Starting phenix.real_space_refine on Fri Jun 27 13:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yez_39205/06_2025/8yez_39205_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yez_39205/06_2025/8yez_39205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yez_39205/06_2025/8yez_39205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yez_39205/06_2025/8yez_39205.map" model { file = "/net/cci-nas-00/data/ceres_data/8yez_39205/06_2025/8yez_39205_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yez_39205/06_2025/8yez_39205_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 183 5.16 5 C 20988 2.51 5 N 5181 2.21 5 O 5241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10431 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10431 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10431 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'L9Q': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'L9Q': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.09, per 1000 atoms: 0.73 Number of scatterers: 31599 At special positions: 0 Unit cell: (226.683, 219.042, 156.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 183 16.00 P 6 15.00 O 5241 8.00 N 5181 7.00 C 20988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2411 " - pdb=" SG CYS A2415 " distance=2.04 Simple disulfide: pdb=" SG CYS B2411 " - pdb=" SG CYS B2415 " distance=2.04 Simple disulfide: pdb=" SG CYS C2411 " - pdb=" SG CYS C2415 " distance=2.04 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: 8.54 Conformation dependent library (CDL) restraints added in 4.1 seconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7314 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 9 sheets defined 71.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS A 584 " --> pdb=" O TRP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.554A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 626 through 644 removed outlier: 3.566A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 701 Proline residue: A 687 - end of helix removed outlier: 3.532A pdb=" N GLN A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 834 through 841 removed outlier: 3.521A pdb=" N VAL A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 930 through 956 Processing helix chain 'A' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP A 976 " --> pdb=" O ARG A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 995 through 1010 removed outlier: 3.718A pdb=" N ASN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A1008 " --> pdb=" O VAL A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.502A pdb=" N ALA A1024 " --> pdb=" O CYS A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1164 Processing helix chain 'A' and resid 1166 through 1179 Processing helix chain 'A' and resid 1183 through 1199 removed outlier: 3.826A pdb=" N LEU A1187 " --> pdb=" O SER A1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A1188 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A1189 " --> pdb=" O PHE A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 removed outlier: 3.701A pdb=" N LEU A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1232 removed outlier: 3.562A pdb=" N ASN A1222 " --> pdb=" O LEU A1218 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A1230 " --> pdb=" O ILE A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG A1300 " --> pdb=" O LEU A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1370 Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1514 through 1533 Processing helix chain 'A' and resid 1533 through 1557 removed outlier: 3.516A pdb=" N LEU A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU A1565 " --> pdb=" O HIS A1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A1568 " --> pdb=" O VAL A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1652 Processing helix chain 'A' and resid 1656 through 1668 removed outlier: 4.012A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1686 Processing helix chain 'A' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 Processing helix chain 'A' and resid 1726 through 1747 Processing helix chain 'A' and resid 1784 through 1803 Processing helix chain 'A' and resid 1941 through 1951 Processing helix chain 'A' and resid 1960 through 1978 Processing helix chain 'A' and resid 2002 through 2024 Processing helix chain 'A' and resid 2026 through 2045 removed outlier: 3.527A pdb=" N LYS A2030 " --> pdb=" O THR A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2084 Processing helix chain 'A' and resid 2100 through 2112 removed outlier: 3.547A pdb=" N VAL A2112 " --> pdb=" O GLY A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2114 through 2127 Processing helix chain 'A' and resid 2133 through 2159 Processing helix chain 'A' and resid 2168 through 2185 Processing helix chain 'A' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU A2191 " --> pdb=" O ILE A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2236 through 2248 Processing helix chain 'A' and resid 2250 through 2258 Processing helix chain 'A' and resid 2281 through 2295 Processing helix chain 'A' and resid 2311 through 2314 Processing helix chain 'A' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU A2342 " --> pdb=" O LEU A2338 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 Processing helix chain 'A' and resid 2437 through 2460 removed outlier: 3.550A pdb=" N MET A2441 " --> pdb=" O GLY A2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A2458 " --> pdb=" O PHE A2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A2459 " --> pdb=" O VAL A2455 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2490 removed outlier: 3.582A pdb=" N PHE A2485 " --> pdb=" O CYS A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2505 removed outlier: 3.715A pdb=" N GLU A2497 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A2502 " --> pdb=" O GLU A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2517 Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS B 584 " --> pdb=" O TRP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 618 removed outlier: 3.555A pdb=" N GLN B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 