null Sun 23 Dec 22:22:53 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 2i9w-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-3.6-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/2i9w-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-3.6-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 22:23:03 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/2i9w-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-3.6-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 123 and 0 Target number of residues in the AU: 123 Target solvent content: 0.6493 Checking the provided sequence file Detected sequence length: 184 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 184 Adjusted target solvent content: 0.48 Input MTZ file: 2i9w-3.6-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: 19 Cell parameters: 41.450 54.640 83.800 90.000 90.000 90.000 Input sequence file: 2i9w-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1472 target number of atoms Had to go as low as 0.75 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: 45.770 3.600 Wilson plot Bfac: 76.16 2412 reflections ( 99.50 % complete ) and 0 restraints for refining 1636 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3697 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3409 (Rfree = 0.000) for 1636 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 1661 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.263 Round 2: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.337 Round 3: 89 peptides, 16 chains. Longest chain 13 peptides. Score 0.397 Round 4: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.396 Round 5: 82 peptides, 11 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 5 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 3192 restraints for refining 1333 atoms. 2919 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2974 (Rfree = 0.000) for 1333 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 2: After refmac, R = 0.3064 (Rfree = 0.000) for 1310 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2921 (Rfree = 0.000) for 1295 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2797 (Rfree = 0.000) for 1287 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.2799 (Rfree = 0.000) for 1284 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 1330 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.246 Round 2: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.339 Round 3: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.363 Round 4: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.492 Round 5: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.397 Taking the results from Round 4 Chains 13, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 2827 restraints for refining 1260 atoms. 2540 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2630 (Rfree = 0.000) for 1260 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 7: After refmac, R = 0.2780 (Rfree = 0.000) for 1253 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2773 (Rfree = 0.000) for 1249 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 9: After refmac, R = 0.2344 (Rfree = 0.000) for 1239 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2563 (Rfree = 0.000) for 1235 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 1284 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.361 Round 2: 81 peptides, 13 chains. Longest chain 9 peptides. Score 0.437 Round 3: 94 peptides, 14 chains. Longest chain 12 peptides. Score 0.504 Round 4: 86 peptides, 13 chains. Longest chain 12 peptides. Score 0.477 Round 5: 83 peptides, 13 chains. Longest chain 10 peptides. Score 0.453 Taking the results from Round 3 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 2833 restraints for refining 1270 atoms. 2527 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2599 (Rfree = 0.000) for 1270 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 12: After refmac, R = 0.2551 (Rfree = 0.000) for 1260 atoms. Found 2 (8 requested) and removed 56 (4 requested) atoms. Cycle 13: After refmac, R = 0.2563 (Rfree = 0.000) for 1204 atoms. Found 2 (7 requested) and removed 10 (3 requested) atoms. Cycle 14: After refmac, R = 0.2788 (Rfree = 0.000) for 1192 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.2639 (Rfree = 0.000) for 1188 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 1249 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.307 Round 2: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.422 Round 3: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.407 Round 4: 79 peptides, 13 chains. Longest chain 10 peptides. Score 0.421 Round 5: 78 peptides, 13 chains. Longest chain 9 peptides. Score 0.413 Taking the results from Round 2 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 2819 restraints for refining 1240 atoms. 2531 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 1240 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 17: After refmac, R = 0.2327 (Rfree = 0.000) for 1240 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 18: After refmac, R = 0.2274 (Rfree = 0.000) for 1236 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2229 (Rfree = 0.000) for 1232 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2170 (Rfree = 0.000) for 1230 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.328 Round 2: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.405 Round 3: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.370 Round 4: 89 peptides, 15 chains. Longest chain 8 peptides. Score 0.432 Round 5: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.416 Taking the results from Round 4 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 3089 restraints for refining 1334 atoms. 2808 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2798 (Rfree = 0.000) for 1334 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.2280 (Rfree = 0.000) for 1322 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.2104 (Rfree = 0.000) for 1317 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2102 (Rfree = 0.000) for 1311 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2103 (Rfree = 0.000) for 1308 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 1345 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.253 Round 2: 86 peptides, 16 chains. Longest chain 12 peptides. Score 0.372 Round 3: 92 peptides, 16 chains. Longest chain 14 peptides. Score 0.422 Round 4: 100 peptides, 17 chains. Longest chain 13 peptides. Score 0.451 Round 5: 94 peptides, 14 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 5 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 3067 restraints for refining 1334 atoms. 2761 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2424 (Rfree = 0.000) for 1334 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2348 (Rfree = 0.000) for 1328 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2340 (Rfree = 0.000) for 1325 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2325 (Rfree = 0.000) for 1322 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2313 (Rfree = 0.000) for 1317 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 1347 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.257 Round 2: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.339 Round 3: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.404 Round 4: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.359 Round 5: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.381 Taking the results from Round 3 Chains 13, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 3166 restraints for refining 1334 atoms. 2923 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2308 (Rfree = 0.000) for 1334 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.2126 (Rfree = 0.000) for 1328 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2071 (Rfree = 0.000) for 1324 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2058 (Rfree = 0.000) for 1321 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2067 (Rfree = 0.000) for 1316 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 1340 seeds are put forward Round 1: 50 peptides, 12 chains. Longest chain 5 peptides. Score 0.188 Round 2: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.292 Round 3: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.337 Round 4: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.402 Round 5: 56 peptides, 9 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 4 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 3303 restraints for refining 1333 atoms. 3086 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2256 (Rfree = 0.000) for 1333 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2584 (Rfree = 0.000) for 1328 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2116 (Rfree = 0.000) for 1326 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2071 (Rfree = 0.000) for 1314 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2327 (Rfree = 0.000) for 1316 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 1341 seeds are put forward Round 1: 50 peptides, 12 chains. Longest chain 6 peptides. Score 0.188 Round 2: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.288 Round 3: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.265 Round 4: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.273 Round 5: 45 peptides, 9 chains. Longest chain 11 peptides. Score 0.268 Taking the results from Round 2 Chains 9, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2412 reflections ( 99.50 % complete ) and 3158 restraints for refining 1281 atoms. 3015 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2655 (Rfree = 0.000) for 1281 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.2889 (Rfree = 0.000) for 1275 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2869 (Rfree = 0.000) for 1273 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2865 (Rfree = 0.000) for 1268 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2438 (Rfree = 0.000) for 1268 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 1307 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 7 peptides. Score 0.212 Round 2: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.249 Round 3: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.309 Round 4: 57 peptides, 11 chains. Longest chain 11 peptides. Score 0.302 Round 5: 58 peptides, 11 chains. Longest chain 12 peptides. Score 0.312 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 47, 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 2i9w-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2412 reflections ( 99.50 % complete ) and 2991 restraints for refining 1276 atoms. 2814 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2410 (Rfree = 0.000) for 1276 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2834 (Rfree = 0.000) for 1271 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2701 (Rfree = 0.000) for 1264 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2732 (Rfree = 0.000) for 1258 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:40 GMT 2018 Job finished. TimeTaking 25.8 Used memory is bytes: 14012128