Starting phenix.real_space_refine on Wed Feb 21 01:30:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8imz_35577/02_2024/8imz_35577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8imz_35577/02_2024/8imz_35577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8imz_35577/02_2024/8imz_35577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8imz_35577/02_2024/8imz_35577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8imz_35577/02_2024/8imz_35577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8imz_35577/02_2024/8imz_35577.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.168 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 19236 2.51 5 N 4941 2.21 5 O 5055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1025": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1134": "NH1" <-> "NH2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A ARG 1318": "NH1" <-> "NH2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A ARG 1518": "NH1" <-> "NH2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "A ARG 1547": "NH1" <-> "NH2" Residue "A ARG 1552": "NH1" <-> "NH2" Residue "A ARG 1553": "NH1" <-> "NH2" Residue "A GLU 1661": "OE1" <-> "OE2" Residue "A ARG 1664": "NH1" <-> "NH2" Residue "A ARG 1671": "NH1" <-> "NH2" Residue "A ARG 1724": "NH1" <-> "NH2" Residue "A ARG 1728": "NH1" <-> "NH2" Residue "A GLU 1777": "OE1" <-> "OE2" Residue "A ARG 2098": "NH1" <-> "NH2" Residue "A ARG 2104": "NH1" <-> "NH2" Residue "A ARG 2135": "NH1" <-> "NH2" Residue "A ARG 2318": "NH1" <-> "NH2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A GLU 2396": "OE1" <-> "OE2" Residue "A ARG 2402": "NH1" <-> "NH2" Residue "A GLU 2408": "OE1" <-> "OE2" Residue "A GLU 2515": "OE1" <-> "OE2" Residue "A ARG 2517": "NH1" <-> "NH2" Residue "A GLU 2524": "OE1" <-> "OE2" Residue "A GLU 2537": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "C ARG 967": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1024": "NH1" <-> "NH2" Residue "C ARG 1025": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "C ARG 1134": "NH1" <-> "NH2" Residue "C ARG 1147": "NH1" <-> "NH2" Residue "C ARG 1204": "NH1" <-> "NH2" Residue "C ARG 1318": "NH1" <-> "NH2" Residue "C GLU 1416": "OE1" <-> "OE2" Residue "C ARG 1518": "NH1" <-> "NH2" Residue "C GLU 1544": "OE1" <-> "OE2" Residue "C ARG 1547": "NH1" <-> "NH2" Residue "C ARG 1552": "NH1" <-> "NH2" Residue "C ARG 1553": "NH1" <-> "NH2" Residue "C GLU 1661": "OE1" <-> "OE2" Residue "C ARG 1664": "NH1" <-> "NH2" Residue "C ARG 1671": "NH1" <-> "NH2" Residue "C ARG 1724": "NH1" <-> "NH2" Residue "C ARG 1728": "NH1" <-> "NH2" Residue "C GLU 1777": "OE1" <-> "OE2" Residue "C ARG 2098": "NH1" <-> "NH2" Residue "C ARG 2104": "NH1" <-> "NH2" Residue "C ARG 2135": "NH1" <-> "NH2" Residue "C ARG 2318": "NH1" <-> "NH2" Residue "C GLU 2343": "OE1" <-> "OE2" Residue "C ARG 2377": "NH1" <-> "NH2" Residue "C GLU 2396": "OE1" <-> "OE2" Residue "C ARG 2402": "NH1" <-> "NH2" Residue "C GLU 2408": "OE1" <-> "OE2" Residue "C GLU 2515": "OE1" <-> "OE2" Residue "C ARG 2517": "NH1" <-> "NH2" Residue "C GLU 2524": "OE1" <-> "OE2" Residue "C GLU 2537": "OE1" <-> "OE2" Residue "B ARG 967": "NH1" <-> "NH2" Residue "B ARG 1005": "NH1" <-> "NH2" Residue "B ARG 1024": "NH1" <-> "NH2" Residue "B ARG 1025": "NH1" <-> "NH2" Residue "B ARG 1031": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "B ARG 1147": "NH1" <-> "NH2" Residue "B ARG 1204": "NH1" <-> "NH2" Residue "B ARG 1318": "NH1" <-> "NH2" Residue "B GLU 1416": "OE1" <-> "OE2" Residue "B ARG 1518": "NH1" <-> "NH2" Residue "B GLU 1544": "OE1" <-> "OE2" Residue "B ARG 1547": "NH1" <-> "NH2" Residue "B ARG 1552": "NH1" <-> "NH2" Residue "B ARG 1553": "NH1" <-> "NH2" Residue "B GLU 1661": "OE1" <-> "OE2" Residue "B ARG 1664": "NH1" <-> "NH2" Residue "B ARG 1671": "NH1" <-> "NH2" Residue "B ARG 1724": "NH1" <-> "NH2" Residue "B ARG 1728": "NH1" <-> "NH2" Residue "B GLU 1777": "OE1" <-> "OE2" Residue "B ARG 2098": "NH1" <-> "NH2" Residue "B ARG 2104": "NH1" <-> "NH2" Residue "B ARG 2135": "NH1" <-> "NH2" Residue "B ARG 2318": "NH1" <-> "NH2" Residue "B GLU 2343": "OE1" <-> "OE2" Residue "B ARG 2377": "NH1" <-> "NH2" Residue "B GLU 2396": "OE1" <-> "OE2" Residue "B ARG 2402": "NH1" <-> "NH2" Residue "B GLU 2408": "OE1" <-> "OE2" Residue "B GLU 2515": "OE1" <-> "OE2" Residue "B ARG 2517": "NH1" <-> "NH2" Residue "B GLU 2524": "OE1" <-> "OE2" Residue "B GLU 2537": "OE1" <-> "OE2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F GLU 239": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29409 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9653 Classifications: {'peptide': 1223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 235 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 150 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "E" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 150 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "C" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9653 Classifications: {'peptide': 1223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 235 Chain: "B" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9653 Classifications: {'peptide': 1223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 235 Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 150 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 19} Time building chain proxies: 14.37, per 1000 atoms: 0.49 Number of scatterers: 29409 At special positions: 0 Unit cell: (186.735, 204.67, 154.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 5055 8.00 N 4941 7.00 C 19236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.61 Conformation dependent library (CDL) restraints added in 5.1 seconds 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7164 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 12 sheets defined 70.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 784 through 824 removed outlier: 4.159A pdb=" N ALA A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.822A pdb=" N LEU A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 832 " --> pdb=" O MET A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 858 removed outlier: 4.436A pdb=" N THR A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.880A pdb=" N VAL A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 950 removed outlier: 3.680A pdb=" N ALA A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1006 removed outlier: 6.349A pdb=" N PHE A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1023 removed outlier: 4.171A pdb=" N HIS A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1053 removed outlier: 3.544A pdb=" N ILE A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A1031 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Proline residue: A1034 - end of helix removed outlier: 3.584A pdb=" N CYS A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A1052 " --> pdb=" O TYR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1080 Processing helix chain 'A' and resid 1093 through 1114 removed outlier: 4.154A pdb=" N ASP A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1159 Processing helix chain 'A' and resid 1161 through 1176 removed outlier: 4.732A pdb=" N VAL A1167 " --> pdb=" O TRP A1163 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1199 removed outlier: 3.571A pdb=" N LEU A1193 " --> pdb=" O PHE A1189 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1228 Processing helix chain 'A' and resid 1229 through 1232 Processing helix chain 'A' and resid 1244 through 1250 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.770A pdb=" N CYS A1286 " --> pdb=" O TRP A1282 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A1299 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1365 removed outlier: 5.074A pdb=" N SER A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1321 " --> pdb=" O SER A1317 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1510 through 1546 removed outlier: 4.215A pdb=" N ASP A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N HIS A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A1527 " --> pdb=" O PHE A1523 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A1540 " --> pdb=" O ALA A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1558 removed outlier: 3.967A pdb=" N VAL A1555 " --> pdb=" O VAL A1551 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A1556 " --> pdb=" O ARG A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1664 removed outlier: 4.035A pdb=" N ARG A1664 " --> pdb=" O GLU A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1669 removed outlier: 3.623A pdb=" N GLN A1668 " --> pdb=" O ARG A1664 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A1669 " --> pdb=" O PHE A1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1664 through 1669' Processing helix chain 'A' and resid 1672 through 1686 Processing helix chain 'A' and resid 1686 through 1701 removed outlier: 3.806A pdb=" N TYR A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1707 Processing helix chain 'A' and resid 1708 through 1717 removed outlier: 3.730A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1749 removed outlier: 3.603A pdb=" N TRP A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A1744 " --> pdb=" O MET A1740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1749 " --> pdb=" O TYR A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1775 Processing helix chain 'A' and resid 1786 through 1803 Processing helix chain 'A' and resid 1958 through 1968 Processing helix chain 'A' and resid 1976 through 1997 Processing helix chain 'A' and resid 2016 through 2041 removed outlier: 4.110A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2069 removed outlier: 4.523A pdb=" N LEU A2065 " --> pdb=" O MET A2061 " (cutoff:3.500A) Proline residue: A2066 - end of helix Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2115 through 2128 removed outlier: 4.113A pdb=" N LEU A2119 " --> pdb=" O ASN A2115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A2120 " --> pdb=" O HIS A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 removed outlier: 3.702A pdb=" N LEU A2134 " --> pdb=" O PHE A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2175 Processing helix chain 'A' and resid 2184 through 2214 removed outlier: 3.806A pdb=" N ILE A2203 " --> pdb=" O LEU A2199 " (cutoff:3.500A) Proline residue: A2206 - end of helix removed outlier: 3.896A pdb=" N ARG A2214 " --> pdb=" O MET A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2252 through 2262 Processing helix chain 'A' and resid 2266 through 2273 removed outlier: 4.232A pdb=" N MET A2270 " --> pdb=" O TYR A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2274 through 2276 No H-bonds generated for 'chain 'A' and resid 2274 through 2276' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2326 through 2330 removed outlier: 3.829A pdb=" N LYS A2329 " --> pdb=" O ASP A2326 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2359 removed outlier: 3.769A pdb=" N GLN A2356 " --> pdb=" O ARG A2352 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A2359 " --> pdb=" O ALA A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2391 removed outlier: 3.732A pdb=" N LEU A2390 " --> pdb=" O VAL A2387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2483 Processing helix chain 'A' and resid 2500 through 2516 Processing helix chain 'A' and resid 2519 through 2533 Processing helix chain 'A' and resid 2537 through 2542 Processing helix chain 'D' and resid 230 through 245 removed outlier: 3.594A pdb=" N LEU D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 244 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 245 " --> pdb=" O CYS D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.594A pdb=" N LEU E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS E 244 " --> pdb=" O CYS E 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 245 " --> pdb=" O CYS E 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 824 removed outlier: 5.423A pdb=" N PHE C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C 815 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR C 816 " --> pdb=" O LEU C 812 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR C 817 " --> pdb=" O VAL C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 840 removed outlier: 3.822A pdb=" N LEU C 831 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 845 through 858 removed outlier: 4.436A pdb=" N THR C 854 " --> pdb=" O SER C 850 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 868 removed outlier: 3.880A pdb=" N VAL C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 950 removed outlier: 3.680A pdb=" N ALA C 938 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1006 removed outlier: 6.350A pdb=" N PHE C 986 " --> pdb=" O ILE C 982 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU C 991 " --> pdb=" O TYR C 987 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1023 removed outlier: 4.172A pdb=" N HIS C1013 " --> pdb=" O MET C1009 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1053 removed outlier: 3.544A pdb=" N ILE C1029 " --> pdb=" O ARG C1025 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C1031 " --> pdb=" O GLU C1027 " (cutoff:3.500A) Proline residue: C1034 - end of helix removed outlier: 3.584A pdb=" N CYS C1051 " --> pdb=" O GLN C1047 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C1052 " --> pdb=" O TYR C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1080 Processing helix chain 'C' and resid 1093 through 1114 removed outlier: 4.154A pdb=" N ASP C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1159 Processing helix chain 'C' and resid 1161 through 1176 removed outlier: 4.732A pdb=" N VAL C1167 " --> pdb=" O TRP C1163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C1176 " --> pdb=" O ALA C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1199 removed outlier: 3.571A pdb=" N LEU C1193 " --> pdb=" O PHE C1189 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1228 Processing helix chain 'C' and resid 1229 through 1232 Processing helix chain 'C' and resid 1244 through 1250 Processing helix chain 'C' and resid 1282 through 1299 removed outlier: 3.771A pdb=" N CYS C1286 " --> pdb=" O TRP C1282 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C1287 " --> pdb=" O ASP C1283 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C1298 " --> pdb=" O ARG C1294 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C1299 " --> pdb=" O ARG C1295 " (cutoff:3.500A) Processing helix chain 'C' and resid 1302 through 1365 removed outlier: 5.073A pdb=" N SER C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C1320 " --> pdb=" O ALA C1316 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C1321 " --> pdb=" O SER C1317 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C1365 " --> pdb=" O GLN C1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1408 Processing helix chain 'C' and resid 1510 through 1546 removed outlier: 4.215A pdb=" N ASP C1514 " --> pdb=" O GLN C1510 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS C1527 " --> pdb=" O PHE C1523 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C1540 " --> pdb=" O ALA C1536 " (cutoff:3.500A) Processing helix chain 'C' and resid 1551 through 1558 removed outlier: 3.968A pdb=" N VAL C1555 " --> pdb=" O VAL C1551 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C1556 " --> pdb=" O ARG C1552 " (cutoff:3.500A) Processing helix chain 'C' and resid 1656 through 1664 removed outlier: 4.034A pdb=" N ARG C1664 " --> pdb=" O GLU C1660 " (cutoff:3.500A) Processing helix chain 'C' and resid 1664 through 1669 removed outlier: 3.622A pdb=" N GLN C1668 " --> pdb=" O ARG C1664 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C1669 " --> pdb=" O PHE C1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1664 through 1669' Processing helix chain 'C' and resid 1672 through 1686 Processing helix chain 'C' and resid 1686 through 1701 removed outlier: 3.806A pdb=" N TYR C1692 " --> pdb=" O GLU C1688 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1707 Processing helix chain 'C' and resid 1708 through 1717 removed outlier: 3.730A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1749 removed outlier: 3.603A pdb=" N TRP C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C1744 " --> pdb=" O MET