644 removed outlier: 5.642A pdb=" N LYS B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 Proline residue: B 687 - end of helix removed outlier: 3.532A pdb=" N GLN B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 829 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL B 838 " --> pdb=" O ASN B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 871 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 930 through 956 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP B 976 " --> pdb=" O ARG B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 995 through 1010 removed outlier: 3.718A pdb=" N ASN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B1008 " --> pdb=" O VAL B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1026 removed outlier: 3.502A pdb=" N ALA B1024 " --> pdb=" O CYS B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG B1036 " --> pdb=" O GLN B1032 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) Proline residue: B1039 - end of helix Processing helix chain 'B' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU B1105 " --> pdb=" O SER B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1164 Processing helix chain 'B' and resid 1166 through 1179 Processing helix chain 'B' and resid 1183 through 1199 removed outlier: 3.826A pdb=" N LEU B1187 " --> pdb=" O SER B1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B1188 " --> pdb=" O ILE B1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B1189 " --> pdb=" O PHE B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1199 through 1204 removed outlier: 3.701A pdb=" N LEU B1203 " --> pdb=" O PHE B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1232 removed outlier: 3.834A pdb=" N ASN B1230 " --> pdb=" O ILE B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG B1300 " --> pdb=" O LEU B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL B1310 " --> pdb=" O TYR B1306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B1318 " --> pdb=" O LEU B1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1320 through 1370 Processing helix chain 'B' and resid 1408 through 1412 Processing helix chain 'B' and resid 1514 through 1533 Processing helix chain 'B' and resid 1533 through 1557 removed outlier: 3.516A pdb=" N LEU B1549 " --> pdb=" O ALA B1545 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU B1565 " --> pdb=" O HIS B1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B1568 " --> pdb=" O VAL B1564 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1652 Processing helix chain 'B' and resid 1656 through 1668 removed outlier: 4.012A pdb=" N GLU B1660 " --> pdb=" O ILE B1656 " (cutoff:3.500A) Processing helix chain 'B' and resid 1670 through 1686 Processing helix chain 'B' and resid 1687 through 1702 removed outlier: 3.608A pdb=" N HIS B1699 " --> pdb=" O ILE B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1718 Processing helix chain 'B' and resid 1726 through 1747 Processing helix chain 'B' and resid 1784 through 1803 Processing helix chain 'B' and resid 1941 through 1951 Processing helix chain 'B' and resid 1960 through 1978 Processing helix chain 'B' and resid 2002 through 2024 Processing helix chain 'B' and resid 2026 through 2045 removed outlier: 3.527A pdb=" N LYS B2030 " --> pdb=" O THR B2026 " (cutoff:3.500A) Processing helix chain 'B' and resid 2061 through 2084 Processing helix chain 'B' and resid 2100 through 2112 removed outlier: 3.547A pdb=" N VAL B2112 " --> pdb=" O GLY B2108 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2127 Processing helix chain 'B' and resid 2133 through 2159 Processing helix chain 'B' and resid 2168 through 2185 Processing helix chain 'B' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU B2191 " --> pdb=" O ILE B2187 " (cutoff:3.500A) Processing helix chain 'B' and resid 2236 through 2248 Processing helix chain 'B' and resid 2250 through 2258 Processing helix chain 'B' and resid 2281 through 2295 Processing helix chain 'B' and resid 2311 through 2314 Processing helix chain 'B' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU B2342 " --> pdb=" O LEU B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2382 Processing helix chain 'B' and resid 2437 through 2460 removed outlier: 3.550A pdb=" N MET B2441 " --> pdb=" O GLY B2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B2458 " --> pdb=" O PHE B2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B2459 " --> pdb=" O VAL B2455 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE B2485 " --> pdb=" O CYS B2481 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2505 removed outlier: 3.714A pdb=" N GLU B2497 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B2502 " --> pdb=" O GLU B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2517 Processing helix chain 'C' and resid 571 through 577 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS C 584 " --> pdb=" O TRP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 618 removed outlier: 3.555A pdb=" N GLN C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 644 removed outlier: 5.587A pdb=" N LYS C 627 " --> pdb=" O ARG C 623 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 628 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 701 Proline residue: C 687 - end of helix removed outlier: 3.532A pdb=" N GLN C 697 " --> pdb=" O ALA C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 709 Processing helix chain 'C' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 829 Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL C 838 " --> pdb=" O ASN C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 871 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 930 through 956 Processing helix chain 'C' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP C 976 " --> pdb=" O ARG C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.718A pdb=" N ASN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C1008 " --> pdb=" O VAL C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1026 removed outlier: 3.502A pdb=" N ALA C1024 " --> pdb=" O CYS C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG C1036 " --> pdb=" O GLN C1032 