Starting phenix.real_space_refine on Fri Mar 6 02:06:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lqi_0946/03_2026/6lqi_0946.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lqi_0946/03_2026/6lqi_0946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lqi_0946/03_2026/6lqi_0946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lqi_0946/03_2026/6lqi_0946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lqi_0946/03_2026/6lqi_0946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lqi_0946/03_2026/6lqi_0946.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.002 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 102 5.16 5 C 17346 2.51 5 N 4752 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26934 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1301, 8978 Classifications: {'peptide': 1301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 493} Link IDs: {'PTRANS': 45, 'TRANS': 1255} Chain breaks: 15 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1860 Unresolved non-hydrogen angles: 2420 Unresolved non-hydrogen dihedrals: 1568 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLU:plan': 26, 'TYR:plan': 27, 'TRP:plan': 12, 'PHE:plan': 31, 'ARG:plan': 30, 'GLN:plan1': 32, 'HIS:plan': 8, 'ASP:plan': 15, 'ASN:plan1': 17} Unresolved non-hydrogen planarities: 1001 Chain: "B" Number of atoms: 8978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1301, 8978 Classifications: {'peptide': 1301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 493} Link IDs: {'PTRANS': 45, 'TRANS': 1255} Chain breaks: 15 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1860 Unresolved non-hydrogen angles: 2420 Unresolved non-hydrogen dihedrals: 1568 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLU:plan': 26, 'TYR:plan': 27, 'TRP:plan': 12, 'PHE:plan': 31, 'ARG:plan': 30, 'GLN:plan1': 32, 'HIS:plan': 8, 'ASP:plan': 15, 'ASN:plan1': 17} Unresolved non-hydrogen planarities: 1001 Chain: "C" Number of atoms: 8978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1301, 8978 Classifications: {'peptide': 1301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 493} Link IDs: {'PTRANS': 45, 'TRANS': 1255} Chain breaks: 15 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 1860 Unresolved non-hydrogen angles: 2420 Unresolved non-hydrogen dihedrals: 1568 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLU:plan': 26, 'TYR:plan': 27, 'TRP:plan': 12, 'PHE:plan': 31, 'ARG:plan': 30, 'GLN:plan1': 32, 'HIS:plan': 8, 'ASP:plan': 15, 'ASN:plan1': 17} Unresolved non-hydrogen planarities: 1001 Time building chain proxies: 6.62, per 1000 atoms: 0.25 Number of scatterers: 26934 At special positions: 0 Unit cell: (216.48, 201.96, 153.12, 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 102 16.00 O 4734 8.00 N 4752 7.00 C 17346 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 - 3.00 Amino acid : True - 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7488 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 11 sheets defined 68.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 577 through 585 removed outlier: 4.124A pdb=" N ILE A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 604 through 625 removed outlier: 4.333A pdb=" N ILE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 625 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 650 removed outlier: 3.552A pdb=" N VAL A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 709 Processing helix chain 'A' and resid 710 through 716 Processing helix chain 'A' and resid 785 through 804 removed outlier: 4.496A pdb=" N SER A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 Processing helix chain 'A' and resid 828 through 840 removed outlier: 4.203A pdb=" N LEU A 832 " --> pdb=" O MET A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 866 Processing helix chain 'A' and resid 924 through 950 removed outlier: 4.135A pdb=" N ILE A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 removed outlier: 3.581A pdb=" N PHE A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1006 removed outlier: 3.780A pdb=" N MET A1006 " --> pdb=" O ILE A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 3.863A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1053 removed outlier: 3.713A pdb=" N ARG A1031 " --> pdb=" O GLU A1027 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Proline residue: A1034 - end of helix removed outlier: 4.003A pdb=" N TYR A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1111 Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.670A pdb=" N HIS A1145 " --> pdb=" O ASN A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1159 removed outlier: 4.070A pdb=" N ALA A1156 " --> pdb=" O MET A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1175 removed outlier: 3.769A pdb=" N TRP A1163 " --> pdb=" O ARG A1159 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1166 " --> pdb=" O PHE A1162 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A1167 " --> pdb=" O TRP A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1200 removed outlier: 3.841A pdb=" N LEU A1185 " --> pdb=" O GLY A1181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1192 " --> pdb=" O CYS A1188 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1224 removed outlier: 3.783A pdb=" N ILE A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1299 Processing helix chain 'A' and resid 1302 through 1315 Processing helix chain 'A' and resid 1315 through 1365 removed outlier: 3.520A pdb=" N GLY A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1391 Processing helix chain 'A' and resid 1481 through 1521 removed outlier: 5.632A pdb=" N HIS A1502 " --> pdb=" O ALA A1498 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS A1503 " --> pdb=" O PHE A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1645 removed outlier: 3.783A pdb=" N GLN A1645 " --> pdb=" O PHE A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1662 removed outlier: 3.873A pdb=" N LEU A1651 " --> pdb=" O ARG A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1677 removed outlier: 3.926A pdb=" N HIS A1675 " --> pdb=" O ILE A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1683 No H-bonds generated for 'chain 'A' and resid 1681 through 1683' Processing helix chain 'A' and resid 1684 through 1695 removed outlier: 4.063A pdb=" N VAL A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A1689 " --> pdb=" O VAL A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1720 Processing helix chain 'A' and resid 1756 through 1777 removed outlier: 3.766A pdb=" N LYS A1760 " --> pdb=" O ASP A1756 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1777 " --> pdb=" O ARG A1773 