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 2hcf-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-3.4-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/2hcf-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-3.4-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 154 and 0 Target number of residues in the AU: 154 Target solvent content: 0.6293 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 65.22 3355 reflections ( 99.38 % complete ) and 0 restraints for refining 2084 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3358 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2927 (Rfree = 0.000) for 2084 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2132 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.327 Round 2: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.499 Round 3: 127 peptides, 17 chains. Longest chain 34 peptides. Score 0.585 Round 4: 122 peptides, 17 chains. Longest chain 13 peptides. Score 0.557 Round 5: 130 peptides, 18 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 3 Chains 17, Residues 110, Estimated correctness of the model 23.6 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 3657 restraints for refining 1702 atoms. 3096 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2640 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 2: After refmac, R = 0.2398 (Rfree = 0.000) for 1652 atoms. Found 7 (12 requested) and removed 18 (6 requested) atoms. Cycle 3: After refmac, R = 0.2375 (Rfree = 0.000) for 1633 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.2191 (Rfree = 0.000) for 1626 atoms. Found 6 (12 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.2785 (Rfree = 0.000) for 1616 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 1700 seeds are put forward Round 1: 126 peptides, 24 chains. Longest chain 12 peptides. Score 0.393 Round 2: 123 peptides, 19 chains. Longest chain 17 peptides. Score 0.511 Round 3: 128 peptides, 20 chains. Longest chain 18 peptides. Score 0.515 Round 4: 132 peptides, 21 chains. Longest chain 15 peptides. Score 0.514 Round 5: 127 peptides, 18 chains. Longest chain 20 peptides. Score 0.561 Taking the results from Round 5 Chains 19, Residues 109, Estimated correctness of the model 15.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 3650 restraints for refining 1702 atoms. 3164 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2338 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.2186 (Rfree = 0.000) for 1682 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2152 (Rfree = 0.000) for 1681 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2037 (Rfree = 0.000) for 1680 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.1899 (Rfree = 0.000) for 1680 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 1751 seeds are put forward Round 1: 112 peptides, 20 chains. Longest chain 15 peptides. Score 0.412 Round 2: 108 peptides, 19 chains. Longest chain 9 peptides. Score 0.414 Round 3: 124 peptides, 20 chains. Longest chain 13 peptides. Score 0.491 Round 4: 123 peptides, 21 chains. Longest chain 13 peptides. Score 0.457 Round 5: 121 peptides, 20 chains. Longest chain 10 peptides. Score 0.472 Taking the results from Round 3 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 3715 restraints for refining 1701 atoms. 3277 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2071 (Rfree = 0.000) for 1701 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.1864 (Rfree = 0.000) for 1696 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.1817 (Rfree = 0.000) for 1685 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1849 (Rfree = 0.000) for 1683 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.1760 (Rfree = 0.000) for 1682 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 1763 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 9 peptides. Score 0.258 Round 2: 101 peptides, 17 chains. Longest chain 13 peptides. Score 0.425 Round 3: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.436 Round 4: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.409 Round 5: 111 peptides, 20 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 3 Chains 18, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 3926 restraints for refining 1702 atoms. 3588 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1921 (Rfree = 0.000) for 1702 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 17: After refmac, R = 0.1833 (Rfree = 0.000) for 1703 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1760 (Rfree = 0.000) for 1698 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1795 (Rfree = 0.000) for 1695 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1734 (Rfree = 0.000) for 1691 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 1767 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 7 peptides. Score 0.248 Round 2: 103 peptides, 20 chains. Longest chain 10 peptides. Score 0.348 Round 3: 101 peptides, 19 chains. Longest chain 11 peptides. Score 0.364 Round 4: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.351 Round 5: 99 peptides, 18 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 5 Chains 18, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 4022 restraints for refining 1702 atoms. 3716 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2026 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.1914 (Rfree = 0.000) for 1701 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2019 (Rfree = 0.000) for 1699 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2008 (Rfree = 0.000) for 1700 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1932 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 1789 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 9 peptides. Score 0.277 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.387 Round 3: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.394 Round 4: 88 peptides, 14 chains. Longest chain 14 peptides. Score 0.425 Round 5: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 4 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 4043 restraints for refining 1702 atoms. 3761 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2131 (Rfree = 0.000) for 1702 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.1935 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.1759 (Rfree = 0.000) for 1704 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1640 (Rfree = 0.000) for 1707 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1564 (Rfree = 0.000) for 1709 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 1774 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 2: 96 peptides, 17 chains. Longest chain 11 peptides. Score 0.390 Round 3: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.375 Round 4: 97 peptides, 17 chains. Longest chain 12 peptides. Score 0.397 Round 5: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 5 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 3895 restraints for refining 1702 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1963 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.1815 (Rfree = 0.000) for 1699 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.1879 (Rfree = 0.000) for 1699 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1764 (Rfree = 0.000) for 1703 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1808 (Rfree = 0.000) for 1699 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 1754 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.261 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.295 Round 3: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.352 Round 4: 87 peptides, 15 chains. Longest chain 17 peptides. Score 0.387 Round 5: 84 peptides, 14 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 4112 restraints for refining 1702 atoms. 3846 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2185 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2280 (Rfree = 0.000) for 1703 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2112 (Rfree = 0.000) for 1699 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2073 (Rfree = 0.000) for 1701 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2094 (Rfree = 0.000) for 1705 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 1761 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 8 peptides. Score 0.240 Round 2: 78 peptides, 15 chains. Longest chain 13 peptides. Score 0.319 Round 3: 82 peptides, 16 chains. Longest chain 7 peptides. Score 0.317 Round 4: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.260 Round 5: 81 peptides, 17 chains. Longest chain 9 peptides. Score 0.276 Taking the results from Round 2 Chains 15, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 99.38 % complete ) and 4150 restraints for refining 1702 atoms. 3913 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2095 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2155 (Rfree = 0.000) for 1704 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 1704 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.2169 (Rfree = 0.000) for 1704 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.1960 (Rfree = 0.000) for 1706 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.58 Search for helices and strands: 0 residues in 0 chains, 1765 seeds are put forward Round 1: 67 peptides, 16 chains. Longest chain 6 peptides. Score 0.193 Round 2: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.252 Round 3: 74 peptides, 16 chains. Longest chain 9 peptides. Score 0.253 Round 4: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.329 Round 5: 67 peptides, 14 chains. Longest chain 9 peptides. Score 0.264 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 61, 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. 3355 reflections ( 99.38 % complete ) and 4049 restraints for refining 1702 atoms. 3819 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2032 (Rfree = 0.000) for 1702 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2128 (Rfree = 0.000) for 1689 atoms. Found 0 (12 requested) and removed 4 (6 requested) atoms. Cycle 48: After refmac, R = 0.1996 (Rfree = 0.000) for 1684 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2052 (Rfree = 0.000) for 1677 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:36 GMT 2018 Job finished. TimeTaking 29.88 Used memory is bytes: 15728656