null Tue 25 Dec 19:27:55 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 1vk2-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-2.1-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/1vk2-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-2.1-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 ============================================================ Tue 25 Dec 19:28:05 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/1vk2-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-2.1-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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.5432 Checking the provided sequence file Detected sequence length: 204 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 204 Adjusted target solvent content: 0.54 Input MTZ file: 1vk2-2.1-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: 96 Cell parameters: 61.120 61.120 127.494 90.000 90.000 90.000 Input sequence file: 1vk2-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 1632 target number of atoms Had to go as low as 0.50 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 1 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: 55.114 2.100 Wilson plot Bfac: 33.18 14709 reflections ( 99.45 % complete ) and 0 restraints for refining 1798 atoms. Observations/parameters ratio is 2.05 ------------------------------------------------------ Starting model: R = 0.3459 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2959 (Rfree = 0.000) for 1798 atoms. Found 41 (53 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.44 2.31 Round 1: 144 peptides, 16 chains. Longest chain 18 peptides. Score 0.672 Round 2: 161 peptides, 11 chains. Longest chain 42 peptides. Score 0.811 Round 3: 177 peptides, 7 chains. Longest chain 43 peptides. Score 0.889 Round 4: 176 peptides, 8 chains. Longest chain 68 peptides. Score 0.878 Round 5: 177 peptides, 7 chains. Longest chain 56 peptides. Score 0.889 Taking the results from Round 5 Chains 8, Residues 170, Estimated correctness of the model 98.5 % 4 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 84 A Built loop between residues 184 A and 187 A 5 chains (178 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1965 restraints for refining 1688 atoms. 644 conditional restraints added. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3264 (Rfree = 0.000) for 1688 atoms. Found 44 (50 requested) and removed 27 (25 requested) atoms. Cycle 2: After refmac, R = 0.2998 (Rfree = 0.000) for 1687 atoms. Found 39 (49 requested) and removed 25 (25 requested) atoms. Cycle 3: After refmac, R = 0.2792 (Rfree = 0.000) for 1688 atoms. Found 32 (48 requested) and removed 25 (25 requested) atoms. Cycle 4: After refmac, R = 0.2677 (Rfree = 0.000) for 1686 atoms. Found 22 (47 requested) and removed 25 (25 requested) atoms. Cycle 5: After refmac, R = 0.2601 (Rfree = 0.000) for 1671 atoms. Found 32 (46 requested) and removed 24 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.30 2.18 Round 1: 181 peptides, 4 chains. Longest chain 98 peptides. Score 0.921 Round 2: 179 peptides, 4 chains. Longest chain 84 peptides. Score 0.919 Round 3: 183 peptides, 5 chains. Longest chain 80 peptides. Score 0.915 Round 4: 183 peptides, 4 chains. Longest chain 72 peptides. Score 0.924 Round 5: 178 peptides, 7 chains. Longest chain 48 peptides. Score 0.891 Taking the results from Round 4 Chains 5, Residues 179, Estimated correctness of the model 99.3 % 3 chains (165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 41 A Built loop between residues 110 A and 117 A 3 chains (187 residues) following loop building 1 chains (173 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1701 restraints for refining 1649 atoms. 