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1942 removed outlier: 3.627A pdb=" N PHE A1938 " --> pdb=" O LEU A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1970 removed outlier: 4.022A pdb=" N MET A1956 " --> pdb=" O VAL A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2016 removed outlier: 3.796A pdb=" N ALA A1995 " --> pdb=" O GLN A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2037 removed outlier: 3.920A pdb=" N VAL A2031 " --> pdb=" O VAL A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2076 Processing helix chain 'A' and resid 2091 through 2102 Processing helix chain 'A' and resid 2107 through 2119 removed outlier: 3.560A pdb=" N ARG A2111 " --> pdb=" O LEU A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2150 removed outlier: 3.748A pdb=" N GLU A2148 " --> pdb=" O SER A2144 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2181 removed outlier: 3.906A pdb=" N TYR A2165 " --> pdb=" O LYS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2188 Processing helix chain 'A' and resid 2228 through 2238 Processing helix chain 'A' and resid 2242 through 2252 removed outlier: 3.991A pdb=" N TYR A2252 " --> pdb=" O PHE A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2273 through 2287 Processing helix chain 'A' and resid 2324 through 2334 Processing helix chain 'A' and resid 2397 through 2401 Processing helix chain 'A' and resid 2442 through 2458 removed outlier: 3.640A pdb=" N TYR A2446 " --> pdb=" O ILE A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2467 through 2472 Processing helix chain 'A' and resid 2476 through 2493 removed outlier: 3.899A pdb=" N LEU A2482 " --> pdb=" O ARG A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2511 Processing helix chain 'A' and resid 2512 through 2517 removed outlier: 3.647A pdb=" N ILE A2516 " --> pdb=" O PRO A2512 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 585 removed outlier: 4.048A pdb=" N ILE B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 585 " --> pdb=" O ILE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 596 Processing helix chain 'B' and resid 604 through 625 removed outlier: 4.348A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR B 610 " --> pdb=" O TYR B 606 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 650 removed outlier: 3.525A pdb=" N VAL B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 709 Processing helix chain 'B' and resid 710 through 716 Processing helix chain 'B' and resid 785 through 804 removed outlier: 4.405A pdb=" N SER B 789 " --> pdb=" O ASP B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 821 Processing helix chain 'B' and resid 828 through 840 removed outlier: 4.167A pdb=" N LEU B 832 " --> pdb=" O MET B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 866 Processing helix chain 'B' and resid 924 through 950 removed outlier: 4.097A pdb=" N ILE B 930 " --> pdb=" O ASN B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 984 removed outlier: 3.591A pdb=" N PHE B 984 " --> pdb=" O TYR B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1006 removed outlier: 3.754A pdb=" N MET B1006 " --> pdb=" O ILE B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1023 removed outlier: 3.863A pdb=" N ARG B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1053 removed outlier: 3.750A pdb=" N ARG B1031 " --> pdb=" O GLU B1027 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B1032 " --> pdb=" O ALA B1028 " (cutoff:3.500A) Proline residue: B1034 - end of helix removed outlier: 4.052A pdb=" N TYR B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1111 Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.657A pdb=" N HIS B1145 " --> pdb=" O ASN B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1159 removed outlier: 4.034A pdb=" N ALA B1156 " --> pdb=" O MET B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1175 removed outlier: 3.786A pdb=" N TRP B1163 " --> pdb=" O ARG B1159 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B1166 " --> pdb=" O PHE B1162 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B1167 " --> pdb=" O TRP B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1200 removed outlier: 3.806A pdb=" N LEU B1185 " --> pdb=" O GLY B1181 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B1192 " --> pdb=" O CYS B1188 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR B1196 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1224 removed outlier: 3.775A pdb=" N ILE B1222 " --> pdb=" O VAL B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1299 Processing helix chain 'B' and resid 1302 through 1315 Processing helix chain 'B' and resid 1315 through 1365 Processing helix chain 'B' and resid 1387 through 1391 Processing helix chain 'B' and resid 1481 through 1521 removed outlier: 5.600A pdb=" N HIS B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS B1503 " --> pdb=" O PHE B1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 1632 through 1645 removed outlier: 3.778A pdb=" N GLN B1645 " --> pdb=" O PHE B1641 " (cutoff:3.500A) Processing helix chain 'B' and resid 1647 through 1662 removed outlier: 3.865A pdb=" N LEU B1651 " --> pdb=" O ARG B1647 " (cutoff:3.500A) Processing helix chain 'B' and resid 1663 through 1677 removed outlier: 3.917A pdb=" N HIS B1675 " --> pdb=" O ILE B1671 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B1677 " --> pdb=" O LEU B1673 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1683 No H-bonds generated for 'chain 'B' and resid 1681 through 1683' Processing helix chain 'B' and resid 1684 through 1695 removed outlier: 4.144A pdb=" N VAL B1688 " --> pdb=" O LEU B1684 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B1689 " --> pdb=" O VAL B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1720 Processing helix chain 'B' and resid 1756 through 1777 removed outlier: 3.779A pdb=" N LYS B1760 " --> pdb=" O ASP B1756 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B1777 " --> pdb=" O ARG B1773 " (cutoff:3.500A) Processing helix chain 'B' and resid 1934 through 1942 removed outlier: 3.630A pdb=" N PHE B1938 " --> pdb=" O LEU B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1970 removed outlier: 4.028A pdb=" N MET B1956 " --> pdb=" O VAL B1952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1991 through 2016 removed outlier: 3.764A pdb=" N ALA B1995 " --> pdb=" O GLN B1991 " (cutoff:3.500A) Processing helix chain 'B' and resid 2019 through 2037 removed outlier: 3.909A pdb=" N VAL B2031 " --> pdb=" O VAL B2027 " (cutoff:3.500A) Processing helix chain 'B' and resid 2049 through 2076 Processing helix chain 'B' and resid 2091 through 2102 Processing helix chain 'B' and resid 2107 through 2119 