null Sun 23 Dec 22:23:01 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 2a6b-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-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/2a6b-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-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 22:23:11 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/2a6b-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-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 262 and 0 Target number of residues in the AU: 262 Target solvent content: 0.5688 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: 0.61 Input MTZ file: 2a6b-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: 90 Cell parameters: 119.176 119.176 46.302 90.000 90.000 90.000 Input sequence file: 2a6b-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.80 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: 29.794 3.200 Wilson plot Bfac: 41.02 5858 reflections ( 99.36 % complete ) and 0 restraints for refining 2060 atoms. Observations/parameters ratio is 0.71 ------------------------------------------------------ Starting model: R = 0.3041 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2242 (Rfree = 0.000) for 2060 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.86 2.46 Search for helices and strands: 0 residues in 0 chains, 2113 seeds are put forward Round 1: 151 peptides, 26 chains. Longest chain 13 peptides. Score 0.417 Round 2: 154 peptides, 21 chains. Longest chain 13 peptides. Score 0.528 Round 3: 170 peptides, 18 chains. Longest chain 19 peptides. Score 0.640 Round 4: 176 peptides, 21 chains. Longest chain 18 peptides. Score 0.612 Round 5: 175 peptides, 19 chains. Longest chain 20 peptides. Score 0.641 Taking the results from Round 5 Chains 19, Residues 156, Estimated correctness of the model 51.6 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 3000 restraints for refining 1729 atoms. 2179 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2621 (Rfree = 0.000) for 1729 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 2: After refmac, R = 0.2445 (Rfree = 0.000) for 1719 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2336 (Rfree = 0.000) for 1715 atoms. Found 11 (15 requested) and removed 7 (7 requested) atoms. Cycle 4: After refmac, R = 0.2242 (Rfree = 0.000) for 1712 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2207 (Rfree = 0.000) for 1707 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.84 2.45 Search for helices and strands: 0 residues in 0 chains, 1787 seeds are put forward Round 1: 158 peptides, 21 chains. Longest chain 15 peptides. Score 0.544 Round 2: 176 peptides, 20 chains. Longest chain 27 peptides. Score 0.628 Round 3: 181 peptides, 18 chains. Longest chain 31 peptides. Score 0.675 Round 4: 171 peptides, 20 chains. Longest chain 19 peptides. Score 0.611 Round 5: 180 peptides, 18 chains. Longest chain 21 peptides. Score 0.672 Taking the results from Round 3 Chains 20, Residues 163, Estimated correctness of the model 59.7 % 4 chains (77 residues) have been docked in sequence ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2784 restraints for refining 1709 atoms. 1814 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2617 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 7: After refmac, R = 0.2427 (Rfree = 0.000) for 1697 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 8: After refmac, R = 0.2300 (Rfree = 0.000) for 1699 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.2240 (Rfree = 0.000) for 1702 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2178 (Rfree = 0.000) for 1697 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.80 2.41 Search for helices and strands: 0 residues in 0 chains, 1779 seeds are put forward Round 1: 157 peptides, 18 chains. Longest chain 22 peptides. Score 0.593 Round 2: 169 peptides, 17 chains. Longest chain 36 peptides. Score 0.652 Round 3: 172 peptides, 19 chains. Longest chain 21 peptides. Score 0.631 Round 4: 166 peptides, 19 chains. Longest chain 23 peptides. Score 0.609 Round 5: 183 peptides, 15 chains. Longest chain 42 peptides. Score 0.723 Taking the results from Round 5 Chains 15, Residues 168, Estimated correctness of the model 69.9 % 3 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 57 A 13 chains (172 residues) following loop building 2 chains (93 residues) in sequence following loop building ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2515 restraints for refining 1709 atoms. 