Sun 23 Dec 22:22:59 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 2hyt-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.2-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/2hyt-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.2-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 22:23:07 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/2hyt-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.2-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 161 and 0 Target number of residues in the AU: 161 Target solvent content: 0.6085 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 197 Adjusted target solvent content: 0.52 Input MTZ file: 2hyt-3.2-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: 150 Cell parameters: 82.957 82.957 56.010 90.000 90.000 120.000 Input sequence file: 2hyt-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1576 target number of atoms Had to go as low as 0.85 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: 71.843 3.201 Wilson plot Bfac: 55.35 3864 reflections ( 99.69 % complete ) and 0 restraints for refining 1764 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3338 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3660 (Rfree = 0.000) for 1764 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 1820 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.262 Round 2: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.402 Round 3: 101 peptides, 15 chains. Longest chain 17 peptides. Score 0.485 Round 4: 99 peptides, 15 chains. Longest chain 11 peptides. Score 0.472 Round 5: 102 peptides, 14 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 5 Chains 14, Residues 88, Estimated correctness of the model 17.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 3281 restraints for refining 1439 atoms. 2943 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3553 (Rfree = 0.000) for 1439 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.3494 (Rfree = 0.000) for 1412 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.3280 (Rfree = 0.000) for 1395 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.3167 (Rfree = 0.000) for 1375 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.3183 (Rfree = 0.000) for 1360 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.04 Search for helices and strands: 0 residues in 0 chains, 1448 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 12 peptides. Score 0.339 Round 2: 99 peptides, 17 chains. Longest chain 15 peptides. Score 0.413 Round 3: 96 peptides, 15 chains. Longest chain 15 peptides. Score 0.452 Round 4: 104 peptides, 14 chains. Longest chain 16 peptides. Score 0.532 Round 5: 105 peptides, 13 chains. Longest chain 16 peptides. Score 0.565 Taking the results from Round 5 Chains 15, Residues 92, Estimated correctness of the model 31.2 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 2988 restraints for refining 1421 atoms. 2590 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3371 (Rfree = 0.000) for 1421 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.3227 (Rfree = 0.000) for 1387 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.3264 (Rfree = 0.000) for 1365 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.3255 (Rfree = 0.000) for 1353 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.3188 (Rfree = 0.000) for 1345 atoms. Found 5 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.04 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.336 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.388 Round 3: 94 peptides, 14 chains. Longest chain 11 peptides. Score 0.468 Round 4: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.438 Round 5: 98 peptides, 13 chains. Longest chain 20 peptides. Score 0.523 Taking the results from Round 5 Chains 13, Residues 85, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 2989 restraints for refining 1354 atoms. 2662 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3505 (Rfree = 0.000) for 1354 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.3213 (Rfree = 0.000) for 1336 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.3083 (Rfree = 0.000) for 1332 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.3019 (Rfree = 0.000) for 1323 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.3141 (Rfree = 0.000) for 1325 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.06 Search for helices and strands: 0 residues in 0 chains, 1393 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 6 peptides. Score 0.285 Round 2: 94 peptides, 16 chains. Longest chain 12 peptides. Score 0.408 Round 3: 110 peptides, 15 chains. Longest chain 16 peptides. Score 0.542 Round 4: 106 peptides, 13 chains. Longest chain 15 peptides. Score 0.571 Round 5: 96 peptides, 12 chains. Longest chain 16 peptides. Score 0.539 Taking the results from Round 4 Chains 13, Residues 93, Estimated correctness of the model 32.9 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 2909 restraints for refining 1389 atoms. 2534 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3024 (Rfree = 0.000) for 1389 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.3087 (Rfree = 0.000) for 1379 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.3082 (Rfree = 0.000) for 1373 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 19: After refmac, R = 0.3001 (Rfree = 0.000) for 1363 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.2943 (Rfree = 0.000) for 1359 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.05 Search for helices and strands: 0 residues in 0 chains, 1448 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.320 Round 2: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.434 Round 3: 91 peptides, 14 chains. Longest chain 11 peptides. Score 0.448 Round 4: 93 peptides, 14 chains. Longest chain 15 peptides. Score 0.462 Round 5: 89 peptides, 13 chains. Longest chain 13 peptides. Score 0.465 Taking the results from Round 5 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 3236 restraints for refining 1439 atoms. 2945 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3365 (Rfree = 0.000) for 1439 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.3195 (Rfree = 0.000) for 1421 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.3089 (Rfree = 0.000) for 1414 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.3191 (Rfree = 0.000) for 1407 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 25: After refmac, R = 0.3068 (Rfree = 0.000) for 1399 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1466 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.263 Round 2: 91 peptides, 14 chains. Longest chain 11 peptides. Score 0.448 Round 3: 93 peptides, 15 chains. Longest chain 19 peptides. Score 0.431 Round 4: 95 peptides, 15 chains. Longest chain 9 peptides. Score 0.445 Round 5: 93 peptides, 14 chains. Longest chain 10 peptides. Score 0.462 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 3176 restraints for refining 1411 atoms. 2874 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3183 (Rfree = 0.000) for 1411 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 27: After refmac, R = 0.3238 (Rfree = 0.000) for 1378 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.3179 (Rfree = 0.000) for 1377 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.3148 (Rfree = 0.000) for 1376 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.3131 (Rfree = 0.000) for 1372 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 1454 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 6 peptides. Score 0.263 Round 2: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.371 Round 3: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.388 Round 4: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.369 Round 5: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 5 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 2991 restraints for refining 1401 atoms. 2663 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3335 (Rfree = 0.000) for 1401 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.3139 (Rfree = 0.000) for 1383 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.3234 (Rfree = 0.000) for 1376 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.3092 (Rfree = 0.000) for 1372 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2911 (Rfree = 0.000) for 1371 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1443 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.262 Round 2: 89 peptides, 14 chains. Longest chain 10 peptides. Score 0.434 Round 3: 91 peptides, 15 chains. Longest chain 14 peptides. Score 0.417 Round 4: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.381 Round 5: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 2 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 3135 restraints for refining 1388 atoms. 2849 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3164 (Rfree = 0.000) for 1388 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 37: After refmac, R = 0.3029 (Rfree = 0.000) for 1358 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.3116 (Rfree = 0.000) for 1357 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.3108 (Rfree = 0.000) for 1348 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.3010 (Rfree = 0.000) for 1343 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.273 Round 2: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.346 Round 3: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.348 Round 4: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.384 Round 5: 77 peptides, 11 chains. Longest chain 15 peptides. Score 0.444 Taking the results from Round 5 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3864 reflections ( 99.69 % complete ) and 3098 restraints for refining 1414 atoms. 2811 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3035 (Rfree = 0.000) for 1414 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.3224 (Rfree = 0.000) for 1409 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.3012 (Rfree = 0.000) for 1401 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.3162 (Rfree = 0.000) for 1395 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.3100 (Rfree = 0.000) for 1383 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 1455 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.225 Round 2: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.333 Round 3: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.338 Round 4: 64 peptides, 10 chains. Longest chain 14 peptides. Score 0.381 Round 5: 73 peptides, 15 chains. Longest chain 10 peptides. Score 0.280 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 54, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2hyt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3864 reflections ( 99.69 % complete ) and 2882 restraints for refining 1377 atoms. 2634 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3300 (Rfree = 0.000) for 1377 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3084 (Rfree = 0.000) for 1356 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2623 (Rfree = 0.000) for 1342 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3027 (Rfree = 0.000) for 1332 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 32.12