removed outlier: 3.572A pdb=" N ARG B2111 " --> pdb=" O LEU B2107 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2150 removed outlier: 3.770A pdb=" N GLU B2148 " --> pdb=" O SER B2144 " (cutoff:3.500A) Processing helix chain 'B' and resid 2160 through 2181 removed outlier: 3.537A pdb=" N LYS B2164 " --> pdb=" O LYS B2160 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B2165 " --> pdb=" O LYS B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2181 through 2188 Processing helix chain 'B' and resid 2228 through 2238 Processing helix chain 'B' and resid 2242 through 2252 removed outlier: 4.012A pdb=" N TYR B2252 " --> pdb=" O PHE B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2255 No H-bonds generated for 'chain 'B' and resid 2253 through 2255' Processing helix chain 'B' and resid 2273 through 2287 Processing helix chain 'B' and resid 2324 through 2334 Processing helix chain 'B' and resid 2397 through 2401 Processing helix chain 'B' and resid 2442 through 2458 removed outlier: 3.586A pdb=" N TYR B2446 " --> pdb=" O ILE B2442 " (cutoff:3.500A) Processing helix chain 'B' and resid 2467 through 2472 Processing helix chain 'B' and resid 2476 through 2493 removed outlier: 3.906A pdb=" N LEU B2482 " --> pdb=" O ARG B2478 " (cutoff:3.500A) Processing helix chain 'B' and resid 2494 through 2511 removed outlier: 3.501A pdb=" N GLU B2498 " --> pdb=" O GLU B2494 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2517 removed outlier: 3.673A pdb=" N ILE B2516 " --> pdb=" O PRO B2512 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 585 removed outlier: 4.014A pdb=" N ILE C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 585 " --> pdb=" O ILE C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 596 Processing helix chain 'C' and resid 604 through 625 removed outlier: 4.387A pdb=" N ILE C 608 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR C 610 " --> pdb=" O TYR C 606 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET C 611 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C 625 " --> pdb=" O PHE C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 650 removed outlier: 3.503A pdb=" N VAL C 650 " --> pdb=" O VAL C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 709 Processing helix chain 'C' and resid 710 through 716 Processing helix chain 'C' and resid 785 through 804 removed outlier: 4.417A pdb=" N SER C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 821 Processing helix chain 'C' and resid 828 through 840 removed outlier: 4.192A pdb=" N LEU C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 866 removed outlier: 4.561A pdb=" N MET C 848 " --> pdb=" O ARG C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 950 removed outlier: 4.170A pdb=" N ILE C 930 " --> pdb=" O ASN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 984 removed outlier: 3.539A pdb=" N PHE C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1006 removed outlier: 3.761A pdb=" N MET C1006 " --> pdb=" O ILE C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1023 removed outlier: 3.840A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1053 removed outlier: 3.751A pdb=" N ARG C1031 " --> pdb=" O GLU C1027 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C1032 " --> pdb=" O ALA C1028 " (cutoff:3.500A) Proline residue: C1034 - end of helix removed outlier: 3.994A pdb=" N TYR C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1111 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.663A pdb=" N HIS C1145 " --> pdb=" O ASN C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1159 removed outlier: 4.073A pdb=" N ALA C1156 " --> pdb=" O MET C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1175 removed outlier: 3.767A pdb=" N TRP C1163 " --> pdb=" O ARG C1159 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C1166 " --> pdb=" O PHE C1162 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C1167 " --> pdb=" O TRP C1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1200 removed outlier: 3.820A pdb=" N LEU C1185 " --> pdb=" O GLY C1181 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C1192 " --> pdb=" O CYS C1188 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1224 removed outlier: 3.771A pdb=" N ILE C1222 " --> pdb=" O VAL C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1299 Processing helix chain 'C' and resid 1302 through 1315 Processing helix chain 'C' and resid 1315 through 1365 removed outlier: 3.506A pdb=" N GLY C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1387 through 1391 Processing helix chain 'C' and resid 1481 through 1521 removed outlier: 5.623A pdb=" N HIS C1502 " --> pdb=" O ALA C1498 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1503 " --> pdb=" O PHE C1499 " (cutoff:3.500A) Processing helix chain 'C' and resid 1632 through 1645 removed outlier: 3.826A pdb=" N GLN C1645 " --> pdb=" O PHE C1641 " (cutoff:3.500A) Processing helix chain 'C' and resid 1647 through 1662 removed outlier: 3.851A pdb=" N LEU C1651 " --> pdb=" O ARG C1647 " (cutoff:3.500A) Processing helix chain 'C' and resid 1663 through 1677 removed outlier: 3.901A pdb=" N HIS C1675 " --> pdb=" O ILE C1671 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C1677 " --> pdb=" O LEU C1673 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1683 No H-bonds generated for 'chain 'C' and resid 1681 through 1683' Processing helix chain 'C' and resid 1684 through 1695 removed outlier: 4.086A pdb=" N VAL C1688 " --> pdb=" O LEU C1684 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU C1689 " --> pdb=" O VAL C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1720 Processing helix chain 'C' and resid 1756 through 1777 removed outlier: 3.778A pdb=" N LYS C1760 " --> pdb=" O ASP C1756 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C1777 " --> pdb=" O ARG C1773 " (cutoff:3.500A) Processing helix chain 'C' and resid 1934 through 1942 removed outlier: 3.701A pdb=" N PHE C1938 " --> pdb=" O LEU C1934 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1970 removed outlier: 4.007A pdb=" N MET C1956 " --> pdb=" O VAL C1952 " (cutoff:3.500A) Processing helix chain 'C' and resid 1991 through 2016 removed outlier: 3.843A pdb=" N ALA C1995 " --> pdb=" O GLN C1991 " (cutoff:3.500A) Processing helix chain 'C' and resid 2019 through 2037 removed outlier: 3.928A pdb=" N VAL C2031 " --> pdb=" O VAL C2027 " (cutoff:3.500A) Processing helix chain 'C' and resid 2049 through 2076 Processing helix chain 'C' and resid 2091 through 2102 Processing helix chain 'C' and resid 2107 through 2119 removed outlier: 3.587A pdb=" N ARG C2111 " --> pdb=" O LEU C2107 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2150 