C1740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C1749 " --> pdb=" O TYR C1745 " (cutoff:3.500A) Processing helix chain 'C' and resid 1771 through 1775 Processing helix chain 'C' and resid 1786 through 1803 Processing helix chain 'C' and resid 1958 through 1968 Processing helix chain 'C' and resid 1976 through 1997 Processing helix chain 'C' and resid 2016 through 2041 removed outlier: 4.109A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2069 removed outlier: 4.523A pdb=" N LEU C2065 " --> pdb=" O MET C2061 " (cutoff:3.500A) Proline residue: C2066 - end of helix Processing helix chain 'C' and resid 2076 through 2100 Processing helix chain 'C' and resid 2115 through 2128 removed outlier: 4.113A pdb=" N LEU C2119 " --> pdb=" O ASN C2115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C2120 " --> pdb=" O HIS C2116 " (cutoff:3.500A) Processing helix chain 'C' and resid 2130 through 2142 removed outlier: 3.701A pdb=" N LEU C2134 " --> pdb=" O PHE C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2175 Processing helix chain 'C' and resid 2184 through 2214 removed outlier: 3.804A pdb=" N ILE C2203 " --> pdb=" O LEU C2199 " (cutoff:3.500A) Proline residue: C2206 - end of helix removed outlier: 3.897A pdb=" N ARG C2214 " --> pdb=" O MET C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2252 through 2262 Processing helix chain 'C' and resid 2266 through 2273 removed outlier: 4.233A pdb=" N MET C2270 " --> pdb=" O TYR C2266 " (cutoff:3.500A) Processing helix chain 'C' and resid 2274 through 2276 No H-bonds generated for 'chain 'C' and resid 2274 through 2276' Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2326 through 2330 removed outlier: 3.830A pdb=" N LYS C2329 " --> pdb=" O ASP C2326 " (cutoff:3.500A) Processing helix chain 'C' and resid 2348 through 2359 removed outlier: 3.768A pdb=" N GLN C2356 " --> pdb=" O ARG C2352 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C2359 " --> pdb=" O ALA C2355 " (cutoff:3.500A) Processing helix chain 'C' and resid 2387 through 2391 removed outlier: 3.731A pdb=" N LEU C2390 " --> pdb=" O VAL C2387 " (cutoff:3.500A) Processing helix chain 'C' and resid 2466 through 2483 Processing helix chain 'C' and resid 2500 through 2516 Processing helix chain 'C' and resid 2519 through 2533 Processing helix chain 'C' and resid 2537 through 2542 Processing helix chain 'B' and resid 785 through 824 removed outlier: 5.423A pdb=" N PHE B 810 " --> pdb=" O GLU B 806 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 815 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR B 817 " --> pdb=" O VAL B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 840 removed outlier: 3.822A pdb=" N LEU B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 832 " --> pdb=" O MET B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 845 through 858 removed outlier: 4.437A pdb=" N THR B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 868 removed outlier: 3.880A pdb=" N VAL B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 950 removed outlier: 3.679A pdb=" N ALA B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 1006 removed outlier: 6.350A pdb=" N PHE B 986 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 991 " --> pdb=" O TYR B 987 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1023 removed outlier: 4.171A pdb=" N HIS B1013 " --> pdb=" O MET B1009 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1053 removed outlier: 3.543A pdb=" N ILE B1029 " --> pdb=" O ARG B1025 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B1031 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix removed outlier: 3.584A pdb=" N CYS B1051 " --> pdb=" O GLN B1047 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B1052 " --> pdb=" O TYR B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1080 Processing helix chain 'B' and resid 1093 through 1114 removed outlier: 4.154A pdb=" N ASP B1097 " --> pdb=" O ASN B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1161 through 1176 removed outlier: 4.732A pdb=" N VAL B1167 " --> pdb=" O TRP B1163 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B1176 " --> pdb=" O ALA B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1199 removed outlier: 3.571A pdb=" N LEU B1193 " --> pdb=" O PHE B1189 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B1196 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1228 Processing helix chain 'B' and resid 1229 through 1232 Processing helix chain 'B' and resid 1244 through 1250 Processing helix chain 'B' and resid 1282 through 1299 removed outlier: 3.770A pdb=" N CYS B1286 " --> pdb=" O TRP B1282 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1287 " --> pdb=" O ASP B1283 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B1298 " --> pdb=" O ARG B1294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B1299 " --> pdb=" O ARG B1295 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1365 removed outlier: 5.073A pdb=" N SER B1317 " --> pdb=" O ALA B1313 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG B1318 " --> pdb=" O LEU B1314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B1321 " --> pdb=" O SER B1317 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B1365 " --> pdb=" O GLN B1361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1408 Processing helix chain 'B' and resid 1510 through 1546 removed outlier: 4.216A pdb=" N ASP B1514 " --> pdb=" O GLN B1510 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS B1526 " --> pdb=" O ALA B1522 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS B1527 " --> pdb=" O PHE B1523 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B1540 " --> pdb=" O ALA B1536 " (cutoff:3.500A) Processing helix chain 'B' and resid 1551 through 1558 removed outlier: 3.967A pdb=" N VAL B1555 " --> pdb=" O VAL B1551 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B1556 " --> pdb=" O ARG B1552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1656 through 1664 removed outlier: 4.034A pdb=" N ARG B1664 " --> pdb=" O GLU B1660 " (cutoff:3.500A) Processing helix chain 'B' and resid 1664 through 1669 removed outlier: 3.623A pdb=" N GLN B1668 " --> pdb=" O ARG B1664 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B1669 " --> pdb=" O PHE B1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1664 through 1669' Processing helix chain 'B' and resid 1672 through 1686 Processing helix chain 'B' and resid 1686 through 1701 removed outlier: 3.807A pdb=" N TYR B1692 " --> pdb=" O GLU B1688 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1707 Processing helix chain 'B' and resid 1708 through 1717 removed outlier: 3.730A pdb=" N VAL B1712 " --> pdb=" O LEU B1708 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1713 " --> pdb=" O VAL B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1749 removed outlier: 3.603A pdb=" N TRP B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B1744 " --> pdb=" O MET B1740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B1749 " --> pdb=" O TYR B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1771 through 1775 Processing helix chain 'B' and resid 1786 through 1803 Processing helix chain 'B' and resid 1958 through 1968 Processing helix chain 'B' and resid 1976 through 1997 Processing helix chain 'B' and resid 2016 through 2041 removed outlier: 4.109A pdb=" N PHE B2022 " --> pdb=" O GLN B2018 " (cutoff:3.500A) Processing helix chain 'B' and resid 2042 through 2069 removed outlier: 4.524A pdb=" N LEU B2065 " --> pdb=" O MET B2061 " (cutoff:3.500A) Proline residue: B2066 - end of helix Processing helix chain 'B' and resid 2076 through 2100 Processing helix chain 'B' and resid 2115 through 2128 removed outlier: 4.113A pdb=" N LEU B2119 " --> pdb=" O ASN B2115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B2120 " --> pdb=" O HIS B2116 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2142 removed outlier: 3.702A pdb=" N LEU B2134 " --> pdb=" O PHE B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2175 Processing helix chain 'B' and resid 2184 through 2214 removed outlier: 3.805A pdb=" N ILE B2203 " --> pdb=" O LEU B2199 " (cutoff:3.500A) Proline residue: B2206 - end of helix removed outlier: 3.897A pdb=" N ARG B2214 " --> pdb=" O MET B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2252 through 2262 Processing helix chain 'B' and resid 2266 through 2273 removed outlier: 4.233A pdb=" N MET B2270 " --> pdb=" O TYR B2266 " (cutoff:3.500A) Processing helix chain 'B' and resid 2274 through 2276 No H-bonds generated for 'chain 'B' and resid 2274 through 2276' Processing helix chain 'B' and resid 2277 through 2279 No H-bonds generated for 'chain 'B' and resid 2277 through 2279' Processing helix chain 'B' and resid 2297 through 2311 Processing helix chain 'B' and resid 2326 through 2330 removed outlier: 3.829A pdb=" N LYS B2329 " --> pdb=" O ASP B2326 " (cutoff:3.500A) Processing helix chain 'B' and resid 2348 through 2359 removed outlier: 3.769A pdb=" N GLN B2356 " --> pdb=" O ARG B2352 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B2359 " --> pdb=" O ALA B2355 " (cutoff:3.500A) Processing helix chain 'B' and resid 2387 through 2391 removed outlier: 3.731A pdb=" N LEU B2390 " --> pdb=" O VAL B2387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2483 Processing helix chain 'B' and resid 2500 through 2516 Processing helix chain 'B' and resid 2519 through 2533 Processing helix chain 'B' and resid 2537 through 2542 Processing helix chain 'F' and resid 230 through 245 removed outlier: 3.595A pdb=" N LEU F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS F 244 " --> pdb=" O CYS F 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE F 245 " --> pdb=" O CYS F 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU A2230 " --> pdb=" O LEU A2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A2240 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A2228 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A2242 " --> pdb=" O VAL A2226 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A2226 " --> pdb=" O SER A2242 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A2338 " --> pdb=" O TRP A2321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU A2230 " --> pdb=" O LEU A2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A2240 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A2228 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A2242 " --> pdb=" O VAL A2226 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A2226 " --> pdb=" O SER A2242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A2315 " --> pdb=" O LEU A2344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 6.465A pdb=" N ILE A2376 " --> pdb=" O PHE A2449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 5.216A pdb=" N VAL A2367 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A2403 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A2401 " --> pdb=" O PRO A2369 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A2399 " --> pdb=" O LEU A2371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU C2230 " --> pdb=" O LEU C2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C2240 " --> pdb=" O VAL C2228 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C2228 " --> pdb=" O THR C2240 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C2242 " --> pdb=" O VAL C2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C2226 " --> pdb=" O SER C2242 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C2338 " --> pdb=" O TRP C2321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU C2230 " --> pdb=" O LEU C2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C2240 " --> pdb=" O VAL C2228 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C2228 " --> pdb=" O THR C2240 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C2242 " --> pdb=" O VAL C2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C2226 " --> pdb=" O SER C2242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C2315 " --> pdb=" O LEU C2344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2248 through 2250 removed outlier: 6.465A pdb=" N ILE C2376 " --> pdb=" O PHE C2449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 5.216A pdb=" N VAL C2367 " --> pdb=" O ILE C2403 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C2403 " --> pdb=" O VAL C2367 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C2401 " --> pdb=" O PRO C2369 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C2399 " --> pdb=" O LEU C2371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU B2230 " --> pdb=" O LEU B2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B2240 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B2228 " --> pdb=" O THR B2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B2242 " --> pdb=" O VAL B2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B2226 " --> pdb=" O SER B2242 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B2338 " --> pdb=" O TRP B2321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU B2230 " --> pdb=" O LEU B2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B2240 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B2228 " --> pdb=" O THR B2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B2242 " --> pdb=" O VAL B2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B2226 " --> pdb=" O SER B2242 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B2315 " --> pdb=" O LEU B2344 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 6.466A pdb=" N ILE B2376 " --> pdb=" O PHE B2449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 5.216A pdb=" N VAL B2367 " --> pdb=" O ILE B2403 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B2403 " --> pdb=" O VAL B2367 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B2401 " --> pdb=" O PRO B2369 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B2399 " --> pdb=" O LEU B2371 " (cutoff:3.500A) 1887 hydrogen bonds defined for protein. 5589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.05 Time building geometry restraints manager: 12.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9220 1.34 - 1.46: 4772 1.46 - 1.57: 15831 1.57 - 1.69: 0 1.69 - 1.81: 261 Bond restraints: 30084 Sorted by residual: bond pdb=" CG GLU C2133 " pdb=" CD GLU C2133 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.29e+00 bond pdb=" CG GLU B2133 " pdb=" CD GLU B2133 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.29e+00 bond pdb=" CG GLU A2133 " pdb=" CD GLU A2133 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.17e+00 bond pdb=" C ASN B2221 " pdb=" N GLN B2222 " ideal model delta sigma weight residual 1.327 1.293 0.034 2.31e-02 1.87e+03 2.10e+00 bond pdb=" C ASN C2221 " pdb=" N GLN C2222 " ideal model delta sigma weight residual 1.327 1.294 0.033 2.31e-02 1.87e+03 2.07e+00 ... (remaining 30079 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.87: 536 105.87 - 112.95: 16315 112.95 - 120.02: 10823 120.02 - 127.10: 12820 127.10 - 134.18: 321 Bond angle restraints: 40815 Sorted by residual: angle pdb=" N PHE C1180 " pdb=" CA PHE C1180 " pdb=" C PHE C1180 " ideal model delta sigma weight residual 114.62 107.04 7.58 1.14e+00 7.69e-01 4.42e+01 angle pdb=" N PHE B1180 " pdb=" CA PHE B1180 " pdb=" C PHE B1180 " ideal model delta sigma weight residual 114.62 107.10 7.52 1.14e+00 7.69e-01 4.35e+01 angle pdb=" N PHE A1180 " pdb=" CA PHE A1180 " pdb=" C PHE A1180 " ideal model delta sigma weight residual 114.62 107.11 7.51 1.14e+00 7.69e-01 4.34e+01 angle pdb=" C PHE C1180 " pdb=" N GLY C1181 " pdb=" CA GLY C1181 " ideal model delta sigma weight residual 119.98 124.43 -4.45 1.11e+00 8.12e-01 1.61e+01 angle pdb=" C PHE A1180 " pdb=" N GLY A1181 " pdb=" CA GLY A1181 " ideal model delta sigma weight residual 119.98 124.42 -4.44 1.11e+00 8.12e-01 1.60e+01 ... (remaining 40810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16027 17.76 - 35.52: 1484 35.52 - 53.29: 225 53.29 - 71.05: 33 71.05 - 88.81: 33 Dihedral angle restraints: 17802 sinusoidal: 6822 harmonic: 10980 Sorted by residual: dihedral pdb=" CA PRO B2265 " pdb=" C PRO B2265 " pdb=" N TYR B2266 " pdb=" CA TYR B2266 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO C2265 " pdb=" C PRO C2265 " pdb=" N TYR C2266 " pdb=" CA TYR C2266 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO A2265 " pdb=" C PRO A2265 " pdb=" N TYR