null Sun 23 Dec 22:22:43 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 2pg3-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-4.0-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/2pg3-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-4.0-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 22:22:52 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/2pg3-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-4.0-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 143 and 0 Target number of residues in the AU: 143 Target solvent content: 0.6741 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.47 Input MTZ file: 2pg3-4.0-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: 92 Cell parameters: 78.154 78.154 77.755 90.000 90.000 90.000 Input sequence file: 2pg3-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 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: 27.561 4.000 Wilson plot Bfac: 95.15 2257 reflections ( 99.52 % complete ) and 0 restraints for refining 2070 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3817 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3681 (Rfree = 0.000) for 2070 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.86 4.02 Search for helices and strands: 0 residues in 0 chains, 2098 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.234 Round 2: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.266 Round 3: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.264 Round 4: 67 peptides, 13 chains. Longest chain 7 peptides. Score 0.294 Round 5: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.284 Taking the results from Round 4 Chains 13, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 4126 restraints for refining 1674 atoms. 3923 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3124 (Rfree = 0.000) for 1674 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 2: After refmac, R = 0.3192 (Rfree = 0.000) for 1645 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 3: After refmac, R = 0.2679 (Rfree = 0.000) for 1618 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2965 (Rfree = 0.000) for 1604 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2972 (Rfree = 0.000) for 1591 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.87 4.03 Search for helices and strands: 0 residues in 0 chains, 1630 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 6 peptides. Score 0.195 Round 2: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.272 Round 3: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.272 Round 4: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.291 Round 5: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.288 Taking the results from Round 4 Chains 11, Residues 47, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3334 restraints for refining 1412 atoms. 3137 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2818 (Rfree = 0.000) for 1412 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 7: After refmac, R = 0.2984 (Rfree = 0.000) for 1394 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 8: After refmac, R = 0.2588 (Rfree = 0.000) for 1376 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.2252 (Rfree = 0.000) for 1370 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. Cycle 10: After refmac, R = 0.2115 (Rfree = 0.000) for 1361 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.92 4.08 Search for helices and strands: 0 residues in 0 chains, 1407 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 10 peptides. Score 0.268 Round 2: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.345 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.345 Round 4: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.325 Round 5: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.332 Taking the results from Round 3 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 2937 restraints for refining 1331 atoms. 2695 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2637 (Rfree = 0.000) for 1331 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 12: After refmac, R = 0.2548 (Rfree = 0.000) for 1321 atoms. Found 6 (6 requested) and removed 38 (3 requested) atoms. Cycle 13: After refmac, R = 0.2625 (Rfree = 0.000) for 1282 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 14: After refmac, R = 0.2728 (Rfree = 0.000) for 1268 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 15: After refmac, R = 0.2565 (Rfree = 0.000) for 1245 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.87 4.03 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.226 Round 2: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.311 Round 3: 87 peptides, 17 chains. Longest chain 7 peptides. Score 0.317 Round 4: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.288 Round 5: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 5 Chains 13, Residues 58, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3102 restraints for refining 1368 atoms. 2865 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2765 (Rfree = 0.000) for 1368 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 17: After refmac, R = 0.2496 (Rfree = 0.000) for 1339 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 18: After refmac, R = 0.2563 (Rfree = 0.000) for 1324 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2503 (Rfree = 0.000) for 1315 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 20: After refmac, R = 0.2453 (Rfree = 0.000) for 1310 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.99 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 6 peptides. Score 0.262 Round 2: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.353 Round 3: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.320 Round 4: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.346 Round 5: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.357 Taking the results from Round 5 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3006 restraints for refining 1363 atoms. 2782 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2775 (Rfree = 0.000) for 1363 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 22: After refmac, R = 0.2437 (Rfree = 0.000) for 1339 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 23: After refmac, R = 0.2495 (Rfree = 0.000) for 1328 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 24: After refmac, R = 0.2505 (Rfree = 0.000) for 1317 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 25: After refmac, R = 0.2412 (Rfree = 0.000) for 1311 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 4.00 Search for helices and strands: 0 residues in 0 chains, 1379 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.244 Round 2: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.288 Round 3: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.264 Round 4: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.299 Round 5: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.299 Taking the results from Round 5 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3158 restraints for refining 1385 atoms. 2977 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2818 (Rfree = 0.000) for 1385 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 27: After refmac, R = 0.2458 (Rfree = 0.000) for 1364 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2555 (Rfree = 0.000) for 1355 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 29: After refmac, R = 0.2253 (Rfree = 0.000) for 1346 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2519 (Rfree = 0.000) for 1345 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.88 4.04 Search for helices and strands: 0 residues in 0 chains, 1394 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.227 Round 2: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.355 Round 3: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.350 Round 4: 77 peptides, 14 chains. Longest chain 13 peptides. Score 0.337 Round 5: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.357 Taking the results from Round 5 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3201 restraints for refining 1448 atoms. 2940 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2700 (Rfree = 0.000) for 1448 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.2237 (Rfree = 0.000) for 1419 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.2413 (Rfree = 0.000) for 1407 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.2201 (Rfree = 0.000) for 1400 atoms. Found 4 (6 requested) and removed 11 (3 requested) atoms. Cycle 35: After refmac, R = 0.2131 (Rfree = 0.000) for 1391 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 4.03 Search for helices and strands: 0 residues in 0 chains, 1437 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.284 Round 2: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.364 Round 3: 83 peptides, 15 chains. Longest chain 12 peptides. Score 0.350 Round 4: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.395 Round 5: 87 peptides, 14 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3233 restraints for refining 1429 atoms. 2955 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2718 (Rfree = 0.000) for 1429 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 37: After refmac, R = 0.2491 (Rfree = 0.000) for 1408 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.2556 (Rfree = 0.000) for 1398 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 39: After refmac, R = 0.2447 (Rfree = 0.000) for 1377 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 40: After refmac, R = 0.2673 (Rfree = 0.000) for 1374 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.97 4.13 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.214 Round 2: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.272 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.299 Round 4: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.286 Round 5: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.296 Taking the results from Round 3 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2257 reflections ( 99.52 % complete ) and 3151 restraints for refining 1391 atoms. 2970 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2858 (Rfree = 0.000) for 1391 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 42: After refmac, R = 0.2540 (Rfree = 0.000) for 1374 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.2498 (Rfree = 0.000) for 1369 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.2530 (Rfree = 0.000) for 1367 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.2515 (Rfree = 0.000) for 1362 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.91 4.07 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.211 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.270 Round 3: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.270 Round 4: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.270 Round 5: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.294 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 54, 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 2pg3-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2257 reflections ( 99.52 % complete ) and 3042 restraints for refining 1352 atoms. 2839 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2705 (Rfree = 0.000) for 1352 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2532 (Rfree = 0.000) for 1343 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2744 (Rfree = 0.000) for 1338 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2345 (Rfree = 0.000) for 1330 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:54 GMT 2018 Job finished. TimeTaking 27.18 Used memory is bytes: 11701624