null 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 2hcf-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-3.8-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/2hcf-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-3.8-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 22:23:08 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/2hcf-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-3.8-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 145 and 0 Target number of residues in the AU: 145 Target solvent content: 0.6510 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.44 Input MTZ file: 2hcf-3.8-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: 37.750 71.590 83.200 90.000 90.000 90.000 Input sequence file: 2hcf-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 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: 54.266 3.801 Wilson plot Bfac: 78.12 2425 reflections ( 99.22 % complete ) and 0 restraints for refining 2066 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3455 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 54 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.305 Round 2: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.327 Round 3: 97 peptides, 14 chains. Longest chain 15 peptides. Score 0.486 Round 4: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.420 Round 5: 107 peptides, 16 chains. Longest chain 18 peptides. Score 0.493 Taking the results from Round 5 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3986 restraints for refining 1692 atoms. 3620 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2560 (Rfree = 0.000) for 1692 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 2: After refmac, R = 0.2361 (Rfree = 0.000) for 1655 atoms. Found 8 (9 requested) and removed 22 (4 requested) atoms. Cycle 3: After refmac, R = 0.2383 (Rfree = 0.000) for 1620 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 4: After refmac, R = 0.1968 (Rfree = 0.000) for 1608 atoms. Found 4 (8 requested) and removed 14 (4 requested) atoms. Cycle 5: After refmac, R = 0.1831 (Rfree = 0.000) for 1590 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.79 Search for helices and strands: 0 residues in 0 chains, 1660 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.323 Round 2: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.432 Round 3: 110 peptides, 18 chains. Longest chain 10 peptides. Score 0.456 Round 4: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.450 Round 5: 122 peptides, 18 chains. Longest chain 12 peptides. Score 0.532 Taking the results from Round 5 Chains 18, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3493 restraints for refining 1548 atoms. 3095 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2204 (Rfree = 0.000) for 1548 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2082 (Rfree = 0.000) for 1533 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 8: After refmac, R = 0.1994 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 9: After refmac, R = 0.1606 (Rfree = 0.000) for 1522 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1635 (Rfree = 0.000) for 1515 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.79 Search for helices and strands: 0 residues in 0 chains, 1597 seeds are put forward Round 1: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.414 Round 2: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.474 Round 3: 127 peptides, 18 chains. Longest chain 13 peptides. Score 0.561 Round 4: 128 peptides, 18 chains. Longest chain 13 peptides. Score 0.566 Round 5: 124 peptides, 14 chains. Longest chain 15 peptides. Score 0.640 Taking the results from Round 5 Chains 14, Residues 110, Estimated correctness of the model 16.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3779 restraints for refining 1633 atoms. 3353 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2099 (Rfree = 0.000) for 1633 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.1869 (Rfree = 0.000) for 1623 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 13: After refmac, R = 0.1993 (Rfree = 0.000) for 1611 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2074 (Rfree = 0.000) for 1608 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.2226 (Rfree = 0.000) for 1603 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 1669 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.305 Round 2: 108 peptides, 20 chains. Longest chain 8 peptides. Score 0.384 Round 3: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.420 Round 4: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.414 Round 5: 99 peptides, 17 chains. Longest chain 9 peptides. Score 0.411 Taking the results from Round 3 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3835 restraints for refining 1634 atoms. 3531 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1998 (Rfree = 0.000) for 1634 atoms. Found 1 (8 requested) and removed 22 (4 requested) atoms. Cycle 17: After refmac, R = 0.2019 (Rfree = 0.000) for 1606 atoms. Found 6 (8 requested) and removed 16 (4 requested) atoms. Cycle 18: After refmac, R = 0.1516 (Rfree = 0.000) for 1591 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.1589 (Rfree = 0.000) for 1583 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.1522 (Rfree = 0.000) for 1576 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 1635 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.246 Round 2: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.303 Round 3: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.350 Round 4: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.383 Round 5: 86 peptides, 15 chains. Longest chain 8 peptides. Score 0.380 Taking the results from Round 4 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3915 restraints for refining 1663 atoms. 3620 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1991 (Rfree = 0.000) for 1663 atoms. Found 3 (9 requested) and removed 19 (4 requested) atoms. Cycle 22: After refmac, R = 0.2238 (Rfree = 0.000) for 1640 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.2051 (Rfree = 0.000) for 1629 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2067 (Rfree = 0.000) for 1618 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1995 (Rfree = 0.000) for 1611 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 1679 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.235 Round 2: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.380 Round 3: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.443 Round 4: 101 peptides, 18 chains. Longest chain 13 peptides. Score 0.395 Round 5: 90 peptides, 14 chains. Longest chain 13 peptides. Score 0.439 Taking the results from Round 3 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3636 restraints for refining 1657 atoms. 3281 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.1978 (Rfree = 0.000) for 1639 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2025 (Rfree = 0.000) for 1631 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 1620 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2061 (Rfree = 0.000) for 1609 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 1672 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 10 peptides. Score 0.290 Round 2: 86 peptides, 14 chains. Longest chain 11 peptides. Score 0.411 Round 3: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.365 Round 4: 85 peptides, 13 chains. Longest chain 15 peptides. Score 0.435 Round 5: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 4 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3690 restraints for refining 1643 atoms. 3386 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1973 (Rfree = 0.000) for 1643 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.1710 (Rfree = 0.000) for 1634 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.1704 (Rfree = 0.000) for 1629 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.1746 (Rfree = 0.000) for 1627 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.1622 (Rfree = 0.000) for 1628 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.90 Search for helices and strands: 0 residues in 0 chains, 1657 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.299 Round 2: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.397 Round 3: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.350 Round 4: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.399 Round 5: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 4 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3944 restraints for refining 1686 atoms. 3666 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1836 (Rfree = 0.000) for 1686 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 37: After refmac, R = 0.2004 (Rfree = 0.000) for 1672 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 38: After refmac, R = 0.2157 (Rfree = 0.000) for 1666 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 39: After refmac, R = 0.2024 (Rfree = 0.000) for 1647 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.2268 (Rfree = 0.000) for 1638 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.89 Search for helices and strands: 0 residues in 0 chains, 1684 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.268 Round 2: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.327 Round 3: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.342 Round 4: 72 peptides, 14 chains. Longest chain 6 peptides. Score 0.305 Round 5: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.283 Taking the results from Round 3 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2425 reflections ( 99.22 % complete ) and 3697 restraints for refining 1586 atoms. 3485 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2024 (Rfree = 0.000) for 1586 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.2128 (Rfree = 0.000) for 1572 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.1991 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1826 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 1620 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.223 Round 2: 66 peptides, 14 chains. Longest chain 6 peptides. Score 0.256 Round 3: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.264 Round 4: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.310 Round 5: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.249 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 52, 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 2hcf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2425 reflections ( 99.22 % complete ) and 3420 restraints for refining 1532 atoms. 3224 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2155 (Rfree = 0.000) for 1532 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1976 (Rfree = 0.000) for 1519 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1990 (Rfree = 0.000) for 1512 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1941 (Rfree = 0.000) for 1505 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:43 GMT 2018 Job finished. TimeTaking 28.74 Used memory is bytes: -769064