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C1037 " --> pdb=" O ALA C1033 " (cutoff:3.500A) Proline residue: C1039 - end of helix Processing helix chain 'C' and resid 1100 through 1116 removed outlier: 3.506A pdb=" N LEU C1105 " --> pdb=" O SER C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1155 through 1164 Processing helix chain 'C' and resid 1166 through 1179 Processing helix chain 'C' and resid 1183 through 1199 removed outlier: 3.826A pdb=" N LEU C1187 " --> pdb=" O SER C1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C1188 " --> pdb=" O ILE C1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C1189 " --> pdb=" O PHE C1185 " (cutoff:3.500A) Processing helix chain 'C' and resid 1199 through 1204 removed outlier: 3.701A pdb=" N LEU C1203 " --> pdb=" O PHE C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1232 removed outlier: 3.782A pdb=" N LEU C1218 " --> pdb=" O LEU C1214 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C1219 " --> pdb=" O TRP C1215 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1220 " --> pdb=" O ASP C1216 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C1230 " --> pdb=" O ILE C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1302 removed outlier: 3.669A pdb=" N ARG C1300 " --> pdb=" O LEU C1296 " (cutoff:3.500A) Processing helix chain 'C' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL C1310 " --> pdb=" O TYR C1306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1370 Processing helix chain 'C' and resid 1408 through 1412 Processing helix chain 'C' and resid 1514 through 1533 Processing helix chain 'C' and resid 1533 through 1557 removed outlier: 3.517A pdb=" N LEU C1549 " --> pdb=" O ALA C1545 " (cutoff:3.500A) Processing helix chain 'C' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU C1565 " --> pdb=" O HIS C1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU C1568 " --> pdb=" O VAL C1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 1646 through 1652 Processing helix chain 'C' and resid 1656 through 1668 removed outlier: 4.012A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) Processing helix chain 'C' and resid 1670 through 1686 Processing helix chain 'C' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 Processing helix chain 'C' and resid 1726 through 1747 Processing helix chain 'C' and resid 1784 through 1803 Processing helix chain 'C' and resid 1941 through 1951 Processing helix chain 'C' and resid 1960 through 1978 Processing helix chain 'C' and resid 2002 through 2024 Processing helix chain 'C' and resid 2026 through 2045 removed outlier: 3.527A pdb=" N LYS C2030 " --> pdb=" O THR C2026 " (cutoff:3.500A) Processing helix chain 'C' and resid 2061 through 2084 Processing helix chain 'C' and resid 2100 through 2112 removed outlier: 3.546A pdb=" N VAL C2112 " --> pdb=" O GLY C2108 " (cutoff:3.500A) Processing helix chain 'C' and resid 2114 through 2127 Processing helix chain 'C' and resid 2133 through 2159 Processing helix chain 'C' and resid 2168 through 2185 Processing helix chain 'C' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU C2191 " --> pdb=" O ILE C2187 " (cutoff:3.500A) Processing helix chain 'C' and resid 2236 through 2248 Processing helix chain 'C' and resid 2250 through 2258 Processing helix chain 'C' and resid 2281 through 2295 Processing helix chain 'C' and resid 2311 through 2314 Processing helix chain 'C' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU C2342 " --> pdb=" O LEU C2338 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2382 Processing helix chain 'C' and resid 2437 through 2460 removed outlier: 3.550A pdb=" N MET C2441 " --> pdb=" O GLY C2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C2458 " --> pdb=" O PHE C2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C2459 " --> pdb=" O VAL C2455 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE C2485 " --> pdb=" O CYS C2481 " (cutoff:3.500A) Processing helix chain 'C' and resid 2493 through 2505 removed outlier: 3.714A pdb=" N GLU C2497 " --> pdb=" O LEU C2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C2502 " --> pdb=" O GLU C2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2517 Processing sheet with id=AA1, first strand: chain 'A' and resid 2223 through 2228 removed outlier: 3.596A pdb=" N ASP A2209 " --> pdb=" O GLN A2308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A2299 " --> pdb=" O LEU A2328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2232 through 2234 Processing sheet with id=AA3, first strand: chain 'A' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN A2354 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A2383 " --> pdb=" O ASN A2354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2223 through 2228 removed outlier: 3.596A pdb=" N ASP B2209 " --> pdb=" O GLN B2308 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B2299 " --> pdb=" O LEU B2328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2232 through 2234 Processing sheet with id=AA6, first strand: chain 'B' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN B2354 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU B2383 " --> pdb=" O ASN B2354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2223 through 2228 removed outlier: 3.595A pdb=" N ASP C2209 " --> pdb=" O GLN C2308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C2299 " --> pdb=" O LEU C2328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2232 through 2234 Processing sheet with id=AA9, first strand: chain 'C' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN C2354 " --> pdb=" O LEU C2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C2383 " --> pdb=" O ASN C2354 " (cutoff:3.500A) 2059 hydrogen bonds defined for protein. 