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 2pc1-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.2-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/2pc1-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.2-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 22:22:53 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/2pc1-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.2-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6093 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.42 Input MTZ file: 2pc1-3.2-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: 1 Cell parameters: 35.480 37.650 41.500 94.220 109.420 113.080 Input sequence file: 2pc1-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.60 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: 25.956 3.201 Wilson plot Bfac: 56.52 2850 reflections ( 95.57 % complete ) and 0 restraints for refining 1773 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2979 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2421 (Rfree = 0.000) for 1773 atoms. Found 13 (15 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.45 Search for helices and strands: 0 residues in 0 chains, 1796 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.295 Round 2: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.381 Round 3: 100 peptides, 17 chains. Longest chain 10 peptides. Score 0.455 Round 4: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.488 Round 5: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.520 Taking the results from Round 5 Chains 18, Residues 95, Estimated correctness of the model 17.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3189 restraints for refining 1468 atoms. 2807 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2020 (Rfree = 0.000) for 1468 atoms. Found 8 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.1828 (Rfree = 0.000) for 1438 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.1754 (Rfree = 0.000) for 1424 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.1667 (Rfree = 0.000) for 1421 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.1635 (Rfree = 0.000) for 1411 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.49 Search for helices and strands: 0 residues in 0 chains, 1460 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.374 Round 2: 105 peptides, 16 chains. Longest chain 17 peptides. Score 0.525 Round 3: 103 peptides, 16 chains. Longest chain 12 peptides. Score 0.510 Round 4: 95 peptides, 13 chains. Longest chain 16 peptides. Score 0.547 Round 5: 107 peptides, 17 chains. Longest chain 14 peptides. Score 0.508 Taking the results from Round 4 Chains 14, Residues 82, Estimated correctness of the model 25.9 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3178 restraints for refining 1435 atoms. 2804 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1986 (Rfree = 0.000) for 1435 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 7: After refmac, R = 0.1944 (Rfree = 0.000) for 1432 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.1831 (Rfree = 0.000) for 1432 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.1750 (Rfree = 0.000) for 1426 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.1620 (Rfree = 0.000) for 1426 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.46 Search for helices and strands: 0 residues in 0 chains, 1461 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 11 peptides. Score 0.348 Round 2: 104 peptides, 14 chains. Longest chain 16 peptides. Score 0.578 Round 3: 94 peptides, 14 chains. Longest chain 17 peptides. Score 0.508 Round 4: 106 peptides, 15 chains. Longest chain 26 peptides. Score 0.562 Round 5: 104 peptides, 15 chains. Longest chain 13 peptides. Score 0.548 Taking the results from Round 2 Chains 15, Residues 90, Estimated correctness of the model 34.9 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3108 restraints for refining 1441 atoms. 2664 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1865 (Rfree = 0.000) for 1441 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 12: After refmac, R = 0.1740 (Rfree = 0.000) for 1436 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2221 (Rfree = 0.000) for 1430 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 14: After refmac, R = 0.1878 (Rfree = 0.000) for 1427 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.1701 (Rfree = 0.000) for 1424 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.49 Search for helices and strands: 0 residues in 0 chains, 1464 seeds are put forward Round 1: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.475 Round 2: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.486 Round 3: 111 peptides, 16 chains. Longest chain 18 peptides. Score 0.566 Round 4: 117 peptides, 17 chains. Longest chain 18 peptides. Score 0.577 Round 5: 111 peptides, 16 chains. Longest chain 18 peptides. Score 0.566 Taking the results from Round 4 Chains 17, Residues 100, Estimated correctness of the model 34.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3180 restraints for refining 1420 atoms. 2797 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1948 (Rfree = 0.000) for 1420 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.1670 (Rfree = 0.000) for 1418 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.2041 (Rfree = 0.000) for 1414 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.1563 (Rfree = 0.000) for 1415 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1573 (Rfree = 0.000) for 1412 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.51 Search for helices and strands: 0 residues in 0 chains, 1462 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.338 Round 2: 97 peptides, 13 chains. Longest chain 20 peptides. Score 0.561 Round 3: 109 peptides, 14 chains. Longest chain 18 peptides. Score 0.610 Round 4: 108 peptides, 16 chains. Longest chain 16 peptides. Score 0.546 Round 5: 110 peptides, 14 chains. Longest chain 18 peptides. Score 0.616 Taking the results from Round 5 Chains 14, Residues 96, Estimated correctness of the model 45.