1429 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2566 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2362 (Rfree = 0.000) for 1709 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2285 (Rfree = 0.000) for 1707 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2247 (Rfree = 0.000) for 1704 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2139 (Rfree = 0.000) for 1705 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.83 2.44 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward Round 1: 177 peptides, 17 chains. Longest chain 39 peptides. Score 0.677 Round 2: 171 peptides, 14 chains. Longest chain 30 peptides. Score 0.703 Round 3: 177 peptides, 16 chains. Longest chain 33 peptides. Score 0.692 Round 4: 184 peptides, 17 chains. Longest chain 30 peptides. Score 0.698 Round 5: 177 peptides, 16 chains. Longest chain 24 peptides. Score 0.692 Taking the results from Round 2 Chains 15, Residues 157, Estimated correctness of the model 65.8 % 4 chains (83 residues) have been docked in sequence Building loops using Loopy2018 15 chains (157 residues) following loop building 4 chains (83 residues) in sequence following loop building ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2767 restraints for refining 1708 atoms. 1801 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2479 (Rfree = 0.000) for 1708 atoms. Found 13 (13 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.2320 (Rfree = 0.000) for 1707 atoms. Found 13 (13 requested) and removed 13 (7 requested) atoms. Cycle 18: After refmac, R = 0.2232 (Rfree = 0.000) for 1706 atoms. Found 7 (13 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2163 (Rfree = 0.000) for 1701 atoms. Found 6 (13 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2109 (Rfree = 0.000) for 1700 atoms. Found 3 (12 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.82 2.43 Search for helices and strands: 0 residues in 0 chains, 1767 seeds are put forward Round 1: 165 peptides, 17 chains. Longest chain 32 peptides. Score 0.638 Round 2: 165 peptides, 16 chains. Longest chain 27 peptides. Score 0.654 Round 3: 170 peptides, 18 chains. Longest chain 18 peptides. Score 0.640 Round 4: 184 peptides, 19 chains. Longest chain 21 peptides. Score 0.670 Round 5: 181 peptides, 17 chains. Longest chain 43 peptides. Score 0.690 Taking the results from Round 5 Chains 17, Residues 164, Estimated correctness of the model 63.0 % 1 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 3165 restraints for refining 1709 atoms. 2349 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2515 (Rfree = 0.000) for 1709 atoms. Found 12 (12 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.2236 (Rfree = 0.000) for 1705 atoms. Found 8 (12 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.2163 (Rfree = 0.000) for 1699 atoms. Found 7 (12 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.2083 (Rfree = 0.000) for 1698 atoms. Found 3 (12 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2065 (Rfree = 0.000) for 1690 atoms. Found 5 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.85 2.46 Search for helices and strands: 0 residues in 0 chains, 1741 seeds are put forward Round 1: 168 peptides, 19 chains. Longest chain 22 peptides. Score 0.617 Round 2: 178 peptides, 16 chains. Longest chain 28 peptides. Score 0.695 Round 3: 182 peptides, 14 chains. Longest chain 29 peptides. Score 0.733 Round 4: 177 peptides, 14 chains. Longest chain 34 peptides. Score 0.720 Round 5: 191 peptides, 11 chains. Longest chain 47 peptides. Score 0.791 Taking the results from Round 5 Chains 16, Residues 180, Estimated correctness of the model 82.0 % 5 chains (109 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 90 A Built loop between residues 142 A and 146 A 13 chains (184 residues) following loop building 3 chains (115 residues) in sequence following loop building ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2377 restraints for refining 1709 atoms. 1178 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2568 (Rfree = 0.000) for 1709 atoms. Found 12 (12 requested) and removed 23 (7 requested) atoms. Cycle 27: After refmac, R = 0.2264 (Rfree = 0.000) for 1691 atoms. Found 12 (12 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2154 (Rfree = 0.000) for 1692 atoms. Found 11 (11 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.2114 (Rfree = 0.000) for 1694 atoms. Found 6 (11 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.2060 (Rfree = 0.000) for 1689 atoms. Found 6 (11 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.85 2.46 Search for helices and strands: 0 residues in 0 chains, 1771 seeds are put forward Round 1: 183 peptides, 17 chains. Longest chain 27 peptides. Score 0.695 Round 2: 190 peptides, 14 chains. Longest chain 39 peptides. Score 0.754 Round 3: 188 peptides, 12 chains. Longest chain 37 peptides. Score 0.773 Round 4: 181 peptides, 15 chains. Longest chain 31 peptides. Score 0.717 Round 5: 189 peptides, 13 chains. Longest chain 54 peptides. Score 0.764 Taking the results from Round 3 Chains 13, Residues 176, Estimated correctness of the model 79.1 % 5 chains (127 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 169 A Built loop between residues 180 A and 184 A 10 chains (183 residues) following loop building 3 chains (135 residues) in sequence following loop building ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2268 restraints for refining 1729 atoms. 