6096 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: 11.97 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4720 1.30 - 1.43: 9167 1.43 - 1.56: 18183 1.56 - 1.69: 12 1.69 - 1.82: 288 Bond restraints: 32370 Sorted by residual: bond pdb=" C39 L9Q A2601 " pdb=" C40 L9Q A2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C39 L9Q B2601 " pdb=" C40 L9Q B2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C39 L9Q A2603 " pdb=" C40 L9Q A2603 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C39 L9Q C2601 " pdb=" C40 L9Q C2601 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" C39 L9Q B2602 " pdb=" C40 L9Q B2602 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 ... (remaining 32365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 42246 3.40 - 6.80: 1354 6.80 - 10.21: 170 10.21 - 13.61: 27 13.61 - 17.01: 12 Bond angle restraints: 43809 Sorted by residual: angle pdb=" N ILE C 684 " pdb=" CA ILE C 684 " pdb=" C ILE C 684 " ideal model delta sigma weight residual 111.90 103.43 8.47 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE B 684 " pdb=" CA ILE B 684 " pdb=" C ILE B 684 " ideal model delta sigma weight residual 111.90 103.43 8.47 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE A 684 " pdb=" CA ILE A 684 " pdb=" C ILE A 684 " ideal model delta sigma weight residual 111.90 103.44 8.46 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE C1025 " pdb=" CA ILE C1025 " pdb=" C ILE C1025 " ideal model delta sigma weight residual 111.90 103.61 8.29 8.10e-01 1.52e+00 1.05e+02 angle pdb=" N ILE A1025 " pdb=" CA ILE A1025 " pdb=" C ILE A1025 " ideal model delta sigma weight residual 111.90 103.62 8.28 8.10e-01 1.52e+00 1.04e+02 ... (remaining 43804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 17260 35.45 - 70.91: 1713 70.91 - 106.36: 68 106.36 - 141.82: 0 141.82 - 177.27: 18 Dihedral angle restraints: 19059 sinusoidal: 7779 harmonic: 11280 Sorted by residual: dihedral pdb=" CA PHE A 923 " pdb=" C PHE A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" C ILE A1722 " pdb=" N ILE A1722 " pdb=" CA ILE A1722 " pdb=" CB ILE A1722 " ideal model delta harmonic sigma weight residual -122.00 -135.49 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" C ILE C1722 " pdb=" N ILE C1722 " pdb=" CA ILE C1722 " pdb=" CB ILE C1722 " ideal model delta harmonic sigma weight residual -122.00 -134.95 12.95 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 19056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3722 0.098 - 0.196: 1047 0.196 - 0.295: 174 0.295 - 0.393: 26 0.393 - 0.491: 14 Chirality restraints: 4983 Sorted by residual: chirality pdb=" CA ILE A1722 " pdb=" N ILE A1722 " pdb=" C ILE A1722 " pdb=" CB ILE A1722 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA ILE C1722 " pdb=" N ILE C1722 " pdb=" C ILE C1722 " pdb=" CB ILE C1722 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA LEU C2493 " pdb=" N LEU C2493 " pdb=" C LEU C2493 " pdb=" CB LEU C2493 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 ... (remaining 4980 not shown) Planarity restraints: 5325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q C2601 " 0.184 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C39 L9Q C2601 " -0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q C2601 " -0.183 2.00e-02 2.50e+03 pdb=" C41 L9Q C2601 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B2602 " 0.184 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C39 L9Q B2602 " -0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q B2602 " -0.183 2.00e-02 2.50e+03 pdb=" C41 L9Q B2602 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A2602 " 0.184 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C39 L9Q A2602 " -0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q A2602 " -0.183 2.00e-02 2.50e+03 pdb=" C41 L9Q A2602 " 0.184 2.00e-02 2.50e+03 ... (remaining 5322 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 9 1.88 - 2.64: 716 2.64 - 3.39: 40880 3.39 - 4.15: 77631 4.15 - 4.90: 133557 Nonbonded interactions: 252793 Sorted by model distance: nonbonded pdb=" N GLU A 679 " pdb=" OE1 GLU A 679 " model vdw 1.126 3.120 nonbonded pdb=" N GLU B 679 " pdb=" OE1 GLU B 679 " model vdw 1.126 3.120 nonbonded pdb=" N GLU C 679 " pdb=" OE1 GLU C 679 " model vdw 1.126 3.120 nonbonded pdb=" CB LYS A2157 " pdb=" NZ LYS A2157 " model vdw 1.702 3.520 nonbonded pdb=" CB LYS C2157 " pdb=" NZ LYS C2157 " model vdw 1.702 3.520 ... (remaining 252788 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 570 through 2521 or resid 2601)) selection = (chain 'B' and (resid 570 through 2521 or resid 2601)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 394.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 76.220 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 477.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 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 : 0.011 0.191 32373 Z= 0.765 Angle : 1.476 17.008 43815 Z= 0.969 Chirality : 0.094 0.491 4983 Planarity : 0.010 0.184 5325 Dihedral : 23.842 177.270 11736 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.62 % Favored : 90.26 % Rotamer: Outliers : 25.90 % Allowed : 12.93 % Favored : 61.17 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.11), residues: 3747 helix: -2.00 (0.08), residues: 2688 sheet: -1.85 (0.29), residues: 246 loop : -3.10 (0.18), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP B2403 HIS 0.004 0.001 HIS A2324 PHE 0.037 0.003 PHE B2307 TYR 0.109 0.005 TYR A2319 ARG 0.007 0.001 ARG A2336 Details of bonding type rmsd hydrogen bonds : bond 0.23562 ( 2059) hydrogen bonds : angle 7.70177 ( 6096) SS BOND : bond 0.01094 ( 3) SS BOND : angle 0.75212 ( 6) covalent geometry : bond 0.01129 (32370) covalent geometry : angle 1.47633 (43809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 867 poor density : 516 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.6211 (tpt) cc_final: 0.4236 (tmm) REVERT: A 699 HIS cc_start: 0.6193 (OUTLIER) cc_final: 0.5376 (m-70) REVERT: A 702 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6279 (t70) REVERT: A 820 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.4835 (tt) REVERT: A 877 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.7010 (m) REVERT: A 929 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6839 (mt) REVERT: A 972 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.4242 (mmt90) REVERT: A 984 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7341 (mmtt) REVERT: A 997 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: A 998 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 1011 