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3276 restraints for refining 1415 atoms. 2906 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1831 (Rfree = 0.000) for 1415 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.1638 (Rfree = 0.000) for 1415 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.1531 (Rfree = 0.000) for 1411 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1509 (Rfree = 0.000) for 1406 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1477 (Rfree = 0.000) for 1400 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.54 Search for helices and strands: 0 residues in 0 chains, 1437 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.327 Round 2: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.431 Round 3: 106 peptides, 17 chains. Longest chain 15 peptides. Score 0.500 Round 4: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.475 Round 5: 101 peptides, 17 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 3 Chains 17, Residues 89, Estimated correctness of the model 11.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3296 restraints for refining 1418 atoms. 2957 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1814 (Rfree = 0.000) for 1418 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 27: After refmac, R = 0.1686 (Rfree = 0.000) for 1416 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1663 (Rfree = 0.000) for 1412 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1621 (Rfree = 0.000) for 1411 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1601 (Rfree = 0.000) for 1404 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.51 Search for helices and strands: 0 residues in 0 chains, 1433 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 10 peptides. Score 0.287 Round 2: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.460 Round 3: 109 peptides, 18 chains. Longest chain 15 peptides. Score 0.491 Round 4: 100 peptides, 17 chains. Longest chain 14 peptides. Score 0.455 Round 5: 105 peptides, 17 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 5 Chains 17, Residues 88, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3287 restraints for refining 1414 atoms. 2952 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1817 (Rfree = 0.000) for 1414 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.1785 (Rfree = 0.000) for 1412 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.1685 (Rfree = 0.000) for 1413 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.1569 (Rfree = 0.000) for 1408 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1541 (Rfree = 0.000) for 1406 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.52 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.330 Round 2: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.379 Round 3: 90 peptides, 16 chains. Longest chain 15 peptides. Score 0.408 Round 4: 89 peptides, 14 chains. Longest chain 15 peptides. Score 0.470 Round 5: 93 peptides, 14 chains. Longest chain 15 peptides. Score 0.501 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 11.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3270 restraints for refining 1409 atoms. 2968 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1752 (Rfree = 0.000) for 1409 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.1645 (Rfree = 0.000) for 1409 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1552 (Rfree = 0.000) for 1409 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.1403 (Rfree = 0.000) for 1404 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1412 (Rfree = 0.000) for 1400 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.47 Search for helices and strands: 0 residues in 0 chains, 1440 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 11 peptides. Score 0.295 Round 2: 84 peptides, 15 chains. Longest chain 15 peptides. Score 0.394 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.408 Round 4: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.376 Round 5: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.366 Taking the results from Round 3 Chains 16, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2850 reflections ( 95.57 % complete ) and 3342 restraints for refining 1426 atoms. 3062 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1575 (Rfree = 0.000) for 1426 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1549 (Rfree = 0.000) for 1422 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1575 (Rfree = 0.000) for 1419 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1311 (Rfree = 0.000) for 1423 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1369 (Rfree = 0.000) for 1419 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 3.46 Search for helices and strands: 0 residues in 0 chains, 1470 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.275 Round 2: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.321 Round 3: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.379 Round 4: 77 peptides, 13 chains. Longest chain 12 peptides. Score 0.407 Round 5: 76 peptides, 13 chains. Longest chain 13 peptides. Score 0.399 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 64, 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 2pc1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2850 reflections ( 95.57 % complete ) and 3431 restraints for refining 1421 atoms. 3188 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1569 (Rfree = 0.000) for 1421 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1596 (Rfree = 0.000) for 1414 atoms. Found 0 (12 requested) and removed 5 (6 requested) atoms. Cycle 48: After refmac, R = 0.1398 (Rfree = 0.000) for 1407 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1747 (Rfree = 0.000) for 1400 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:53 GMT 2018 Job finished. TimeTaking 28.17 Used memory is bytes: 3217296