Sun 23 Dec 22:23:14 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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/2hyt-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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 22:23:22 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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 150 and 0 Target number of residues in the AU: 150 Target solvent content: 0.6352 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-3.6-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: 150 Cell parameters: 82.957 82.957 56.010 90.000 90.000 120.000 Input sequence file: 2hyt-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1576 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 Loops will be built when appropriate and at the last cycle Resolution range: 71.843 3.600 Wilson plot Bfac: 68.14 2736 reflections ( 99.56 % complete ) and 0 restraints for refining 1753 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3498 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2870 (Rfree = 0.000) for 1753 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1799 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 5 peptides. Score 0.211 Round 2: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.364 Round 3: 102 peptides, 17 chains. Longest chain 14 peptides. Score 0.434 Round 4: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.443 Round 5: 105 peptides, 14 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 15, Residues 91, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3292 restraints for refining 1429 atoms. 2917 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2782 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.2517 (Rfree = 0.000) for 1407 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 1396 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2303 (Rfree = 0.000) for 1392 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2244 (Rfree = 0.000) for 1387 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 1480 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 15 peptides. Score 0.422 Round 2: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.485 Round 3: 109 peptides, 15 chains. Longest chain 15 peptides. Score 0.536 Round 4: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.508 Round 5: 107 peptides, 14 chains. Longest chain 19 peptides. Score 0.550 Taking the results from Round 5 Chains 14, Residues 93, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3249 restraints for refining 1429 atoms. 2880 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2899 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2597 (Rfree = 0.000) for 1425 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2436 (Rfree = 0.000) for 1421 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2419 (Rfree = 0.000) for 1413 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2389 (Rfree = 0.000) for 1404 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 1489 seeds are put forward Round 1: 95 peptides, 15 chains. Longest chain 21 peptides. Score 0.445 Round 2: 99 peptides, 13 chains. Longest chain 17 peptides. Score 0.529 Round 3: 108 peptides, 13 chains. Longest chain 19 peptides. Score 0.582 Round 4: 104 peptides, 12 chains. Longest chain 17 peptides. Score 0.586 Round 5: 101 peptides, 14 chains. Longest chain 11 peptides. Score 0.514 Taking the results from Round 4 Chains 14, Residues 92, Estimated correctness of the model 9.1 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3155 restraints for refining 1429 atoms. 2746 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2746 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.2578 (Rfree = 0.000) for 1410 atoms. Found 3 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2388 (Rfree = 0.000) for 1400 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2371 (Rfree = 0.000) for 1387 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2323 (Rfree = 0.000) for 1383 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.315 Round 2: 103 peptides, 17 chains. Longest chain 15 peptides. Score 0.440 Round 3: 100 peptides, 14 chains. Longest chain 18 peptides. Score 0.507 Round 4: 108 peptides, 14 chains. Longest chain 15 peptides. Score 0.556 Round 5: 106 peptides, 13 chains. Longest chain 20 peptides. Score 0.571 Taking the results from Round 5 Chains 13, Residues 93, Estimated correctness of the model 3.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3072 restraints for refining 1429 atoms. 2642 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2595 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 17: After refmac, R = 0.2411 (Rfree = 0.000) for 1416 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2286 (Rfree = 0.000) for 1407 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2224 (Rfree = 0.000) for 1401 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2179 (Rfree = 0.000) for 1396 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 1463 seeds are put forward Round 1: 103 peptides, 17 chains. Longest chain 17 peptides. Score 0.440 Round 2: 112 peptides, 16 chains. Longest chain 19 peptides. Score 0.527 Round 3: 110 peptides, 12 chains. Longest chain 27 peptides. Score 0.618 Round 4: 103 peptides, 14 chains. Longest chain 19 peptides. Score 0.526 Round 5: 106 peptides, 12 chains. Longest chain 19 peptides. Score 0.597 Taking the results from Round 3 Chains 12, Residues 98, Estimated correctness of the model 21.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3051 restraints for refining 1429 atoms. 2618 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2617 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 22: After refmac, R = 0.2458 (Rfree = 0.000) for 1405 atoms. Found 8 (9 requested) and removed 16 (4 requested) atoms. Cycle 23: After refmac, R = 0.2338 (Rfree = 0.000) for 1395 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2220 (Rfree = 0.000) for 1394 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2227 (Rfree = 0.000) for 1392 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.396 Round 2: 99 peptides, 14 chains. Longest chain 18 peptides. Score 0.501 Round 3: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.424 Round 4: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.422 Round 5: 100 peptides, 15 chains. Longest chain 15 peptides. Score 0.479 Taking the results from Round 2 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3295 restraints for refining 1408 atoms. 2952 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2529 (Rfree = 0.000) for 1408 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2309 (Rfree = 0.000) for 1409 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2195 (Rfree = 0.000) for 1405 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2081 (Rfree = 0.000) for 1405 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2054 (Rfree = 0.000) for 1402 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1481 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.353 Round 2: 90 peptides, 14 chains. Longest chain 13 peptides. Score 0.441 Round 3: 97 peptides, 14 chains. Longest chain 22 peptides. Score 0.488 Round 4: 104 peptides, 16 chains. Longest chain 15 peptides. Score 0.476 Round 5: 106 peptides, 14 chains. Longest chain 30 peptides. Score 0.544 Taking the results from Round 5 Chains 14, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3375 restraints for refining 1429 atoms. 3021 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2791 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2542 (Rfree = 0.000) for 1431 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2462 (Rfree = 0.000) for 1430 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2430 (Rfree = 0.000) for 1427 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2413 (Rfree = 0.000) for 1425 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1484 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.270 Round 2: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.431 Round 3: 99 peptides, 14 chains. Longest chain 19 peptides. Score 0.501 Round 4: 100 peptides, 15 chains. Longest chain 16 peptides. Score 0.479 Round 5: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 3 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3388 restraints for refining 1428 atoms. 3062 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2536 (Rfree = 0.000) for 1428 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 37: After refmac, R = 0.2579 (Rfree = 0.000) for 1421 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2409 (Rfree = 0.000) for 1420 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2347 (Rfree = 0.000) for 1420 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2321 (Rfree = 0.000) for 1417 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 1487 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 9 peptides. Score 0.255 Round 2: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.369 Round 3: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.332 Round 4: 87 peptides, 16 chains. Longest chain 13 peptides. Score 0.356 Round 5: 79 peptides, 15 chains. Longest chain 14 peptides. Score 0.328 Taking the results from Round 2 Chains 17, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2736 reflections ( 99.56 % complete ) and 3534 restraints for refining 1429 atoms. 3247 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2439 (Rfree = 0.000) for 1429 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 42: After refmac, R = 0.2245 (Rfree = 0.000) for 1427 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2172 (Rfree = 0.000) for 1426 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2161 (Rfree = 0.000) for 1420 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2098 (Rfree = 0.000) for 1416 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1456 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 5 peptides. Score 0.213 Round 2: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.401 Round 3: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.369 Round 4: 75 peptides, 13 chains. Longest chain 13 peptides. Score 0.363 Round 5: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.351 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 67, 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 2hyt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2736 reflections ( 99.56 % complete ) and 3534 restraints for refining 1429 atoms. 3279 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2325 (Rfree = 0.000) for 1429 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Cycle 47: After refmac, R = 0.2248 (Rfree = 0.000) for 1425 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Cycle 48: After refmac, R = 0.2209 (Rfree = 0.000) for 1422 atoms. Found 0 (9 requested) and removed 0 (4 requested) atoms. Cycle 49: After refmac, R = 0.2189 (Rfree = 0.000) for 1422 atoms. TimeTaking 31.27