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: A 1156 ASP cc_start: 0.5570 (OUTLIER) cc_final: 0.5118 (t0) REVERT: A 1523 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7524 (t0) REVERT: A 1694 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 1719 MET cc_start: 0.8611 (mtp) cc_final: 0.8332 (mtt) REVERT: A 1727 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.6893 (tptm) REVERT: A 2027 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8155 (t) REVERT: A 2045 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7940 (ttt) REVERT: A 2134 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7175 (p) REVERT: A 2169 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7889 (mmtm) REVERT: A 2181 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 2476 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: A 2511 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: A 2515 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: A 2516 TRP cc_start: 0.8331 (t-100) cc_final: 0.7868 (t-100) REVERT: B 605 MET cc_start: 0.6268 (tpt) cc_final: 0.4502 (tmm) REVERT: B 699 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.5333 (m-70) REVERT: B 877 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6816 (m) REVERT: B 929 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6830 (mt) REVERT: B 972 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.4257 (mmt90) REVERT: B 984 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7391 (mmtt) REVERT: B 997 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: B 998 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6553 (tp) REVERT: B 1156 ASP cc_start: 0.5563 (OUTLIER) cc_final: 0.5172 (t0) REVERT: B 1523 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7562 (t0) REVERT: B 1719 MET cc_start: 0.8677 (mtp) cc_final: 0.8387 (mtt) REVERT: B 1727 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.6868 (tptp) REVERT: B 1797 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6625 (ttt-90) REVERT: B 2027 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8312 (t) REVERT: B 2045 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: B 2064 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: B 2100 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7349 (t-90) REVERT: B 2117 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 2134 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7325 (p) REVERT: B 2166 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8619 (mtmm) REVERT: B 2169 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7724 (mtpp) REVERT: B 2181 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8729 (mm) REVERT: B 2200 VAL cc_start: 0.1761 (OUTLIER) cc_final: 0.1531 (p) REVERT: B 2456 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7565 (tpp-160) REVERT: B 2467 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (mtm) REVERT: B 2511 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: B 2515 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: B 2516 TRP cc_start: 0.8337 (t-100) cc_final: 0.7928 (t-100) REVERT: C 605 MET cc_start: 0.6198 (tpt) cc_final: 0.4338 (tmm) REVERT: C 699 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5358 (m-70) REVERT: C 820 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.4887 (tt) REVERT: C 843 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: C 877 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6782 (m) REVERT: C 972 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.4283 (mmt90) REVERT: C 984 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7349 (mmtt) REVERT: C 997 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6220 (tt0) REVERT: C 998 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6509 (tp) REVERT: C 1156 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.5052 (t0) REVERT: C 1523 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7636 (t0) REVERT: C 1694 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7779 (mp) REVERT: C 1696 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 1719 MET cc_start: 0.8660 (mtp) cc_final: 0.8351 (mtt) REVERT: C 1727 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.6937 (tptm) REVERT: C 1797 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6969 (ttt-90) REVERT: C 1971 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7900 (t0) REVERT: C 2122 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: C 2134 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7252 (p) REVERT: C 2169 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7773 (mmtm) REVERT: C 2181 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8718 (mm) REVERT: C 2200 VAL cc_start: 0.1745 (OUTLIER) cc_final: 0.1501 (p) REVERT: C 2231 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6556 (p) REVERT: C 2476 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6394 (mtm180) REVERT: C 2511 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: C 2515 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8089 (ttmt) REVERT: C 2516 TRP cc_start: 0.8326 (t-100) cc_final: 0.7325 (t-100) outliers start: 867 outliers final: 225 residues processed: 1178 average time/residue: 0.4990 time to fit residues: 890.2268 Evaluate side-chains 582 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 286 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1053 TYR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1682 CYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1958 THR Chi-restraints excluded: chain A residue 2024 ARG Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2045 MET Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2169 LYS Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2476 ARG Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2515 LYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 843 PHE Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 998 ILE Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1053 TYR Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1112 GLN Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1180 THR Chi-restraints excluded: chain B residue 1198 LEU Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1338 