removed outlier: 3.762A pdb=" N GLU C2148 " --> pdb=" O SER C2144 " (cutoff:3.500A) Processing helix chain 'C' and resid 2160 through 2181 removed outlier: 3.510A pdb=" N LYS C2164 " --> pdb=" O LYS C2160 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C2165 " --> pdb=" O LYS C2161 " (cutoff:3.500A) Processing helix chain 'C' and resid 2181 through 2188 Processing helix chain 'C' and resid 2228 through 2238 Processing helix chain 'C' and resid 2242 through 2252 removed outlier: 4.011A pdb=" N TYR C2252 " --> pdb=" O PHE C2248 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2255 No H-bonds generated for 'chain 'C' and resid 2253 through 2255' Processing helix chain 'C' and resid 2273 through 2287 Processing helix chain 'C' and resid 2324 through 2334 Processing helix chain 'C' and resid 2397 through 2401 Processing helix chain 'C' and resid 2442 through 2458 removed outlier: 3.634A pdb=" N TYR C2446 " --> pdb=" O ILE C2442 " (cutoff:3.500A) Processing helix chain 'C' and resid 2467 through 2472 Processing helix chain 'C' and resid 2476 through 2493 removed outlier: 3.905A pdb=" N LEU C2482 " --> pdb=" O ARG C2478 " (cutoff:3.500A) Processing helix chain 'C' and resid 2494 through 2511 Processing helix chain 'C' and resid 2512 through 2517 removed outlier: 3.689A pdb=" N ILE C2516 " --> pdb=" O PRO C2512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2215 through 2220 removed outlier: 3.908A pdb=" N TRP A2297 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A2314 " --> pdb=" O TRP A2297 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2215 through 2220 Processing sheet with id=AA3, first strand: chain 'A' and resid 2224 through 2226 Processing sheet with id=AA4, first strand: chain 'A' and resid 2377 through 2385 Processing sheet with id=AA5, first strand: chain 'B' and resid 2215 through 2220 removed outlier: 3.934A pdb=" N TRP B2297 " --> pdb=" O GLU B2314 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B2314 " --> pdb=" O TRP B2297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2215 through 2220 Processing sheet with id=AA7, first strand: chain 'B' and resid 2224 through 2226 Processing sheet with id=AA8, first strand: chain 'B' and resid 2377 through 2385 Processing sheet with id=AA9, first strand: chain 'C' and resid 2215 through 2220 removed outlier: 3.910A pdb=" N TRP C2297 " --> pdb=" O GLU C2314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C2314 " --> pdb=" O TRP C2297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 2224 through 2226 Processing sheet with id=AB2, first strand: chain 'C' and resid 2377 through 2385 2039 hydrogen bonds defined for protein. 6033 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: 5.71 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8972 1.34 - 1.46: 5712 1.46 - 1.58: 12547 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 27393 Sorted by residual: bond pdb=" SD MET C2129 " pdb=" CE MET C2129 " ideal model delta sigma weight residual 1.791 1.753 0.038 2.50e-02 1.60e+03 2.28e+00 bond pdb=" CB VAL B2002 " pdb=" CG1 VAL B2002 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 bond pdb=" CB VAL C2002 " pdb=" CG1 VAL C2002 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL A2002 " pdb=" CG1 VAL A2002 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB VAL C2450 " pdb=" CG1 VAL C2450 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 ... (remaining 27388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 37060 3.43 - 6.85: 275 6.85 - 10.28: 23 10.28 - 13.70: 3 13.70 - 17.13: 4 Bond angle restraints: 37365 Sorted by residual: angle pdb=" CA LEU C1290 " pdb=" CB LEU C1290 " pdb=" CG LEU C1290 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 angle pdb=" C THR B1175 " pdb=" N ARG B1176 " pdb=" CA ARG B1176 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C THR A1175 " pdb=" N ARG A1176 " pdb=" CA ARG A1176 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" C LEU A2184 " pdb=" N PHE A2185 " pdb=" CA PHE A2185 " ideal model delta sigma weight residual 121.94 114.32 7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" C LEU B2184 " pdb=" N PHE B2185 " pdb=" CA PHE B2185 " ideal model delta sigma weight residual 121.94 114.34 7.60 2.00e+00 2.50e-01 1.44e+01 ... (remaining 37360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 14754 17.63 - 35.26: 1079 35.26 - 52.90: 161 52.90 - 70.53: 19 70.53 - 88.16: 34 Dihedral angle restraints: 16047 sinusoidal: 4605 harmonic: 11442 Sorted by residual: dihedral pdb=" CA THR A1175 " pdb=" C THR A1175 " pdb=" N ARG A1176 " pdb=" CA ARG A1176 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA THR B1175 " pdb=" C THR B1175 " pdb=" N ARG B1176 " pdb=" CA ARG B1176 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA THR C1175 " pdb=" C THR C1175 " pdb=" N ARG C1176 " pdb=" CA ARG C1176 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 16044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4219 0.085 - 0.170: 279 0.170 - 0.255: 8 0.255 - 0.340: 0 0.340 - 0.425: 3 Chirality restraints: 4509 Sorted by residual: chirality pdb=" CB VAL B1690 " pdb=" CA VAL B1690 " pdb=" CG1 VAL B1690 " pdb=" CG2 VAL B1690 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CG LEU C1290 " pdb=" CB LEU C1290 " pdb=" CD1 LEU C1290 " pdb=" CD2 LEU C1290 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB VAL C1690 " pdb=" CA VAL C1690 " pdb=" CG1 VAL C1690 " pdb=" CG2 VAL C1690 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 4506 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C2499 " -0.027 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C GLU C2499 " 0.092 2.00e-02 2.50e+03 pdb=" O GLU C2499 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU C2500 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A2499 " 0.027 2.00e-02 2.50e+03 5.28e-02 2.78e+01 pdb=" C GLU A2499 " -0.091 2.00e-02 2.50e+03 pdb=" O GLU A2499 " 0.033 2.00e-02 2.50e+03 pdb=" N GLU A2500 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B2499 " -0.027 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C GLU B2499 " 0.091 2.00e-02 2.50e+03 pdb=" O GLU B2499 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU B2500 " -0.031 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3040 2.74 - 3.28: 27797 3.28 - 3.82: 43729 3.82 - 4.36: 44688 4.36 - 4.90: 75453 Nonbonded interactions: 194707 Sorted by model distance: nonbonded pdb=" O LEU B1303 " pdb=" OG SER B1306 " model vdw 2.203 3.040 nonbonded pdb=" O LEU C1303 " pdb=" OG SER C1306 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A1303 " pdb=" OG SER A1306 " model vdw 2.219 3.040 nonbonded pdb=" O PHE B 707 " pdb=" N MET B 712 " model vdw 2.230 3.120 nonbonded pdb=" O PHE C 707 " pdb=" N MET C 712 " model vdw 2.247 3.120 ... (remaining 194702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 1.360 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 26.