A2266 " pdb=" CA TYR A2266 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 17799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3478 0.049 - 0.097: 1014 0.097 - 0.146: 155 0.146 - 0.195: 24 0.195 - 0.243: 12 Chirality restraints: 4683 Sorted by residual: chirality pdb=" CB ILE C1179 " pdb=" CA ILE C1179 " pdb=" CG1 ILE C1179 " pdb=" CG2 ILE C1179 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A1179 " pdb=" CA ILE A1179 " pdb=" CG1 ILE A1179 " pdb=" CG2 ILE A1179 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B1179 " pdb=" CA ILE B1179 " pdb=" CG1 ILE B1179 " pdb=" CG2 ILE B1179 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4680 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B2381 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B2382 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B2382 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B2382 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2381 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A2382 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A2382 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A2382 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C2381 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO C2382 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C2382 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C2382 " -0.055 5.00e-02 4.00e+02 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 250 2.60 - 3.17: 26614 3.17 - 3.75: 45704 3.75 - 4.32: 58478 4.32 - 4.90: 95546 Nonbonded interactions: 226592 Sorted by model distance: nonbonded pdb=" NE ARG A1971 " pdb=" O ARG A2098 " model vdw 2.020 2.520 nonbonded pdb=" NE ARG C1971 " pdb=" O ARG C2098 " model vdw 2.021 2.520 nonbonded pdb=" NE ARG B1971 " pdb=" O ARG B2098 " model vdw 2.021 2.520 nonbonded pdb=" O MET B2270 " pdb=" OG SER B2274 " model vdw 2.073 2.440 nonbonded pdb=" O MET A2270 " pdb=" OG SER A2274 " model vdw 2.073 2.440 ... (remaining 226587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.340 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 75.610 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 30084 Z= 0.438 Angle : 0.770 10.010 40815 Z= 0.423 Chirality : 0.046 0.243 4683 Planarity : 0.005 0.103 5091 Dihedral : 14.272 88.810 10638 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3636 helix: 1.07 (0.11), residues: 2328 sheet: -2.25 (0.29), residues: 246 loop : -1.75 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2321 HIS 0.008 0.002 HIS B2116 PHE 0.019 0.002 PHE C2426 TYR 0.020 0.002 TYR A1803 ARG 0.012 0.001 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2224 ILE cc_start: 0.8627 (tt) cc_final: 0.8384 (tp) REVERT: A 2270 MET cc_start: 0.5483 (tpt) cc_final: 0.5160 (tpt) REVERT: A 2372 PHE cc_start: 0.8508 (t80) cc_final: 0.7942 (t80) REVERT: A 2517 ARG cc_start: 0.7036 (mpt180) cc_final: 0.6206 (tmm160) REVERT: C 2270 MET cc_start: 0.5204 (tpt) cc_final: 0.4783 (tpt) REVERT: C 2372 PHE cc_start: 0.8637 (t80) cc_final: 0.8409 (t80) REVERT: C 2473 ILE cc_start: 0.8089 (tp) cc_final: 0.7838 (tp) REVERT: C 2517 ARG cc_start: 0.7232 (mpt180) cc_final: 0.6215 (tmm160) REVERT: B 2270 MET cc_start: 0.5113 (tpt) cc_final: 0.4868 (tpt) REVERT: B 2372 PHE cc_start: 0.8562 (t80) cc_final: 0.8099 (t80) REVERT: B 2517 ARG cc_start: 0.7006 (mpt180) cc_final: 0.6116 (tmm160) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.4185 time to fit residues: 262.4031 Evaluate side-chains 305 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 150 optimal weight: 30.0000 chunk 291 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN A2364 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2364 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30084 Z= 0.192 Angle : 0.584 7.234 40815 Z= 0.298 Chirality : 0.040 0.184 4683 Planarity : 0.005 0.083 5091 Dihedral : 4.653 28.389 4026 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.30 % Allowed : 8.77 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3636 helix: 1.64 (0.11), residues: 2385 sheet: -1.91 (0.30), residues: 264 loop : -1.64 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2140 HIS 0.005 0.001 HIS C2116 PHE 0.020 0.001 PHE C1794 TYR 0.013 0.001 TYR B1803 ARG 0.004 0.000 ARG A1971 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 393 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1791 MET cc_start: 0.6519 (tpt) cc_final: 0.6299 (tpt) REVERT: A 2321 TRP cc_start: 0.8906 (p90) cc_final: 0.8648 (p90) REVERT: A 2517 ARG cc_start: 0.7182 (mpt180) cc_final: 0.6569 (tmm160) REVERT: C 2270 MET cc_start: 0.4820 (tpt) cc_final: 0.4285 (tpt) REVERT: C 2315 ILE cc_start: 0.8805 (tp) cc_final: 0.8513 (tp) REVERT: C 2321 TRP cc_start: 0.8771 (p90) cc_final: 0.8307 (p90) REVERT: C 2517 ARG cc_start: 0.7110 (mpt180) cc_final: 0.6281 (tmm160) REVERT: B 1349 MET cc_start: 0.8212 (tpp) cc_final: 0.7940 (mmm) REVERT: B 2061 MET cc_start: 0.7620 (tpt) cc_final: 0.7304 (tpt) REVERT: B 2133 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 2270 MET cc_start: 0.4869 (tpt) cc_final: 0.4422 (tpt) REVERT: B 2276 TYR cc_start: 0.6633 (m-80) cc_final: 0.6397 (m-80) REVERT: B 2321 TRP cc_start: 0.8802 (p90) cc_final: 0.8315 (p90) REVERT: B 2372 PHE cc_start: 0.8428 (t80) cc_final: 0.7968 (t80) REVERT: B 2517 ARG cc_start: 0.7227 (mpt180) cc_final: 0.6596 (tmm160) outliers start: 39 outliers final: 19 residues processed: 410 average time/residue: 0.3840 time to fit residues: 256.3546 Evaluate side-chains 364 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 344 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2227 THR Chi-restraints excluded: chain A residue 2254 GLN Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2464 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.0980 chunk 104 optimal weight: 0.0570 chunk 281 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 338 optimal weight: 0.6980 chunk 365 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 335 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN A2322 ASN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2322 ASN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30084 Z= 0.179 Angle : 0.551 12.432 40815 Z= 0.277 Chirality : 0.039 0.191 4683 Planarity : 0.004 0.064 5091 Dihedral : 4.372 28.069 4026 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.76 % Allowed : 12.96 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3636 helix: 1.79 (0.11), residues: 2421 sheet: -1.70 (0.30), residues: 279 loop : -1.62 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2142 HIS 0.004 0.001 HIS C2116 PHE 0.020 0.001 PHE C2426 TYR 0.012 0.001 TYR B1803 ARG 0.004 0.000 ARG C2104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 384 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1100 LEU cc_start: 0.7806 (tt) cc_final: 0.7307 (tp) REVERT: A 1774 LEU cc_start: 0.8259 (tp) cc_final: 0.7936 (tp) REVERT: A 2321 TRP cc_start: 0.8863 (p90) cc_final: 0.8558 (p90) REVERT: A 2444 LEU cc_start: 0.8895 (mp) cc_final: 0.8644 (mp) REVERT: A 2517 ARG cc_start: 0.7093 (mpt180) cc_final: 0.6481 (tmm160) REVERT: C 2270 MET cc_start: 0.4764 (tpt) cc_final: 0.4474 (tpt) REVERT: C 2315 ILE cc_start: 0.8709 (tp) cc_final: 0.8365 (tp) REVERT: C 2321 TRP cc_start: 0.8726 (p90) cc_final: 0.8243 (p90) REVERT: C 2517 ARG cc_start: 0.7095 (mpt180) cc_final: 0.6342 (tmm160) REVERT: B 1349 MET cc_start: 0.8221 (tpp) cc_final: 0.7990 (mmm) REVERT: B 2061 MET cc_start: 0.7477 (tpt) cc_final: 0.7183 (tpt) REVERT: B 2133 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: B 2259 LEU cc_start: 0.8521 (tp) cc_final: 0.8010 (tt) REVERT: B 2270 MET cc_start: 0.4662 (tpt) cc_final: 0.4277 (tpt) REVERT: B 2321 TRP cc_start: 0.8784 (p90) cc_final: 0.8528 (p90) REVERT: B 2372 PHE cc_start: 0.8389 (t80) cc_final: 0.8045 (t80) REVERT: B 2517 ARG cc_start: 0.7143 (mpt180) cc_final: 0.6525 (tmm160) outliers start: 53 outliers final: 27 residues processed: 415 average time/residue: 0.3896 time to fit residues: 264.4396 Evaluate side-chains 380 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2227 THR Chi-restraints excluded: chain A residue 2254 