 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2473 (Rfree = 0.000) for 1229 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.2312 (Rfree = 0.000) for 1222 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2322 (Rfree = 0.000) for 1218 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 29: After refmac, R = 0.2210 (Rfree = 0.000) for 1214 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2170 (Rfree = 0.000) for 1209 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.21 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1309 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.297 Round 2: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.404 Round 3: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.439 Round 4: 78 peptides, 11 chains. Longest chain 11 peptides. Score 0.454 Round 5: 76 peptides, 11 chains. Longest chain 11 peptides. Score 0.439 Taking the results from Round 4 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2765 restraints for refining 1230 atoms. 2508 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2855 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2474 (Rfree = 0.000) for 1226 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2355 (Rfree = 0.000) for 1221 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 1216 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.2061 (Rfree = 0.000) for 1210 atoms. Found 2 (6 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.15 Search for helices and strands: 0 residues in 0 chains, 1260 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1276 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.304 Round 2: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.359 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.381 Round 4: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.458 Round 5: 90 peptides, 14 chains. Longest chain 14 peptides. Score 0.444 Taking the results from Round 4 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2367 reflections ( 99.71 % complete ) and 2686 restraints for refining 1230 atoms. 2388 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2519 (Rfree = 0.000) for 1230 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2482 (Rfree = 0.000) for 1220 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2324 (Rfree = 0.000) for 1213 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2386 (Rfree = 0.000) for 1207 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2202 (Rfree = 0.000) for 1204 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.22 Search for helices and strands: 0 residues in 0 chains, 1274 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1291 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.263 Round 2: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.337 Round 3: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.361 Round 4: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.328 Round 5: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.361 Taking the results from Round 5 Chains 15, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2367 reflections ( 99.71 % complete ) and 2838 restraints for refining 1230 atoms. 2581 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2658 (Rfree = 0.000) for 1230 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2290 (Rfree = 0.000) for 1224 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2287 (Rfree = 0.000) for 1219 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2152 (Rfree = 0.000) for 1217 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2126 (Rfree = 0.000) for 1216 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.27 Search for helices and strands: 0 residues in 0 chains, 1263 seeds are put forward NCS extension: 0 residues added, 1263 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.289 Round 2: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.371 Round 3: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.386 Round 4: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.389 Round 5: 74 peptides, 11 chains. Longest chain 18 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 63, 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 2750 restraints for refining 1230 atoms. 2509 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2638 (Rfree = 0.000) for 1230 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2483 (Rfree = 0.000) for 1224 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2538 (Rfree = 0.000) for 1220 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2463 (Rfree = 0.000) for 1213 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:02:59 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 35.03