272 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2680 (Rfree = 0.000) for 1649 atoms. Found 36 (44 requested) and removed 25 (24 requested) atoms. Cycle 7: After refmac, R = 0.2437 (Rfree = 0.000) for 1649 atoms. Found 30 (43 requested) and removed 24 (24 requested) atoms. Cycle 8: After refmac, R = 0.2308 (Rfree = 0.000) for 1650 atoms. Found 28 (42 requested) and removed 11 (24 requested) atoms. Cycle 9: After refmac, R = 0.2219 (Rfree = 0.000) for 1665 atoms. Found 21 (42 requested) and removed 9 (24 requested) atoms. Cycle 10: After refmac, R = 0.2157 (Rfree = 0.000) for 1669 atoms. Found 29 (42 requested) and removed 13 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.27 2.15 Round 1: 188 peptides, 3 chains. Longest chain 105 peptides. Score 0.936 Round 2: 186 peptides, 4 chains. Longest chain 84 peptides. Score 0.927 Round 3: 186 peptides, 3 chains. Longest chain 83 peptides. Score 0.934 Round 4: 186 peptides, 3 chains. Longest chain 90 peptides. Score 0.934 Round 5: 183 peptides, 5 chains. Longest chain 68 peptides. Score 0.915 Taking the results from Round 1 Chains 3, Residues 185, Estimated correctness of the model 99.5 % 2 chains (182 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 120 A 2 chains (187 residues) following loop building 1 chains (184 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1647 restraints for refining 1673 atoms. 168 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2357 (Rfree = 0.000) for 1673 atoms. Found 29 (42 requested) and removed 24 (24 requested) atoms. Cycle 12: After refmac, R = 0.2198 (Rfree = 0.000) for 1676 atoms. Found 21 (42 requested) and removed 25 (25 requested) atoms. Cycle 13: After refmac, R = 0.2105 (Rfree = 0.000) for 1670 atoms. Found 33 (40 requested) and removed 21 (24 requested) atoms. Cycle 14: After refmac, R = 0.2067 (Rfree = 0.000) for 1681 atoms. Found 28 (40 requested) and removed 23 (25 requested) atoms. Cycle 15: After refmac, R = 0.2032 (Rfree = 0.000) for 1684 atoms. Found 26 (39 requested) and removed 18 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.28 2.16 Round 1: 188 peptides, 3 chains. Longest chain 105 peptides. Score 0.936 Round 2: 186 peptides, 4 chains. Longest chain 74 peptides. Score 0.927 Round 3: 181 peptides, 5 chains. Longest chain 70 peptides. Score 0.913 Round 4: 189 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 5: 185 peptides, 4 chains. Longest chain 98 peptides. Score 0.926 Taking the results from Round 4 Chains 2, Residues 187, Estimated correctness of the model 99.6 % 2 chains (187 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 86 A 1 chains (190 residues) following loop building 1 chains (190 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1628 restraints for refining 1679 atoms. 107 conditional restraints added. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2307 (Rfree = 0.000) for 1679 atoms. Found 38 (38 requested) and removed 26 (25 requested) atoms. Cycle 17: After refmac, R = 0.2127 (Rfree = 0.000) for 1686 atoms. Found 21 (37 requested) and removed 26 (25 requested) atoms. Cycle 18: After refmac, R = 0.2029 (Rfree = 0.000) for 1680 atoms. Found 30 (36 requested) and removed 26 (25 requested) atoms. Cycle 19: After refmac, R = 0.2001 (Rfree = 0.000) for 1681 atoms. Found 28 (35 requested) and removed 25 (25 requested) atoms. Cycle 20: After refmac, R = 0.1985 (Rfree = 0.000) for 1684 atoms. Found 18 (34 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.26 2.14 Round 1: 187 peptides, 3 chains. Longest chain 105 peptides. Score 0.935 Round 2: 184 peptides, 4 chains. Longest chain 85 peptides. Score 0.925 Round 3: 184 peptides, 4 chains. Longest chain 105 peptides. Score 0.925 Round 4: 186 peptides, 3 chains. Longest chain 98 peptides. Score 0.934 Round 5: 184 peptides, 3 chains. Longest chain 83 peptides. Score 0.932 Taking the results from Round 1 Chains 3, Residues 184, Estimated correctness of the model 99.4 % 3 chains (184 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 120 A Built loop between residues 162 A and 165 A 1 chains (188 residues) following loop building 1 chains (188 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1610 restraints for refining 1659 atoms. 