Sun 23 Dec 22:23:02 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 2o2g-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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/2o2g-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 22:23:12 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/2o2g-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6380 Checking the provided sequence file Detected sequence length: 223 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 223 Adjusted target solvent content: 0.41 Input MTZ file: 2o2g-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: 47.887 62.444 67.988 90.000 90.000 90.000 Input sequence file: 2o2g-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1784 target number of atoms Had to go as low as 0.55 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: 45.990 3.600 Wilson plot Bfac: 70.78 2378 reflections ( 95.23 % complete ) and 0 restraints for refining 1988 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3705 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3735 (Rfree = 0.000) for 1988 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 2014 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.222 Round 2: 57 peptides, 12 chains. Longest chain 11 peptides. Score 0.256 Round 3: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.255 Round 4: 70 peptides, 15 chains. Longest chain 9 peptides. Score 0.261 Round 5: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.309 Taking the results from Round 5 Chains 13, Residues 54, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 4231 restraints for refining 1617 atoms. 4022 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3306 (Rfree = 0.000) for 1617 atoms. Found 4 (10 requested) and removed 17 (5 requested) atoms. Cycle 2: After refmac, R = 0.2993 (Rfree = 0.000) for 1588 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Cycle 3: After refmac, R = 0.2772 (Rfree = 0.000) for 1573 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2865 (Rfree = 0.000) for 1564 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2734 (Rfree = 0.000) for 1551 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.92 Search for helices and strands: 0 residues in 0 chains, 1579 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 7 peptides. Score 0.207 Round 2: 74 peptides, 14 chains. Longest chain 10 peptides. Score 0.333 Round 3: 79 peptides, 16 chains. Longest chain 10 peptides. Score 0.303 Round 4: 90 peptides, 17 chains. Longest chain 12 peptides. Score 0.360 Round 5: 83 peptides, 17 chains. Longest chain 9 peptides. Score 0.302 Taking the results from Round 4 Chains 17, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3587 restraints for refining 1460 atoms. 3312 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2777 (Rfree = 0.000) for 1460 atoms. Found 6 (9 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2587 (Rfree = 0.000) for 1447 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2626 (Rfree = 0.000) for 1440 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2585 (Rfree = 0.000) for 1435 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2610 (Rfree = 0.000) for 1430 atoms. Found 0 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 1467 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.251 Round 2: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.374 Round 3: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.345 Round 4: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.412 Round 5: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 4 Chains 15, Residues 73, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3589 restraints for refining 1533 atoms. 3288 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2822 (Rfree = 0.000) for 1533 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.2650 (Rfree = 0.000) for 1520 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2615 (Rfree = 0.000) for 1512 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2576 (Rfree = 0.000) for 1511 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2605 (Rfree = 0.000) for 1505 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 1549 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.307 Round 2: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.388 Round 3: 87 peptides, 15 chains. Longest chain 13 peptides. Score 0.404 Round 4: 91 peptides, 15 chains. Longest chain 14 peptides. Score 0.435 Round 5: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 5 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3656 restraints for refining 1564 atoms. 3346 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2873 (Rfree = 0.000) for 1564 atoms. Found 5 (10 requested) and removed 13 (5 requested) atoms. Cycle 17: After refmac, R = 0.2696 (Rfree = 0.000) for 1552 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2622 (Rfree = 0.000) for 1540 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2761 (Rfree = 0.000) for 1531 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.2527 (Rfree = 0.000) for 1528 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.91 Search for helices and strands: 0 residues in 0 chains, 1575 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.291 Round 2: 84 peptides, 15 chains. Longest chain 12 peptides. Score 0.380 Round 3: 90 peptides, 13 chains. Longest chain 12 peptides. Score 0.492 Round 4: 80 peptides, 13 chains. Longest chain 15 peptides. Score 0.417 Round 5: 91 peptides, 15 chains. Longest chain 11 peptides. Score 0.435 Taking the results from Round 3 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3634 restraints for refining 1553 atoms. 3334 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2725 (Rfree = 0.000) for 1553 atoms. Found 5 (9 requested) and removed 37 (4 requested) atoms. Cycle 22: After refmac, R = 0.2513 (Rfree = 0.000) for 1519 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2405 (Rfree = 0.000) for 1515 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2665 (Rfree = 0.000) for 1505 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2147 (Rfree = 0.000) for 1505 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 1557 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 8 peptides. Score 0.243 Round 2: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.289 Round 3: 57 peptides, 10 chains. Longest chain 13 peptides. Score 0.335 Round 4: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.311 Round 5: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.314 Taking the results from Round 3 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3645 restraints for refining 1502 atoms. 3467 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2543 (Rfree = 0.000) for 1502 atoms. Found 7 (9 requested) and removed 25 (4 requested) atoms. Cycle 27: After refmac, R = 0.2557 (Rfree = 0.000) for 1479 atoms. Found 8 (9 requested) and removed 18 (4 requested) atoms. Cycle 28: After refmac, R = 0.2929 (Rfree = 0.000) for 1462 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2290 (Rfree = 0.000) for 1460 atoms. Found 3 (9 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2256 (Rfree = 0.000) for 1450 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 1488 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.245 Round 2: 62 peptides, 10 chains. Longest chain 9 peptides. Score 0.378 Round 3: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.366 Round 4: 64 peptides, 11 chains. Longest chain 12 peptides. Score 0.358 Round 5: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 2 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3264 restraints for refining 1435 atoms. 3060 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3097 (Rfree = 0.000) for 1435 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.2700 (Rfree = 0.000) for 1424 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2600 (Rfree = 0.000) for 1419 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2132 (Rfree = 0.000) for 1418 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2378 (Rfree = 0.000) for 1417 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 1452 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.225 Round 2: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.247 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.314 Round 4: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.358 Round 5: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.338 Taking the results from Round 4 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3272 restraints for refining 1433 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2829 (Rfree = 0.000) for 1433 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 37: After refmac, R = 0.2361 (Rfree = 0.000) for 1425 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.2514 (Rfree = 0.000) for 1421 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2455 (Rfree = 0.000) for 1416 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.2273 (Rfree = 0.000) for 1413 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 1463 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 5 peptides. Score 0.210 Round 2: 70 peptides, 14 chains. Longest chain 11 peptides. Score 0.298 Round 3: 69 peptides, 13 chains. Longest chain 12 peptides. Score 0.326 Round 4: 64 peptides, 11 chains. Longest chain 12 peptides. Score 0.358 Round 5: 67 peptides, 11 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 95.23 % complete ) and 3254 restraints for refining 1438 atoms. 3041 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2562 (Rfree = 0.000) for 1438 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2529 (Rfree = 0.000) for 1434 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2823 (Rfree = 0.000) for 1434 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2373 (Rfree = 0.000) for 1426 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2529 (Rfree = 0.000) for 1424 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 1464 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.210 Round 2: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.287 Round 3: 59 peptides, 11 chains. Longest chain 11 peptides. Score 0.314 Round 4: 57 peptides, 10 chains. Longest chain 12 peptides. Score 0.335 Round 5: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.344 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 48, 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 2o2g-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2378 reflections ( 95.23 % complete ) and 3228 restraints for refining 1391 atoms. 3046 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2835 (Rfree = 0.000) for 1391 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2678 (Rfree = 0.000) for 1379 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2231 (Rfree = 0.000) for 1374 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 1370 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. TimeTaking 28.05