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.003 0.049 27393 Z= 0.149 Angle : 0.765 17.125 37365 Z= 0.424 Chirality : 0.045 0.425 4509 Planarity : 0.007 0.060 4797 Dihedral : 13.588 88.160 8559 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.44 % Favored : 93.41 % Rotamer: Outliers : 0.40 % Allowed : 5.41 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.12), residues: 3807 helix: -1.09 (0.09), residues: 2526 sheet: -1.68 (0.34), residues: 207 loop : -4.09 (0.15), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B2011 TYR 0.020 0.001 TYR B2509 PHE 0.027 0.002 PHE A1039 TRP 0.033 0.002 TRP C2128 HIS 0.005 0.001 HIS A1384 Details of bonding type rmsd covalent geometry : bond 0.00287 (27393) covalent geometry : angle 0.76535 (37365) hydrogen bonds : bond 0.10559 ( 2011) hydrogen bonds : angle 5.87520 ( 6033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 PHE cc_start: 0.7719 (m-80) cc_final: 0.7424 (m-80) REVERT: A 1152 MET cc_start: 0.8062 (ttp) cc_final: 0.7817 (ptm) REVERT: A 1202 ASP cc_start: 0.8135 (t70) cc_final: 0.7610 (p0) REVERT: A 1226 MET cc_start: 0.7977 (mmp) cc_final: 0.7666 (mmm) REVERT: A 1295 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8004 (tmt170) REVERT: A 1356 GLN cc_start: 0.9093 (mm110) cc_final: 0.7800 (tm-30) REVERT: A 1496 LEU cc_start: 0.9384 (mp) cc_final: 0.9109 (tp) REVERT: A 1676 MET cc_start: 0.8375 (ttm) cc_final: 0.7822 (mtm) REVERT: A 1765 GLN cc_start: 0.9458 (tt0) cc_final: 0.9052 (tt0) REVERT: A 1960 ASP cc_start: 0.9190 (m-30) cc_final: 0.8799 (m-30) REVERT: A 2033 ILE cc_start: 0.9520 (mm) cc_final: 0.9311 (mm) REVERT: A 2071 TYR cc_start: 0.8988 (t80) cc_final: 0.8610 (t80) REVERT: A 2086 LEU cc_start: 0.9110 (mp) cc_final: 0.8851 (mp) REVERT: A 2110 LEU cc_start: 0.9095 (mt) cc_final: 0.8760 (tt) REVERT: A 2129 MET cc_start: 0.8603 (mtm) cc_final: 0.8201 (mtp) REVERT: A 2190 ARG cc_start: 0.6719 (mtm180) cc_final: 0.6168 (mpt180) REVERT: A 2498 GLU cc_start: 0.9222 (tt0) cc_final: 0.8955 (tt0) REVERT: A 2499 GLU cc_start: 0.8258 (pp20) cc_final: 0.7885 (pp20) REVERT: A 2501 LEU cc_start: 0.9672 (mt) cc_final: 0.9413 (mt) REVERT: A 2515 MET cc_start: 0.9099 (mtp) cc_final: 0.8886 (ttp) REVERT: A 2518 TRP cc_start: 0.9015 (t-100) cc_final: 0.8665 (t-100) outliers start: 3 outliers final: 1 residues processed: 252 average time/residue: 0.0874 time to fit residues: 31.0596 Evaluate side-chains 178 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 968 GLN B1334 HIS ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2026 GLN B2034 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.107421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084206 restraints weight = 35681.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086108 restraints weight = 19245.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087504 restraints weight = 12603.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088313 restraints weight = 9327.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088872 restraints weight = 7699.540| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27393 Z= 0.194 Angle : 0.676 14.822 37365 Z= 0.363 Chirality : 0.041 0.175 4509 Planarity : 0.004 0.052 4797 Dihedral : 4.857 26.680 4104 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.88 % Rotamer: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3807 helix: 0.60 (0.10), residues: 2562 sheet: -1.08 (0.35), residues: 234 loop : -4.05 (0.16), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1514 TYR 0.020 0.002 TYR A1668 PHE 0.031 0.002 PHE B 838 TRP 0.024 0.002 TRP B2180 HIS 0.004 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00387 (27393) covalent geometry : angle 0.67632 (37365) hydrogen bonds : bond 0.04104 ( 2011) hydrogen bonds : angle 4.38661 ( 6033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 845 PHE cc_start: 0.7398 (m-80) cc_final: 0.7084 (m-80) REVERT: B 1152 MET cc_start: 0.8683 (ttp) cc_final: 0.8187 (ptm) REVERT: B 1295 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8014 (tmt170) REVERT: B 1357 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 1716 MET cc_start: 0.9112 (mmm) cc_final: 0.8804 (tmm) REVERT: B 2048 MET cc_start: 0.6850 (ttt) cc_final: 0.6470 (mtm) REVERT: B 2115 ASP cc_start: 0.8993 (m-30) cc_final: 0.8721 (m-30) REVERT: B 2190 ARG cc_start: 0.6489 (mtm180) cc_final: 0.5485 (mmm160) REVERT: B 2493 ARG cc_start: 0.8600 (mpp80) cc_final: 0.8395 (mpp80) REVERT: B 2498 GLU cc_start: 0.9296 (tt0) cc_final: 0.8472 (tm-30) REVERT: B 2499 GLU cc_start: 0.8489 (pp20) cc_final: 0.8242 (pp20) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.0719 time to fit residues: 21.9772 Evaluate side-chains 156 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 386 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 321 optimal weight: 0.2980 chunk 168 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 336 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 296 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1534 GLN B1662 HIS ** B1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2003 GLN B2034 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089498 restraints weight = 34760.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091585 restraints weight = 18857.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092954 restraints weight = 12171.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.093816 restraints weight = 8895.