107 conditional restraints added. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2240 (Rfree = 0.000) for 1659 atoms. Found 32 (32 requested) and removed 25 (24 requested) atoms. Cycle 22: After refmac, R = 0.2066 (Rfree = 0.000) for 1665 atoms. Found 22 (31 requested) and removed 24 (24 requested) atoms. Cycle 23: After refmac, R = 0.2035 (Rfree = 0.000) for 1663 atoms. Found 29 (30 requested) and removed 21 (24 requested) atoms. Cycle 24: After refmac, R = 0.1983 (Rfree = 0.000) for 1670 atoms. Found 29 (29 requested) and removed 24 (24 requested) atoms. Cycle 25: After refmac, R = 0.1974 (Rfree = 0.000) for 1675 atoms. Found 27 (28 requested) and removed 23 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.27 2.15 Round 1: 185 peptides, 3 chains. Longest chain 83 peptides. Score 0.933 Round 2: 185 peptides, 5 chains. Longest chain 72 peptides. Score 0.918 Round 3: 188 peptides, 3 chains. Longest chain 171 peptides. Score 0.936 Round 4: 185 peptides, 6 chains. Longest chain 56 peptides. Score 0.910 Round 5: 188 peptides, 3 chains. Longest chain 71 peptides. Score 0.936 Taking the results from Round 5 Chains 3, Residues 185, Estimated correctness of the model 99.5 % 3 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A Built loop between residues 151 A and 154 A 1 chains (189 residues) following loop building 1 chains (189 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1608 restraints for refining 1657 atoms. 96 conditional restraints added. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2332 (Rfree = 0.000) for 1657 atoms. Found 27 (27 requested) and removed 25 (24 requested) atoms. Cycle 27: After refmac, R = 0.2139 (Rfree = 0.000) for 1658 atoms. Found 26 (26 requested) and removed 24 (24 requested) atoms. Cycle 28: After refmac, R = 0.2039 (Rfree = 0.000) for 1659 atoms. Found 25 (25 requested) and removed 20 (24 requested) atoms. Cycle 29: After refmac, R = 0.2007 (Rfree = 0.000) for 1663 atoms. Found 24 (24 requested) and removed 18 (24 requested) atoms. Cycle 30: After refmac, R = 0.1989 (Rfree = 0.000) for 1668 atoms. Found 22 (24 requested) and removed 22 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.27 2.15 Round 1: 185 peptides, 5 chains. Longest chain 70 peptides. Score 0.918 Round 2: 186 peptides, 4 chains. Longest chain 98 peptides. Score 0.927 Round 3: 186 peptides, 3 chains. Longest chain 90 peptides. Score 0.934 Round 4: 180 peptides, 6 chains. Longest chain 65 peptides. Score 0.903 Round 5: 187 peptides, 4 chains. Longest chain 106 peptides. Score 0.928 Taking the results from Round 3 Chains 4, Residues 183, Estimated correctness of the model 99.4 % 3 chains (182 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 117 A and 120 A 2 chains (187 residues) following loop building 2 chains (187 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1604 restraints for refining 1639 atoms. 120 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2246 (Rfree = 0.000) for 1639 atoms. Found 24 (24 requested) and removed 26 (24 requested) atoms. Cycle 32: After refmac, R = 0.2079 (Rfree = 0.000) for 1637 atoms. Found 22 (24 requested) and removed 12 (24 requested) atoms. Cycle 33: After refmac, R = 0.1992 (Rfree = 0.000) for 1647 atoms. Found 16 (24 requested) and removed 15 (24 requested) atoms. Cycle 34: After refmac, R = 0.1959 (Rfree = 0.000) for 1647 atoms. Found 20 (24 requested) and removed 14 (24 requested) atoms. Cycle 35: After refmac, R = 0.1944 (Rfree = 0.000) for 1651 atoms. Found 23 (24 requested) and removed 13 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.27 2.15 Round 1: 185 peptides, 5 chains. Longest chain 70 peptides. Score 0.918 Round 2: 187 peptides, 3 chains. Longest chain 130 peptides. Score 0.935 Round 3: 183 peptides, 5 chains. Longest chain 83 peptides. Score 0.915 Round 4: 188 peptides, 2 chains. Longest chain 175 peptides. Score 0.943 Round 5: 183 peptides, 6 chains. Longest chain 78 peptides. Score 0.907 Taking the results from Round 4 Chains 2, Residues 186, Estimated correctness of the model 99.6 % 2 chains (186 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 A and 190 A 1 chains (188 residues) following loop building 1 chains (188 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1613 restraints for refining 1653 atoms. 