PHE Chi-restraints excluded: chain B residue 1346 SER Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1646 SER Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1682 CYS Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1728 ARG Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1797 ARG Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1963 LEU Chi-restraints excluded: chain B residue 1966 LEU Chi-restraints excluded: chain B residue 1971 ASP Chi-restraints excluded: chain B residue 2024 ARG Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2028 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2062 VAL Chi-restraints excluded: chain B residue 2064 GLN Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2122 MET Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2166 LYS Chi-restraints excluded: chain B residue 2169 LYS Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2200 VAL Chi-restraints excluded: chain B residue 2456 ARG Chi-restraints excluded: chain B residue 2460 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2467 MET Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2515 LYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 703 ARG Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 855 SER Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 982 CYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 984 LYS Chi-restraints excluded: chain C residue 997 GLU Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1053 TYR Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1180 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1228 SER Chi-restraints excluded: chain C residue 1304 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1336 ILE Chi-restraints excluded: chain C residue 1338 PHE Chi-restraints excluded: chain C residue 1417 ASP Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1523 ASP Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1646 SER Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1682 CYS Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1701 VAL Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1728 ARG Chi-restraints excluded: chain C residue 1797 ARG Chi-restraints excluded: chain C residue 1802 CYS Chi-restraints excluded: chain C residue 1949 ILE Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 1971 ASP Chi-restraints excluded: chain C residue 2026 THR Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2028 LEU Chi-restraints excluded: chain C residue 2045 MET Chi-restraints excluded: chain C residue 2062 VAL Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2119 ARG Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2131 LEU Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2166 LYS Chi-restraints excluded: chain C residue 2169 LYS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2181 LEU Chi-restraints excluded: chain C residue 2186 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2193 PHE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2460 SER Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2476 ARG Chi-restraints excluded: chain C residue 2486 LEU Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2515 LYS Chi-restraints excluded: chain C residue 2518 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 98 optimal weight: 0.0010 chunk 194 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 222 optimal weight: 4.9990 chunk 345 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN A1339 HIS A1535 HIS A1556 GLN A2099 ASN ** A2250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1222 ASN B1230 ASN B1339 HIS B1535 HIS B2064 GLN B2099 ASN ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1230 ASN C1535 HIS C1556 GLN C2099 ASN ** C2228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.192372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130165 restraints weight = 47358.030| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.18 r_work: 0.3321 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32373 Z= 0.166 Angle : 0.701 15.854 43815 Z= 0.363 Chirality : 0.041 0.207 4983 Planarity : 0.006 0.062 5325 Dihedral : 17.993 178.104 5083 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 8.99 % Allowed : 18.55 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3747 helix: 0.49 (0.10), residues: 2685 sheet: -1.01 (0.30), residues: 249 loop : -2.32 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C2136 HIS 0.008 0.001 HIS B1535 PHE 0.044 0.002 PHE C2193 TYR 0.019 0.002 TYR B2219 ARG 0.007 0.001 ARG A1341 Details of bonding type rmsd hydrogen bonds : bond 0.06458 ( 2059) hydrogen bonds : angle 4.77468 ( 6096) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.64091 ( 6) covalent geometry : bond 0.00338 (32370) covalent geometry : angle 0.70094 (43809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 301 poor density : 371 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5844 (tpt) cc_final: 0.4189 (tmm) REVERT: A 702 HIS cc_start: 0.5498 (OUTLIER) cc_final: 0.4822 (t70) REVERT: A 972 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.3940 (mmt90) REVERT: A 1057 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6826 (tp) REVERT: A 1156 ASP cc_start: 0.5152 (OUTLIER) cc_final: 0.4949 (t0) REVERT: A 1230 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7331 (t0) REVERT: A 1727 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6021 (tptm) REVERT: A 1948 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7978 (t0) REVERT: A 2034 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: A 2122 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8487 (mtp) REVERT: A 2166 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8853 (ptpp) REVERT: A 2169 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7457 (mmtm) REVERT: A 2181 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (mm) REVERT: A 2504 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 2516 TRP cc_start: 0.8736 (OUTLIER) cc_final: 0.6984 (m-90) REVERT: B 587 MET cc_start: 0.5295 (mmp) cc_final: 0.5021 (mmp) REVERT: B 605 MET cc_start: 0.5708 (tpt) cc_final: 0.4293 (tmm) REVERT: B 702 HIS cc_start: 0.5252 (OUTLIER) cc_final: 0.4158 (t70) REVERT: B 710 ASP cc_start: 0.5884 (OUTLIER) cc_final: 0.5610 (p0) REVERT: B 942 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: B 972 ARG cc_start: 0.5345 (OUTLIER) cc_final: 0.3811 (mmt90) REVERT: B 974 GLN cc_start: 0.7176 (tt0) cc_final: 0.6878 (tt0) REVERT: B 1057 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6883 (tp) REVERT: B 1112 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7407 (tp40) REVERT: B 1156 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.4867 (t0) REVERT: B 1230 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7189 (t0) REVERT: B 1696 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 1727 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6090 (tptm) REVERT: B 1948 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 2027 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8226 (t) REVERT: B 2034 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: B 2117 GLU cc_start: 0.8487 (mp0) cc_final: 0.8054 (mp0) REVERT: B 2122 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: B 2166 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8743 (ptpp) REVERT: B 2169 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7274 (mmtm) REVERT: B 2181 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8543 (mm) REVERT: B 2486 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7995 (tt) REVERT: B 2504 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8398 (tp) REVERT: C 587 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.5367 (mmp) REVERT: C 605 MET cc_start: 0.5767 (tpt) cc_final: 0.4196 (tmm) REVERT: C 702 HIS cc_start: 0.4787 (OUTLIER) cc_final: 0.4085 (t70) REVERT: C 703 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7453 (mtt90) REVERT: C 710 ASP cc_start: 0.5945 (OUTLIER) cc_final: 0.5674 (p0) REVERT: C 843 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: C 942 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6531 (tt0) REVERT: C 972 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.3792 (mmt90) REVERT: C 974 GLN cc_start: 0.7111 (tt0) cc_final: 0.6775 (tt0) REVERT: C 998 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7074 (tp) REVERT: C 1011 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: C 1057 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6365 (tp) REVERT: C 1156 ASP cc_start: 0.5140 (OUTLIER) cc_final: 0.4793 (t0) REVERT: C 1230 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7143 (t0) REVERT: C 1528 TRP cc_start: 0.8555 (t-100) cc_final: 0.8331 (t-100) REVERT: C 1727 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6081 (tptm) REVERT: C 1948 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7600 (t70) REVERT: C 2034 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: C 2045 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8501 (tpt) REVERT: C 2117 GLU cc_start: 0.8456 (mp0) cc_final: 0.8087 (mp0) REVERT: C 2122 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: C 2169 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7361 (mmtm) REVERT: C 2181 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (mm) REVERT: C 2486 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7931 (tt) REVERT: C 2504 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8255 (tp) outliers start: 301 outliers final: 122 residues processed: 615 average time/residue: 0.4112 time to fit residues: 415.6209 Evaluate side-chains 456 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 280 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1360 LYS Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1682 CYS Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2169 LYS Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1112 GLN Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1535 HIS Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1682 CYS Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2122 MET Chi-restraints excluded: chain B residue 2166 LYS Chi-restraints excluded: chain B residue 2169 LYS Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2435 LEU Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 703 ARG Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 982 CYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1360 LYS Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1682 CYS Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1948 ASP Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2045 MET Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2169 LYS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2181 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2435 LEU Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2486 LEU Chi-restraints excluded: chain C residue 2487 VAL Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 379 optimal weight: 0.8980 chunk 245 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 155 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 GLN A1040 ASN A1535 HIS ** A2250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2308 GLN B 930 GLN B1040 ASN ** B1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2308 GLN C1040 ASN C1114 GLN C1535 HIS ** C2228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.188425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121247 restraints weight = 47887.714| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.70 r_work: 0.3279 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32373 Z= 0.157 Angle : 0.602 8.711 43815 Z= 0.308 Chirality : 0.040 0.193 4983 Planarity : 0.005 0.049 5325 Dihedral : 14.937 178.959 4727 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.81 % Rotamer: Outliers : 6.75 % Allowed : 20.85 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3747 helix: 1.36 (0.10), residues: 2697 sheet: -0.99 (0.31), residues: 252 loop : -1.96 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2188 HIS 0.011 0.001 HIS B1535 PHE 0.027 0.002 PHE B 588 TYR 0.014 0.001 TYR B 952 ARG 0.009 0.000 ARG B1341 Details of bonding type rmsd hydrogen bonds : bond 0.05823 ( 2059) hydrogen bonds : angle 4.34390 ( 6096) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.30608 ( 6) covalent