957 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2541 (Rfree = 0.000) for 1729 atoms. Found 10 (10 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.2276 (Rfree = 0.000) for 1715 atoms. Found 10 (10 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 1711 atoms. Found 10 (10 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.2074 (Rfree = 0.000) for 1710 atoms. Found 9 (10 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2071 (Rfree = 0.000) for 1709 atoms. Found 9 (9 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.83 2.44 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward Round 1: 180 peptides, 14 chains. Longest chain 38 peptides. Score 0.728 Round 2: 190 peptides, 13 chains. Longest chain 33 peptides. Score 0.766 Round 3: 185 peptides, 17 chains. Longest chain 22 peptides. Score 0.701 Round 4: 179 peptides, 14 chains. Longest chain 22 peptides. Score 0.725 Round 5: 183 peptides, 17 chains. Longest chain 23 peptides. Score 0.695 Taking the results from Round 2 Chains 16, Residues 177, Estimated correctness of the model 77.9 % 6 chains (131 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 63 A Built loop between residues 164 A and 170 A Built loop between residues 182 A and 191 A Built loop between residues 204 A and 210 A 7 chains (195 residues) following loop building 2 chains (158 residues) in sequence following loop building ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2197 restraints for refining 1790 atoms. 737 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2682 (Rfree = 0.000) for 1790 atoms. Found 10 (10 requested) and removed 26 (8 requested) atoms. Cycle 37: After refmac, R = 0.2406 (Rfree = 0.000) for 1763 atoms. Found 9 (9 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2288 (Rfree = 0.000) for 1752 atoms. Found 8 (8 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.2188 (Rfree = 0.000) for 1745 atoms. Found 8 (8 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.2089 (Rfree = 0.000) for 1743 atoms. Found 7 (8 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.83 2.44 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward Round 1: 192 peptides, 17 chains. Longest chain 43 peptides. Score 0.721 Round 2: 201 peptides, 14 chains. Longest chain 27 peptides. Score 0.779 Round 3: 191 peptides, 12 chains. Longest chain 43 peptides. Score 0.780 Round 4: 184 peptides, 15 chains. Longest chain 31 peptides. Score 0.726 Round 5: 183 peptides, 14 chains. Longest chain 28 peptides. Score 0.736 Taking the results from Round 3 Chains 13, Residues 179, Estimated correctness of the model 80.3 % 5 chains (130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 45 A Built loop between residues 55 A and 62 A 11 chains (189 residues) following loop building 3 chains (140 residues) in sequence following loop building ------------------------------------------------------ 5858 reflections ( 99.36 % complete ) and 2313 restraints for refining 1767 atoms. 976 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2694 (Rfree = 0.000) for 1767 atoms. Found 7 (7 requested) and removed 34 (7 requested) atoms. Cycle 42: After refmac, R = 0.2327 (Rfree = 0.000) for 1730 atoms. Found 7 (7 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.2211 (Rfree = 0.000) for 1714 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.2120 (Rfree = 0.000) for 1708 atoms. Found 7 (7 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2065 (Rfree = 0.000) for 1708 atoms. Found 7 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.84 2.45 Search for helices and strands: 0 residues in 0 chains, 1778 seeds are put forward Round 1: 186 peptides, 14 chains. Longest chain 39 peptides. Score 0.744 Round 2: 191 peptides, 14 chains. Longest chain 36 peptides. Score 0.756 Round 3: 184 peptides, 13 chains. Longest chain 36 peptides. Score 0.751 Round 4: 190 peptides, 14 chains. Longest chain 40 peptides. Score 0.754 Round 5: 187 peptides, 16 chains. Longest chain 26 peptides. Score 0.720 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 177, Estimated correctness of the model 76.1 % 5 chains (107 residues) have been docked in sequence Sequence coverage is 60 % Consider running further cycles of model building using 2a6b-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 26 A and 30 A 14 chains (180 residues) following loop building 4 chains (110 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5858 reflections ( 99.36 % complete ) and 2583 restraints for refining 1709 atoms. 1416 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2417 (Rfree = 0.000) for 1709 atoms. Found 0 (7 requested) and removed 5 (7 requested) atoms. Cycle 47: After refmac, R = 0.2274 (Rfree = 0.000) for 1695 atoms. Found 0 (7 requested) and removed 2 (7 requested) atoms. Cycle 48: After refmac, R = 0.2185 (Rfree = 0.000) for 1692 atoms. Found 0 (7 requested) and removed 0 (7 requested) atoms. Cycle 49: After refmac, R = 0.2093 (Rfree = 0.000) for 1689 atoms. Found 0 (7 requested) and removed 0 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:57 GMT 2018 Job finished. TimeTaking 45.92 Used memory is bytes: 18938936