GLN Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2227 THR Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2227 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 359 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 321 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS A2254 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30084 Z= 0.323 Angle : 0.618 9.232 40815 Z= 0.311 Chirality : 0.041 0.174 4683 Planarity : 0.004 0.054 5091 Dihedral : 4.476 29.839 4026 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.06 % Allowed : 15.89 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3636 helix: 1.76 (0.11), residues: 2403 sheet: -1.58 (0.31), residues: 264 loop : -1.63 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2142 HIS 0.006 0.001 HIS B2490 PHE 0.027 0.002 PHE C2426 TYR 0.016 0.001 TYR C2533 ARG 0.006 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 362 time to evaluate : 3.259 Fit side-chains revert: symmetry clash REVERT: A 1226 MET cc_start: 0.8053 (tpp) cc_final: 0.7604 (mmm) REVERT: A 1774 LEU cc_start: 0.8307 (tp) cc_final: 0.7999 (tp) REVERT: A 2444 LEU cc_start: 0.8976 (mp) cc_final: 0.8741 (mp) REVERT: A 2517 ARG cc_start: 0.7145 (mpt180) cc_final: 0.6433 (tmm160) REVERT: C 1010 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7632 (m) REVERT: C 1226 MET cc_start: 0.7643 (tpp) cc_final: 0.7271 (mmm) REVERT: C 2270 MET cc_start: 0.4989 (tpt) cc_final: 0.4662 (tpt) REVERT: C 2321 TRP cc_start: 0.8785 (p90) cc_final: 0.8270 (p90) REVERT: C 2517 ARG cc_start: 0.7143 (mpt180) cc_final: 0.6307 (tmm160) REVERT: B 1226 MET cc_start: 0.7983 (tpp) cc_final: 0.7575 (mmm) REVERT: B 1349 MET cc_start: 0.8327 (tpp) cc_final: 0.8040 (mmm) REVERT: B 2133 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: B 2270 MET cc_start: 0.4779 (tpt) cc_final: 0.4413 (tpt) REVERT: B 2321 TRP cc_start: 0.8893 (p90) cc_final: 0.8533 (p90) REVERT: B 2338 GLU cc_start: 0.6549 (pt0) cc_final: 0.6174 (pt0) REVERT: B 2372 PHE cc_start: 0.8519 (t80) cc_final: 0.8035 (t80) REVERT: B 2376 ILE cc_start: 0.9033 (mm) cc_final: 0.8795 (mm) REVERT: B 2407 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7898 (ttm-80) REVERT: B 2517 ARG cc_start: 0.7164 (mpt180) cc_final: 0.6557 (tmm160) outliers start: 92 outliers final: 59 residues processed: 432 average time/residue: 0.3806 time to fit residues: 271.3680 Evaluate side-chains 406 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 345 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2227 THR Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1219 THR Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2227 THR Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1219 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2227 THR Chi-restraints excluded: chain B residue 2228 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 306 optimal weight: 0.6980 chunk 248 optimal weight: 120.0000 chunk 0 optimal weight: 120.0000 chunk 183 optimal weight: 0.8980 chunk 322 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2353 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1304 HIS ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30084 Z= 0.335 Angle : 0.630 12.443 40815 Z= 0.316 Chirality : 0.041 0.170 4683 Planarity : 0.004 0.051 5091 Dihedral : 4.494 28.961 4026 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.89 % Allowed : 17.08 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3636 helix: 1.70 (0.11), residues: 2406 sheet: -1.55 (0.32), residues: 264 loop : -1.70 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2142 HIS 0.020 0.001 HIS A1304 PHE 0.031 0.002 PHE C2426 TYR 0.016 0.001 TYR C2533 ARG 0.007 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 355 time to evaluate : 3.474 Fit side-chains revert: symmetry clash REVERT: A 1226 MET cc_start: 0.8095 (tpp) cc_final: 0.7642 (mmm) REVERT: A 1774 LEU cc_start: 0.8287 (tp) cc_final: 0.7984 (tp) REVERT: A 2042 THR cc_start: 0.8884 (p) cc_final: 0.8615 (p) REVERT: A 2315 ILE cc_start: 0.8821 (tp) cc_final: 0.8156 (tt) REVERT: A 2444 LEU cc_start: 0.8997 (mp) cc_final: 0.8777 (mp) REVERT: A 2517 ARG cc_start: 0.7222 (mpt180) cc_final: 0.6524 (tmm160) REVERT: C 1010 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7580 (m) REVERT: C 1226 MET cc_start: 0.7828 (tpp) cc_final: 0.7474 (mmm) REVERT: C 2285 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7800 (mm110) REVERT: C 2321 TRP cc_start: 0.8809 (p90) cc_final: 0.8280 (p90) REVERT: C 2353 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8358 (mm-40) REVERT: C 2492 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9210 (tt) REVERT: C 2517 ARG cc_start: 0.7067 (mpt180) cc_final: 0.6246 (tmm160) REVERT: B 1226 MET cc_start: 0.8020 (tpp) cc_final: 0.7683 (mmm) REVERT: B 1349 MET cc_start: 0.8378 (tpp) cc_final: 0.8092 (mmm) REVERT: B 1774 LEU cc_start: 0.8214 (tp) cc_final: 0.7932 (tp) REVERT: B 2133 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: B 2258 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7200 (tp30) REVERT: B 2321 TRP cc_start: 0.8902 (p90) cc_final: 0.8562 (p90) REVERT: B 2338 GLU cc_start: 0.6566 (pt0) cc_final: 0.6243 (pt0) REVERT: B 2372 PHE cc_start: 0.8555 (t80) cc_final: 0.8131 (t80) REVERT: B 2517 ARG cc_start: 0.7191 (mpt180) cc_final: 0.6582 (tmm160) outliers start: 117 outliers final: 83 residues processed: 446 average time/residue: 0.3594 time to fit residues: 265.2072 Evaluate side-chains 429 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 343 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1741 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2219 VAL Chi-restraints excluded: chain A residue 2227 THR Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1179 ILE Chi-restraints excluded: chain C residue 1219 THR Chi-restraints excluded: chain C residue 1233 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2219 VAL Chi-restraints excluded: chain C residue 2227 THR Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2293 LEU Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1219 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2227 THR Chi-restraints excluded: chain B residue 2248 ILE Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.9980 chunk 323 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN C1013 HIS ** C1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 HIS C2254 GLN ** B1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30084 Z= 0.167 Angle : 0.566 11.962 40815 Z= 0.280 Chirality : 0.039 0.304 4683 Planarity : 0.004 0.054 5091 Dihedral : 4.243 27.382 4026 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.09 % Allowed : 18.68 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3636 helix: 1.96 (0.11), residues: 2409 sheet: -1.38 (0.32), residues: 264 loop : -1.61 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2142 HIS 0.024 0.001 HIS B1304 PHE 0.029 0.001 PHE C2426 TYR 0.012 0.001 TYR B1977 ARG 0.006 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 377 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1100 LEU cc_start: 0.7809 (tt) cc_final: 0.7319 (tp) REVERT: A 1226 MET cc_start: 0.8161 (tpp) cc_final: 0.7641 (mmm) REVERT: A 1342 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7865 (tp) REVERT: A 1740 MET cc_start: 0.7682 (tpp) cc_final: 0.7427 (tpt) REVERT: A 1774 LEU cc_start: 0.8219 (tp) cc_final: 0.7946 (tp) REVERT: A 2251 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: A 2266 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: A 2315 ILE cc_start: 0.8821 (tp) cc_final: 0.8168 (tt) REVERT: A 2444 LEU cc_start: 0.8927 (mp) cc_final: 0.8711 (mp) REVERT: A 2517 ARG cc_start: 0.7173 (mpt180) cc_final: 0.6558 (tmm160) REVERT: C 1226 MET cc_start: 0.7640 (tpp) cc_final: 0.7356 (mmm) REVERT: C 1342 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7831 (tp) REVERT: C 1740 MET cc_start: 0.7567 (tpp) cc_final: 0.7179 (tpt) REVERT: C 1801 LEU cc_start: 0.8521 (tp) cc_final: 0.8278 (tt) REVERT: C 2023 MET cc_start: 0.8346 (tpt) cc_final: 0.8131 (tpt) REVERT: C 2285 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7799 (mm110) REVERT: C 2353 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8279 (mm-40) REVERT: C 2492 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9053 (tt) REVERT: C 2517 ARG cc_start: 0.7183 (mpt180) cc_final: 0.6356 (tmm160) REVERT: B 1072 MET cc_start: 0.0976 (ptt) cc_final: 0.0426 (ttp) REVERT: B 1226 MET cc_start: 0.7947 (tpp) cc_final: 0.7559 (mmm) REVERT: B 1342 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7831 (tp) REVERT: B 1774 LEU cc_start: 0.8132 (tp) cc_final: 0.7882 (tp) REVERT: B 2034 ASP cc_start: 0.8355 (t0) cc_final: 0.8013 (t0) REVERT: B 2258 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7112 (tp30) REVERT: B 2315 ILE cc_start: 0.8664 (tp) cc_final: 0.8053 (tt) REVERT: B 2321 TRP cc_start: 0.8757 (p90) cc_final: 0.8544 (p90) REVERT: B 2338 GLU cc_start: 0.6378 (pt0) cc_final: 0.6161 (pt0) REVERT: B 2372 PHE cc_start: 0.8500 (t80) cc_final: 0.8263 (t80) REVERT: B 2376 ILE cc_start: 0.9002 (mm) cc_final: 0.8744 (mm) REVERT: B 2517 ARG cc_start: 0.7173 (mpt180) cc_final: 0.6521 (tmm160) outliers start: 93 outliers final: 58 residues processed: 447 average time/residue: 0.3754 time to fit residues: 276.0331 Evaluate side-chains 421 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 357 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 358 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 165 optimal weight: 0.0370 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN C1013 HIS ** C1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** B1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2261 GLN ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30084 Z= 0.195 Angle : 0.566 11.530 40815 Z= 0.281 Chirality : 0.039 0.294 4683 Planarity : 0.004 0.046 5091 Dihedral : 4.187 28.027 4026 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.99 % Allowed : 19.54 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3636 helix: 2.01 (0.11), residues: 2409 sheet: -1.28 (0.32), residues: 264 loop : -1.66 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2142 HIS 0.018 0.001 HIS C1304 PHE 0.027 0.001 PHE C2426 TYR 0.012 0.001 TYR B1977 ARG 0.008 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 365 time to evaluate : 3.634 Fit side-chains revert: symmetry clash REVERT: A 1072 MET cc_start: 0.1116 (ptt) cc_final: 0.0520 (ttp) REVERT: A 1100 LEU cc_start: 0.7848 (tt) cc_final: 0.7364 (tp) REVERT: A 1226 MET cc_start: 0.8170 (tpp) cc_final: 0.7668 (mmm) REVERT: A 1342 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7856 (tp) REVERT: A 1740 MET cc_start: 0.7699 (tpp) cc_final: 0.7444 (tpt) REVERT: A 1774 LEU cc_start: 0.8195 (tp) cc_final: 0.7925 (tp) REVERT: A 2251 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: A 2266 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: A 2306 GLN cc_start: 0.8440 (tp40) cc_final: 0.8236 (tp40) REVERT: A 2315 ILE cc_start: 0.8817 (tp) cc_final: 0.8195 (tt) REVERT: A 2353 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8302 (mm-40) REVERT: A 2444 LEU cc_start: 0.8902 (mp) cc_final: 0.8694 (mp) REVERT: A 2517 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6561 (tmm160) REVERT: C 1226 MET cc_start: 0.7658 (tpp) cc_final: 0.7396 (mmm) REVERT: C 1342 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7838 (tp) REVERT: C 1740 MET cc_start: 0.7553 (tpp) cc_final: 0.7261 (tpt) REVERT: C 1801 LEU cc_start: 0.8517 (tp) cc_final: 0.8256 (tt) REVERT: C 2266 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: C 2353 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8266 (mm-40) REVERT: C 2492 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9136 (tt) REVERT: C 2517 ARG cc_start: 0.7107 (mpt180) cc_final: 0.6420 (tmm160) REVERT: B 1072 MET cc_start: 0.0874 (ptt) cc_final: 0.0606 (ttp) REVERT: B 1226 MET cc_start: 0.8004 (tpp) cc_final: 0.7593 (mmm) REVERT: B 1342 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7855 (tp) REVERT: B 1774 LEU cc_start: 0.8089 (tp) cc_final: 0.7839 (tp) REVERT: B 2034 ASP cc_start: 0.8453 (t0) cc_final: 0.8134 (t0) REVERT: B 2066 PRO cc_start: 0.6783 (Cg_exo) cc_final: 0.6582 (Cg_endo) REVERT: B 2258 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7101 (tp30) REVERT: B 2315 ILE cc_start: 0.8670 (tp) cc_final: 0.8064 (tt) REVERT: B 2321 TRP cc_start: 0.8733 (p90) cc_final: 0.8510 (p90) REVERT: B 2376 ILE cc_start: 0.9019 (mm) cc_final: 0.8760 (mm) REVERT: B 2517 ARG cc_start: 0.7243 (mpt180) cc_final: 0.6414 (tmm160) outliers start: 90 outliers final: 70 residues processed: 436 average time/residue: 0.3709 time to fit residues: 265.2223 Evaluate side-chains 430 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 353 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2266 TYR Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2296 ILE Chi-restraints excluded: chain B residue 2297 SER Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2245 GLN A2254 GLN C1013 HIS C2254 GLN C2285 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30084 Z= 0.238 Angle : 0.584 11.387 40815 Z= 0.290 Chirality : 0.040 0.263 4683 Planarity : 0.004 0.045 5091 Dihedral : 4.224 28.845 4026 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.49 % Allowed : 19.61 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 3636 helix: 2.00 (0.11), residues: 2406 sheet: -1.27 (0.32), residues: 264 loop : -1.62 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2321 HIS 0.003 0.001 HIS B2116 PHE 0.036 0.001 PHE C2426 TYR 0.011 0.001 TYR B1977 ARG 0.007 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 361 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1072 MET cc_start: 0.1040 (ptt) cc_final: 0.0625 (ttp) REVERT: A 1100 LEU cc_start: 0.7873 (tt) cc_final: 0.7385 (tp) REVERT: A 1226 MET cc_start: 0.8162 (tpp) cc_final: 0.7669 (mmm) REVERT: A 1342 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7878 (tp) REVERT: A 1774 LEU cc_start: 0.8212 (tp) cc_final: 0.7959 (tp) REVERT: A 2251 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: A 2266 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6296 (m-80) REVERT: A 2315 ILE cc_start: 0.8832 (tp) cc_final: 0.8204 (tt) REVERT: A 2353 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 2444 LEU cc_start: 0.8912 (mp) cc_final: 0.8702 (mp) REVERT: A 2517 ARG cc_start: 0.7133 (mpt180) cc_final: 0.6645 (tmm160) REVERT: C 1226 MET cc_start: 0.7689 (tpp) cc_final: 0.7415 (mmm) REVERT: C 1342 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7847 (tp) REVERT: C 1740 MET cc_start: 0.7672 (tpp) cc_final: 0.7401 (tpt) REVERT: C 1801 LEU cc_start: 0.8534 (tp) cc_final: 0.8280 (tt) REVERT: C 2266 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: C 2353 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8328 (mm-40) REVERT: C 2492 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9140 (tt) REVERT: C 2517 ARG cc_start: 0.7101 (mpt180) cc_final: 0.6466 (tmm160) REVERT: B 1072 MET cc_start: 0.1030 (ptt) cc_final: 0.0805 (ttp) REVERT: B 1226 MET cc_start: 0.7984 (tpp) cc_final: 0.7646 (mmm) REVERT: B 1342 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7891 (tp) REVERT: B 1774 LEU cc_start: 0.8091 (tp) cc_final: 0.7854 (tp) REVERT: B 2034 ASP cc_start: 0.8473 (t0) cc_final: 0.8145 (t0) REVERT: B 2066 PRO cc_start: 0.6812 (Cg_exo) cc_final: 0.6607 (Cg_endo) REVERT: B 2258 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7053 (tp30) REVERT: B 2315 ILE cc_start: 0.8665 (tp) cc_final: 0.8070 (tt) REVERT: B 2517 ARG cc_start: 0.7202 (mpt180) cc_final: 0.6329 (tmm160) outliers start: 105 outliers final: 78 residues processed: 447 average time/residue: 0.3667 time to fit residues: 272.6968 Evaluate side-chains 433 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 348 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2513 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2266 TYR Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2296 ILE Chi-restraints excluded: chain B residue 2297 SER Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 1.9990 chunk 343 optimal weight: 0.0040 chunk 313 optimal weight: 0.0030 chunk 334 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 301 optimal weight: 10.0000 chunk 316 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN A2261 GLN C1013 HIS ** C1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2261 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2356 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30084 Z= 0.157 Angle : 0.554 11.390 40815 Z= 0.273 Chirality : 0.038 0.251 4683 Planarity : 0.004 0.047 5091 Dihedral : 4.085 27.455 4026 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 20.60 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 3636 helix: 2.14 (0.11), residues: 2412 sheet: -1.18 (0.33), residues: 264 loop : -1.56 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2140 HIS 0.003 0.001 HIS B1699 PHE 0.032 0.001 PHE C2426 TYR 0.012 0.001 TYR B1977 ARG 0.006 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 367 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1072 MET cc_start: 0.1031 (ptt) cc_final: 0.0681 (ttp) REVERT: A 1100 LEU cc_start: 0.7856 (tt) cc_final: 0.7340 (tp) REVERT: A 1226 MET cc_start: 0.8206 (tpp) cc_final: 0.7681 (mmm) REVERT: A 1342 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 1740 MET cc_start: 0.7688 (tpp) cc_final: 0.7423 (tpt) REVERT: A 1774 LEU cc_start: 0.8111 (tp) cc_final: 0.7858 (tp) REVERT: A 1794 PHE cc_start: 0.7730 (m-80) cc_final: 0.7424 (m-80) REVERT: A 2251 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: A 2266 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: A 2315 ILE cc_start: 0.8814 (tp) cc_final: 0.8213 (tt) REVERT: A 2444 LEU cc_start: 0.8872 (mp) cc_final: 0.8636 (mp) REVERT: A 2517 ARG cc_start: 0.7096 (mpt180) cc_final: 0.6555 (tmm160) REVERT: C 1072 MET cc_start: 0.0966 (ptt) cc_final: 0.0543 (ttp) REVERT: C 1226 MET cc_start: 0.7629 (tpp) cc_final: 0.7377 (mmm) REVERT: C 1342 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7826 (tp) REVERT: C 1740 MET cc_start: 0.7631 (tpp) cc_final: 0.7392 (tpt) REVERT: C 1801 LEU cc_start: 0.8435 (tp) cc_final: 0.8188 (tt) REVERT: C 2401 VAL cc_start: 0.8859 (t) cc_final: 0.8322 (m) REVERT: C 2426 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7697 (p90) REVERT: C 2517 ARG cc_start: 0.6978 (mpt180) cc_final: 0.6349 (tmm160) REVERT: B 1215 LEU cc_start: 0.7697 (tt) cc_final: 0.7020 (mp) REVERT: B 1226 MET cc_start: 0.7945 (tpp) cc_final: 0.7593 (mmm) REVERT: B 1342 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 1349 MET cc_start: 0.8315 (mmm) cc_final: 0.7768 (mmp) REVERT: B 1740 MET cc_start: 0.7507 (tpp) cc_final: 0.7238 (tpt) REVERT: B 1774 LEU cc_start: 0.8097 (tp) cc_final: 0.7859 (tp) REVERT: B 2034 ASP cc_start: 0.8473 (t0) cc_final: 0.8134 (t0) REVERT: B 2258 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7016 (tp30) REVERT: B 2266 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: B 2315 ILE cc_start: 0.8622 (tp) cc_final: 0.8062 (tt) REVERT: B 2517 ARG cc_start: 0.7156 (mpt180) cc_final: 0.6585 (tmm160) outliers start: 81 outliers final: 62 residues processed: 432 average time/residue: 0.3900 time to fit residues: 277.7654 Evaluate side-chains 420 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 351 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain C residue 1001 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2426 PHE Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2266 TYR Chi-restraints excluded: chain B residue 2297 SER Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.0070 chunk 353 optimal weight: 3.9990 chunk 215 optimal weight: 0.0970 chunk 167 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 370 optimal weight: 0.0570 chunk 341 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2285 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30084 Z= 0.144 Angle : 0.558 14.545 40815 Z= 0.272 Chirality : 0.038 0.243 4683 Planarity : 0.004 0.050 5091 Dihedral : 3.978 27.393 4026 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.23 % Allowed : 21.34 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3636 helix: 2.29 (0.11), residues: 2403 sheet: -0.89 (0.35), residues: 237 loop : -1.61 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2140 HIS 0.003 0.001 HIS B1699 PHE 0.027 0.001 PHE C2426 TYR 0.011 0.001 TYR B1977 ARG 0.008 0.000 ARG A2104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 382 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 MET cc_start: 0.6506 (mtt) cc_final: 0.6220 (ttm) REVERT: A 1215 LEU cc_start: 0.7532 (tt) cc_final: 0.6933 (mp) REVERT: A 1226 MET cc_start: 0.8131 (tpp) cc_final: 0.7590 (mmm) REVERT: A 1740 MET cc_start: 0.7639 (tpp) cc_final: 0.7352 (tpt) REVERT: A 1774 LEU cc_start: 0.8056 (tp) cc_final: 0.7813 (tp) REVERT: A 1794 PHE cc_start: 0.7638 (m-80) cc_final: 0.7316 (m-80) REVERT: A 2251 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: A 2272 PHE cc_start: 0.8276 (t80) cc_final: 0.8029 (t80) REVERT: A 2315 ILE cc_start: 0.8822 (tp) cc_final: 0.8233 (tt) REVERT: A 2444 LEU cc_start: 0.8763 (mp) cc_final: 0.8526 (mp) REVERT: A 2517 ARG cc_start: 0.6996 (mpt180) cc_final: 0.6470 (tmm160) REVERT: C 1072 MET cc_start: 0.1283 (ptt) cc_final: 0.0899 (ttp) REVERT: C 1215 LEU cc_start: 0.7656 (tt) cc_final: 0.7008 (mp) REVERT: C 1226 MET cc_start: 0.7568 (tpp) cc_final: 0.7333 (mmm) REVERT: C 1342 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7800 (tp) REVERT: C 1519 TRP cc_start: 0.7611 (t-100) cc_final: 0.7308 (t-100) REVERT: C 1801 LEU cc_start: 0.8389 (tp) cc_final: 0.8152 (tt) REVERT: C 2425 ASP cc_start: 0.6769 (t0) cc_final: 0.6511 (t0) REVERT: C 2492 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9054 (tt) REVERT: C 2517 ARG cc_start: 0.6889 (mpt180) cc_final: 0.6242 (tmm160) REVERT: B 1072 MET cc_start: 0.1601 (ttp) cc_final: 0.1342 (ttt) REVERT: B 1215 LEU cc_start: 0.7744 (tt) cc_final: 0.6994 (mp) REVERT: B 1226 MET cc_start: 0.7909 (tpp) cc_final: 0.7581 (mmm) REVERT: B 1342 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7784 (tp) REVERT: B 1664 ARG cc_start: 0.8602 (tpt90) cc_final: 0.8321 (tpt90) REVERT: B 1740 MET cc_start: 0.7442 (tpp) cc_final: 0.7078 (tpt) REVERT: B 1774 LEU cc_start: 0.8063 (tp) cc_final: 0.7835 (tp) REVERT: B 1801 LEU cc_start: 0.8246 (tp) cc_final: 0.8020 (tt) REVERT: B 2034 ASP cc_start: 0.8456 (t0) cc_final: 0.8095 (t0) REVERT: B 2258 GLU cc_start: 0.7615 (tm-30) cc_final: 0.6953 (tp30) REVERT: B 2279 GLU cc_start: 0.8740 (pp20) cc_final: 0.8054 (pp20) REVERT: B 2315 ILE cc_start: 0.8642 (tp) cc_final: 0.8087 (tt) REVERT: B 2339 LYS cc_start: 0.7798 (pttm) cc_final: 0.7424 (pttt) REVERT: B 2407 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7646 (ttm-80) REVERT: B 2517 ARG cc_start: 0.7127 (mpt180) cc_final: 0.6414 (tmm160) outliers start: 67 outliers final: 56 residues processed: 436 average time/residue: 0.3687 time to fit residues: 264.6984 Evaluate side-chains 417 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 357 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain C residue 1001 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2072 MET Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2297 SER Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 0.0270 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN C1013 HIS ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.173828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.154817 restraints weight = 54565.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.156734 restraints weight = 118490.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.156111 restraints weight = 53420.866| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30084 Z= 0.213 Angle : 0.590 11.331 40815 Z= 0.289 Chirality : 0.039 0.273 4683 Planarity : 0.004 0.045 5091 Dihedral : 4.064 27.942 4026 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.73 % Allowed : 21.07 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.15), residues: 3636 helix: 2.19 (0.11), residues: 2415 sheet: -1.30 (0.32), residues: 279 loop : -1.49 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C2321 HIS 0.003 0.001 HIS B2116 PHE 0.031 0.001 PHE C2426 TYR 0.011 0.001 TYR A1977 ARG 0.006 0.000 ARG A2402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5881.76 seconds wall clock time: 107 minutes 54.87 seconds (6474.87 seconds total)