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094414 restraints weight = 7188.120| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27393 Z= 0.112 Angle : 0.568 7.873 37365 Z= 0.296 Chirality : 0.041 0.251 4509 Planarity : 0.003 0.030 4797 Dihedral : 4.256 25.211 4104 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3807 helix: 1.13 (0.10), residues: 2598 sheet: -0.64 (0.36), residues: 234 loop : -3.99 (0.16), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1514 TYR 0.021 0.001 TYR B 947 PHE 0.037 0.002 PHE A2461 TRP 0.018 0.001 TRP C2180 HIS 0.004 0.001 HIS A1943 Details of bonding type rmsd covalent geometry : bond 0.00229 (27393) covalent geometry : angle 0.56835 (37365) hydrogen bonds : bond 0.03379 ( 2011) hydrogen bonds : angle 3.83691 ( 6033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 845 PHE cc_start: 0.7662 (m-80) cc_final: 0.7343 (m-80) REVERT: B 1152 MET cc_start: 0.8188 (ttp) cc_final: 0.7707 (ptm) REVERT: B 1190 TYR cc_start: 0.8362 (t80) cc_final: 0.8015 (t80) REVERT: B 1295 ARG cc_start: 0.8513 (mmt-90) cc_final: 0.7846 (tmt170) REVERT: B 1357 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 1652 LEU cc_start: 0.9247 (mt) cc_final: 0.8935 (tt) REVERT: B 1695 MET cc_start: 0.8527 (mmm) cc_final: 0.8246 (mmm) REVERT: B 1707 MET cc_start: 0.8667 (mpp) cc_final: 0.8295 (mpp) REVERT: B 2003 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8632 (tp40) REVERT: B 2048 MET cc_start: 0.6824 (ttt) cc_final: 0.6426 (mtm) REVERT: B 2114 MET cc_start: 0.8836 (tpp) cc_final: 0.8509 (mmp) REVERT: B 2115 ASP cc_start: 0.8916 (m-30) cc_final: 0.8596 (m-30) REVERT: B 2190 ARG cc_start: 0.6363 (mtm180) cc_final: 0.5521 (mmm160) REVERT: B 2486 ILE cc_start: 0.9471 (tp) cc_final: 0.9237 (tp) REVERT: B 2493 ARG cc_start: 0.8554 (mpp80) cc_final: 0.8345 (mpp80) REVERT: B 2499 GLU cc_start: 0.8390 (pp20) cc_final: 0.8074 (pp20) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0762 time to fit residues: 25.0302 Evaluate side-chains 158 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 375 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 151 optimal weight: 30.0000 chunk 305 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 377 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2034 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087001 restraints weight = 36408.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089004 restraints weight = 20250.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090266 restraints weight = 13374.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091147 restraints weight = 9994.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091676 restraints weight = 8124.926| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27393 Z= 0.130 Angle : 0.568 8.369 37365 Z= 0.300 Chirality : 0.041 0.232 4509 Planarity : 0.003 0.035 4797 Dihedral : 4.137 23.593 4104 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3807 helix: 1.32 (0.10), residues: 2616 sheet: -0.62 (0.34), residues: 234 loop : -3.85 (0.16), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 967 TYR 0.020 0.001 TYR C 947 PHE 0.026 0.001 PHE B 838 TRP 0.055 0.002 TRP B2180 HIS 0.003 0.001 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00274 (27393) covalent geometry : angle 0.56843 (37365) hydrogen bonds : bond 0.03273 ( 2011) hydrogen bonds : angle 3.81119 ( 6033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8387 (ttp) cc_final: 0.7876 (ptm) REVERT: B 1186 LEU cc_start: 0.9030 (mm) cc_final: 0.8827 (mm) REVERT: B 1190 TYR cc_start: 0.8442 (t80) cc_final: 0.8139 (t80) REVERT: B 1295 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.7807 (tmt170) REVERT: B 1357 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 1652 LEU cc_start: 0.9246 (mt) cc_final: 0.8916 (tt) REVERT: B 1670 ILE cc_start: 0.9667 (tt) cc_final: 0.9456 (tt) REVERT: B 1695 MET cc_start: 0.8590 (mmm) cc_final: 0.8321 (mmm) REVERT: B 1707 MET cc_start: 0.8764 (mpp) cc_final: 0.8448 (mpp) REVERT: B 1713 THR cc_start: 0.9462 (p) cc_final: 0.9102 (p) REVERT: B 1716 MET cc_start: 0.8662 (tpt) cc_final: 0.8365 (tpt) REVERT: B 1765 GLN cc_start: 0.9389 (tt0) cc_final: 0.8418 (tm-30) REVERT: B 2003 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8743 (tp40) REVERT: B 2033 ILE cc_start: 0.9513 (mm) cc_final: 0.9306 (mm) REVERT: B 2040 ILE cc_start: 0.8661 (pt) cc_final: 0.8380 (pt) REVERT: B 2048 MET cc_start: 0.7191 (ttt) cc_final: 0.6589 (mtm) REVERT: B 2114 MET cc_start: 0.9048 (tpp) cc_final: 0.8699 (mmp) REVERT: B 2115 ASP cc_start: 0.9057 (m-30) cc_final: 0.8763 (m-30) REVERT: B 2146 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8716 (tp30) REVERT: B 2190 ARG cc_start: 0.6337 (mtm180) cc_final: 0.5991 (mpt180) REVERT: B 2462 SER cc_start: 0.8938 (p) cc_final: 0.8726 (t) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0695 time to fit residues: 21.2778 Evaluate side-chains 161 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 274 optimal weight: 1.9990 chunk 251 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 262 optimal weight: 40.0000 chunk 283 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 243 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087553 restraints weight = 36267.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089459 restraints weight = 20355.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090715 restraints weight = 13664.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091550 restraints weight = 10272.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092027 restraints weight = 8471.570| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27393 Z= 0.110 Angle : 0.559 7.531 37365 Z= 0.291 Chirality : 0.041 0.240 4509 Planarity : 0.003 0.035 4797 Dihedral : 4.013 22.435 4104 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3807 helix: 1.43 (0.10), residues: 2607 sheet: -0.12 (0.33), residues: 234 loop : -3.68 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2458 TYR 0.012 0.001 TYR B1323 PHE 0.025 0.001 PHE B 838 TRP 0.032 0.001 TRP C2180 HIS 0.003 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00225 (27393) covalent geometry : angle 0.55921 (37365) hydrogen bonds : bond 0.03142 ( 2011) hydrogen bonds : angle 3.69011 ( 6033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8389 (ttp) cc_final: 0.7856 (ptm) REVERT: B 1186 LEU cc_start: 0.9009 (mm) cc_final: 0.8783 (mm) REVERT: B 1190 TYR cc_start: 0.8445 (t80) cc_final: 0.8102 (t80) REVERT: B 1295 ARG cc_start: 0.8600 (mmt-90) cc_final: 0.7883 (tmt170) REVERT: B 1302 PHE cc_start: 0.8908 (t80) cc_final: 0.8632 (t80) REVERT: B 1357 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 1506 MET cc_start: 0.9235 (ttt) cc_final: 0.8951 (tpp) REVERT: B 1670 ILE cc_start: 0.9615 (tt) cc_final: 0.9414 (tt) REVERT: B 1695 MET cc_start: 0.8744 (mmm) cc_final: 0.8391 (mmm) REVERT: B 1707 MET cc_start: 0.8787 (mpp) cc_final: 0.8455 (mpp) REVERT: B 1765 GLN cc_start: 0.9362 (tt0) cc_final: 0.8382 (tm-30) REVERT: B 2003 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8544 (tp40) REVERT: B 2033 ILE cc_start: 0.9508 (mm) cc_final: 0.9303 (mm) REVERT: B 2040 ILE cc_start: 0.8666 (pt) cc_final: 0.8289 (pt) REVERT: B 2048 MET cc_start: 0.7171 (ttt) cc_final: 0.6580 (mtm) REVERT: B 2062 LYS cc_start: 0.9463 (tppp) cc_final: 0.9197 (tptm) REVERT: B 2114 MET cc_start: 0.8938 (tpp) cc_final: 0.8536 (mmp) REVERT: B 2115 ASP cc_start: 0.8912 (m-30) cc_final: 0.8678 (m-30) REVERT: B 2146 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8792 (tp30) REVERT: B 2190 ARG cc_start: 0.6302 (mtm180) cc_final: 0.5981 (mpt180) REVERT: B 2493 ARG cc_start: 0.8692 (mpp80) cc_final: 0.8202 (mpp80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0736 time to fit residues: 22.9393 Evaluate side-chains 166 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 44 optimal weight: 9.9990 chunk 306 optimal weight: 0.9990 chunk 386 optimal weight: 1.9990 chunk 276 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 274 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1991 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087140 restraints weight = 36037.