110 conditional restraints added. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2223 (Rfree = 0.000) for 1653 atoms. Found 24 (24 requested) and removed 26 (24 requested) atoms. Cycle 37: After refmac, R = 0.2059 (Rfree = 0.000) for 1649 atoms. Found 24 (24 requested) and removed 22 (24 requested) atoms. Cycle 38: After refmac, R = 0.1976 (Rfree = 0.000) for 1651 atoms. Found 24 (24 requested) and removed 15 (24 requested) atoms. Cycle 39: After refmac, R = 0.1941 (Rfree = 0.000) for 1660 atoms. Found 24 (24 requested) and removed 14 (24 requested) atoms. Cycle 40: After refmac, R = 0.1913 (Rfree = 0.000) for 1670 atoms. Found 24 (24 requested) and removed 17 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.26 2.14 Round 1: 183 peptides, 3 chains. Longest chain 104 peptides. Score 0.931 Round 2: 185 peptides, 4 chains. Longest chain 111 peptides. Score 0.926 Round 3: 186 peptides, 4 chains. Longest chain 98 peptides. Score 0.927 Round 4: 186 peptides, 3 chains. Longest chain 117 peptides. Score 0.934 Round 5: 187 peptides, 3 chains. Longest chain 98 peptides. Score 0.935 Taking the results from Round 5 Chains 3, Residues 184, Estimated correctness of the model 99.4 % 2 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 110 A and 113 A 2 chains (186 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ 14709 reflections ( 99.45 % complete ) and 1670 restraints for refining 1639 atoms. 206 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2256 (Rfree = 0.000) for 1639 atoms. Found 24 (24 requested) and removed 26 (24 requested) atoms. Cycle 42: After refmac, R = 0.2089 (Rfree = 0.000) for 1636 atoms. Found 24 (24 requested) and removed 21 (24 requested) atoms. Cycle 43: After refmac, R = 0.2029 (Rfree = 0.000) for 1639 atoms. Found 24 (24 requested) and removed 20 (24 requested) atoms. Cycle 44: After refmac, R = 0.1995 (Rfree = 0.000) for 1643 atoms. Found 23 (24 requested) and removed 19 (24 requested) atoms. Cycle 45: After refmac, R = 0.1972 (Rfree = 0.000) for 1647 atoms. Found 24 (24 requested) and removed 18 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.28 2.16 Round 1: 185 peptides, 5 chains. Longest chain 77 peptides. Score 0.918 Round 2: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.951 Round 3: 183 peptides, 7 chains. Longest chain 70 peptides. Score 0.898 Round 4: 185 peptides, 5 chains. Longest chain 81 peptides. Score 0.918 Round 5: 181 peptides, 6 chains. Longest chain 67 peptides. Score 0.904 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 188, Estimated correctness of the model 99.7 % 1 chains (188 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14709 reflections ( 99.45 % complete ) and 1503 restraints for refining 1478 atoms. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2844 (Rfree = 0.000) for 1478 atoms. Found 15 (22 requested) and removed 0 (22 requested) atoms. Cycle 47: After refmac, R = 0.2645 (Rfree = 0.000) for 1478 atoms. Found 5 (22 requested) and removed 0 (22 requested) atoms. Cycle 48: After refmac, R = 0.2504 (Rfree = 0.000) for 1478 atoms. Found 13 (22 requested) and removed 1 (22 requested) atoms. Cycle 49: After refmac, R = 0.2352 (Rfree = 0.000) for 1478 atoms. Found 6 (22 requested) and removed 3 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:10:41 GMT 2018 Job finished. TimeTaking 42.76 Used memory is bytes: 17322576