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089051 restraints weight = 20409.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090221 restraints weight = 13705.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091085 restraints weight = 10467.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091560 restraints weight = 8597.722| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27393 Z= 0.117 Angle : 0.570 9.550 37365 Z= 0.294 Chirality : 0.041 0.249 4509 Planarity : 0.003 0.039 4797 Dihedral : 4.006 24.247 4104 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3807 helix: 1.53 (0.10), residues: 2607 sheet: -0.30 (0.33), residues: 252 loop : -3.53 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1700 TYR 0.021 0.001 TYR B 947 PHE 0.024 0.001 PHE C 838 TRP 0.068 0.002 TRP B2180 HIS 0.003 0.001 HIS B1304 Details of bonding type rmsd covalent geometry : bond 0.00243 (27393) covalent geometry : angle 0.57041 (37365) hydrogen bonds : bond 0.03103 ( 2011) hydrogen bonds : angle 3.67106 ( 6033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8464 (ttp) cc_final: 0.7871 (ptm) REVERT: B 1186 LEU cc_start: 0.9033 (mm) cc_final: 0.8807 (mm) REVERT: B 1190 TYR cc_start: 0.8509 (t80) cc_final: 0.8269 (t80) REVERT: B 1302 PHE cc_start: 0.8879 (t80) cc_final: 0.8559 (t80) REVERT: B 1506 MET cc_start: 0.9305 (ttt) cc_final: 0.9044 (tpp) REVERT: B 1671 ILE cc_start: 0.9242 (mt) cc_final: 0.9025 (mt) REVERT: B 1695 MET cc_start: 0.8756 (mmm) cc_final: 0.8365 (mmm) REVERT: B 1707 MET cc_start: 0.8755 (mpp) cc_final: 0.8513 (mpp) REVERT: B 1765 GLN cc_start: 0.9394 (tt0) cc_final: 0.8401 (tm-30) REVERT: B 2001 LEU cc_start: 0.8464 (mm) cc_final: 0.7960 (tt) REVERT: B 2003 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8619 (tp40) REVERT: B 2009 ILE cc_start: 0.8873 (tp) cc_final: 0.8554 (tp) REVERT: B 2040 ILE cc_start: 0.8631 (pt) cc_final: 0.8264 (pt) REVERT: B 2114 MET cc_start: 0.9039 (tpp) cc_final: 0.8827 (tpp) REVERT: B 2190 ARG cc_start: 0.6164 (mtm180) cc_final: 0.5816 (mpt180) REVERT: B 2495 LEU cc_start: 0.9322 (mt) cc_final: 0.9095 (mp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.0685 time to fit residues: 22.0122 Evaluate side-chains 166 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087996 restraints weight = 35998.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088189 restraints weight = 17953.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089064 restraints weight = 13919.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089230 restraints weight = 11917.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089288 restraints weight = 10836.286| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27393 Z= 0.142 Angle : 0.579 9.218 37365 Z= 0.304 Chirality : 0.041 0.260 4509 Planarity : 0.003 0.038 4797 Dihedral : 3.996 20.782 4104 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3807 helix: 1.56 (0.10), residues: 2601 sheet: -0.27 (0.33), residues: 261 loop : -3.49 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2493 TYR 0.007 0.001 TYR B2065 PHE 0.031 0.002 PHE A2185 TRP 0.039 0.002 TRP B2180 HIS 0.003 0.001 HIS C1145 Details of bonding type rmsd covalent geometry : bond 0.00300 (27393) covalent geometry : angle 0.57897 (37365) hydrogen bonds : bond 0.03220 ( 2011) hydrogen bonds : angle 3.78642 ( 6033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8653 (ttp) cc_final: 0.8116 (ptm) REVERT: B 1182 LEU cc_start: 0.8422 (mm) cc_final: 0.7757 (mm) REVERT: B 1186 LEU cc_start: 0.9100 (mm) cc_final: 0.8876 (mm) REVERT: B 1190 TYR cc_start: 0.8519 (t80) cc_final: 0.8254 (t80) REVERT: B 1302 PHE cc_start: 0.8837 (t80) cc_final: 0.8492 (t80) REVERT: B 1356 GLN cc_start: 0.9210 (mm110) cc_final: 0.8821 (mm110) REVERT: B 1506 MET cc_start: 0.9222 (ttt) cc_final: 0.8951 (tpp) REVERT: B 1695 MET cc_start: 0.8807 (mmm) cc_final: 0.8467 (mmm) REVERT: B 1707 MET cc_start: 0.8686 (mpp) cc_final: 0.8342 (mpp) REVERT: B 2040 ILE cc_start: 0.8684 (pt) cc_final: 0.8225 (pt) REVERT: B 2048 MET cc_start: 0.7309 (ttt) cc_final: 0.6614 (mtm) REVERT: B 2056 GLN cc_start: 0.8935 (mm110) cc_final: 0.8548 (mm-40) REVERT: B 2114 MET cc_start: 0.9006 (tpp) cc_final: 0.8640 (mmp) REVERT: B 2129 MET cc_start: 0.8791 (mmt) cc_final: 0.8482 (mmt) REVERT: B 2190 ARG cc_start: 0.6275 (mtm180) cc_final: 0.5889 (mpt180) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0722 time to fit residues: 22.0353 Evaluate side-chains 158 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 176 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 346 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 62 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 chunk 375 optimal weight: 0.0770 chunk 326 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2056 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090959 restraints weight = 35860.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091645 restraints weight = 19339.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092437 restraints weight = 13892.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092638 restraints weight = 12866.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092570 restraints weight = 11088.735| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27393 Z= 0.107 Angle : 0.564 8.886 37365 Z= 0.288 Chirality : 0.040 0.272 4509 Planarity : 0.003 0.040 4797 Dihedral : 3.880 21.487 4104 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3807 helix: 1.60 (0.10), residues: 2589 sheet: -0.17 (0.33), residues: 276 loop : -3.54 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1700 TYR 0.016 0.001 TYR C1216 PHE 0.024 0.001 PHE B 838 TRP 0.055 0.001 TRP B2180 HIS 0.003 0.000 HIS B1943 Details of bonding type rmsd covalent geometry : bond 0.00218 (27393) covalent geometry : angle 0.56390 (37365) hydrogen bonds : bond 0.03029 ( 2011) hydrogen bonds : angle 3.58508 ( 6033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8431 (ttp) cc_final: 0.7812 (ptm) REVERT: B 1182 LEU cc_start: 0.8440 (mm) cc_final: 0.7705 (mm) REVERT: B 1186 LEU cc_start: 0.9076 (mm) cc_final: 0.8874 (mm) REVERT: B 1302 PHE cc_start: 0.8790 (t80) cc_final: 0.8461 (t80) REVERT: B 1520 GLU cc_start: 0.8410 (pp20) cc_final: 0.8106 (pp20) REVERT: B 1670 ILE cc_start: 0.9589 (tt) cc_final: 0.9377 (tt) REVERT: B 1671 ILE cc_start: 0.9278 (mt) cc_final: 0.8995 (mt) REVERT: B 1695 MET cc_start: 0.8763 (mmm) cc_final: 0.8413 (mmm) REVERT: B 1707 MET cc_start: 0.8717 (mpp) cc_final: 0.8429 (mpp) REVERT: B 1765 GLN cc_start: 0.9358 (tt0) cc_final: 0.8589 (tp40) REVERT: B 2040 ILE cc_start: 0.8660 (pt) cc_final: 0.8111 (pt) REVERT: B 2056 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8477 (mm-40) REVERT: B 2114 MET cc_start: 0.9079 (mmt) cc_final: 0.8626 (mmm) REVERT: B 2115 ASP cc_start: 0.8792 (m-30) cc_final: 0.8591 (m-30) REVERT: B 2129 MET cc_start: 0.8974 (mmt) cc_final: 0.8598 (mmt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0737 time to fit residues: 22.5168 Evaluate side-chains 174 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 67 optimal weight: 0.6980 chunk 276 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 292 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 347 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 331 optimal weight: 0.0030 chunk 203 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.110373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088529 restraints weight = 34742.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090533 restraints weight = 19747.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091836 restraints weight = 13231.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092711 restraints weight = 9910.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093145 restraints weight = 8112.902| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27393 Z= 0.109 Angle : 0.582 8.881 37365 Z= 0.296 Chirality : 0.041 0.289 4509 Planarity : 0.003 0.040 4797 Dihedral : 3.822 20.773 4104 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3807 helix: 1.67 (0.10), residues: 2562 sheet: -0.03 (0.34), residues: 276 loop : -3.45 (0.17), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C2493 TYR 0.015 0.001 TYR B1216 PHE 0.024 0.001 PHE A 838 TRP 0.024 0.001 TRP A2180 HIS 0.003 0.001 HIS B1943 Details of bonding type rmsd covalent geometry : bond 0.00230 (27393) covalent geometry : angle 0.58170 (37365) hydrogen bonds : bond 0.03026 ( 2011) hydrogen bonds : angle 3.55327 ( 6033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8429 (ttp) cc_final: 0.7907 (ptm) REVERT: B 1182 LEU cc_start: 0.8354 (mm) cc_final: 0.7568 (mm) REVERT: B 1186 LEU cc_start: 0.9041 (mm) cc_final: 0.8804 (mm) REVERT: B 1302 PHE cc_start: 0.8693 (t80) cc_final: 0.8359 (t80) REVERT: B 1357 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 1520 GLU cc_start: 0.8222 (pp20) cc_final: 0.7997 (pp20) REVERT: B 1671 ILE cc_start: 0.9310 (mt) cc_final: 0.9060 (mt) REVERT: B 1695 MET cc_start: 0.8809 (mmm) cc_final: 0.8494 (mmm) REVERT: B 1713 THR cc_start: 0.9540 (p) cc_final: 0.9267 (p) REVERT: B 1765 GLN cc_start: 0.9314 (tt0) cc_final: 0.8590 (tm-30) REVERT: B 2040 ILE cc_start: 0.8639 (pt) cc_final: 0.8137 (pt) REVERT: B 2114 MET cc_start: 0.8946 (mmt) cc_final: 0.8528 (mmm) REVERT: B 2123 LEU cc_start: 0.9248 (mp) cc_final: 0.9008 (mp) REVERT: B 2129 MET cc_start: 0.8922 (mmt) cc_final: 0.8605 (mmt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0675 time to fit residues: 21.1080 Evaluate side-chains 167 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 109 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 120 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 362 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083748 restraints weight = 36490.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084880 restraints weight = 19617.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085899 restraints weight = 13465.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086196 restraints weight = 11679.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086093 restraints weight = 9679.925| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27393 Z= 0.236 Angle : 0.715 10.230 37365 Z= 0.380 Chirality : 0.045 0.320 4509 Planarity : 0.004 0.039 4797 Dihedral : 4.413 26.846 4104 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3807 helix: 1.20 (0.10), residues: 2592 sheet: -0.10 (0.34), residues: 261 loop : -3.48 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C2522 TYR 0.048 0.002 TYR B2509 PHE 0.024 0.002 PHE A2185 TRP 0.097 0.003 TRP C2180 HIS 0.006 0.002 HIS A2034 Details of bonding type rmsd covalent geometry : bond 0.00489 (27393) covalent geometry : angle 0.71502 (37365) hydrogen bonds : bond 0.03785 ( 2011) hydrogen bonds : angle 4.27220 ( 6033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1152 MET cc_start: 0.8919 (ttp) cc_final: 0.8481 (ptm) REVERT: B 1302 PHE cc_start: 0.8988 (t80) cc_final: 0.8769 (t80) REVERT: B 1695 MET cc_start: 0.8809 (mmm) cc_final: 0.8480 (mmm) REVERT: B 2003 GLN cc_start: 0.8705 (tp40) cc_final: 0.8334 (tp40) REVERT: B 2048 MET cc_start: 0.7180 (ttt) cc_final: 0.6673 (mtm) REVERT: B 2114 MET cc_start: 0.8933 (mmt) cc_final: 0.8627 (mmm) REVERT: B 2129 MET cc_start: 0.8852 (mmt) cc_final: 0.8637 (mmm) REVERT: B 2462 SER cc_start: 0.9040 (p) cc_final: 0.8814 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0683 time to fit residues: 19.0740 Evaluate side-chains 141 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 6 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 375 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083774 restraints weight = 36001.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083143 restraints weight = 21350.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.084090 restraints weight = 16569.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084336 restraints weight = 13363.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084313 restraints weight = 11769.267| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27393 Z= 0.265 Angle : 0.786 17.916 37365 Z= 0.411 Chirality : 0.046 0.323 4509 Planarity : 0.004 0.064 4797 Dihedral : 4.648 45.073 4104 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3807 helix: 0.92 (0.10), residues: 2580 sheet: -0.29 (0.33), residues: 279 loop : -3.61 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C2493 TYR 0.060 0.002 TYR C2509 PHE 0.039 0.002 PHE A2185 TRP 0.153 0.004 TRP B2180 HIS 0.006 0.001 HIS A2034 Details of bonding type rmsd covalent geometry : bond 0.00553 (27393) covalent geometry : angle 0.78613 (37365) hydrogen bonds : bond 0.03996 ( 2011) hydrogen bonds : angle 4.44532 ( 6033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.21 seconds wall clock time: 39 minutes 49.39 seconds (2389.39 seconds total)