geometry : bond 0.00352 (32370) covalent geometry : angle 0.60196 (43809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 283 time to evaluate : 3.611 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: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5701 (tpt) cc_final: 0.4275 (tmm) REVERT: A 702 HIS cc_start: 0.5278 (OUTLIER) cc_final: 0.4458 (t70) REVERT: A 710 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.5797 (p0) REVERT: A 974 GLN cc_start: 0.6989 (tt0) cc_final: 0.6543 (tt0) REVERT: A 979 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7422 (mt) REVERT: A 983 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7326 (mp) REVERT: A 1156 ASP cc_start: 0.5001 (OUTLIER) cc_final: 0.4359 (t0) REVERT: A 1719 MET cc_start: 0.8913 (mtp) cc_final: 0.8703 (mtt) REVERT: A 1727 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.5953 (tptm) REVERT: A 2034 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: A 2122 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8359 (mtp) REVERT: A 2420 MET cc_start: 0.6241 (tmm) cc_final: 0.6034 (tmm) REVERT: A 2504 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8285 (tp) REVERT: A 2511 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: B 587 MET cc_start: 0.5458 (mmp) cc_final: 0.5219 (mmp) REVERT: B 605 MET cc_start: 0.5554 (tpt) cc_final: 0.4224 (tmm) REVERT: B 702 HIS cc_start: 0.4740 (OUTLIER) cc_final: 0.3896 (t70) REVERT: B 708 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6525 (mt) REVERT: B 710 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5767 (p0) REVERT: B 974 GLN cc_start: 0.7136 (tt0) cc_final: 0.6795 (tt0) REVERT: B 1156 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4313 (t0) REVERT: B 1562 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6154 (tpt-90) REVERT: B 1696 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7645 (mt) REVERT: B 1727 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.5942 (tptm) REVERT: B 2027 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7962 (t) REVERT: B 2034 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: B 2117 GLU cc_start: 0.8527 (mp0) cc_final: 0.8016 (mp0) REVERT: B 2194 MET cc_start: 0.7254 (mtp) cc_final: 0.7019 (mtp) REVERT: B 2462 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9089 (mp) REVERT: B 2504 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 605 MET cc_start: 0.5395 (tpt) cc_final: 0.3929 (tmm) REVERT: C 710 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.5992 (p0) REVERT: C 843 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: C 974 GLN cc_start: 0.7218 (tt0) cc_final: 0.6772 (tt0) REVERT: C 1011 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: C 1156 ASP cc_start: 0.5221 (OUTLIER) cc_final: 0.4512 (t0) REVERT: C 1355 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 1422 GLU cc_start: 0.8821 (tp30) cc_final: 0.8583 (mm-30) REVERT: C 1727 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6118 (tptm) REVERT: C 2034 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: C 2117 GLU cc_start: 0.8503 (mp0) cc_final: 0.8085 (mp0) REVERT: C 2122 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8365 (mtm) REVERT: C 2462 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8949 (mp) REVERT: C 2504 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8030 (tp) REVERT: C 2511 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.7495 (tt0) outliers start: 226 outliers final: 130 residues processed: 473 average time/residue: 0.4334 time to fit residues: 345.1611 Evaluate side-chains 429 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 268 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2308 GLN Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2478 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2195 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2308 GLN Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1114 GLN Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1285 ILE Chi-restraints excluded: chain C residue 1304 SER Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 90 optimal weight: 0.7980 chunk 181 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 chunk 362 optimal weight: 0.0370 chunk 92 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 chunk 169 optimal weight: 0.8980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN A2034 GLN ** A2250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2308 GLN B1230 ASN B1535 HIS ** B1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2308 GLN C1230 ASN C1535 HIS ** C2228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2308 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.190682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121064 restraints weight = 47957.188| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.29 r_work: 0.3319 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32373 Z= 0.117 Angle : 0.537 8.522 43815 Z= 0.270 Chirality : 0.037 0.161 4983 Planarity : 0.004 0.046 5325 Dihedral : 13.511 177.926 4615 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.20 % Allowed : 21.65 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.14), residues: 3747 helix: 1.85 (0.10), residues: 2700 sheet: -0.93 (0.30), residues: 252 loop : -1.49 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2188 HIS 0.010 0.001 HIS C1535 PHE 0.022 0.001 PHE B 588 TYR 0.014 0.001 TYR A 952 ARG 0.005 0.000 ARG B1341 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 2059) hydrogen bonds : angle 4.04874 ( 6096) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.27845 ( 6) covalent geometry : bond 0.00246 (32370) covalent geometry : angle 0.53664 (43809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 286 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5662 (tpt) cc_final: 0.4152 (tmm) REVERT: A 702 HIS cc_start: 0.5115 (OUTLIER) cc_final: 0.4354 (t70) REVERT: A 710 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6075 (p0) REVERT: A 974 GLN cc_start: 0.7057 (tt0) cc_final: 0.6540 (tt0) REVERT: A 1057 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 1156 ASP cc_start: 0.5029 (OUTLIER) cc_final: 0.4391 (t0) REVERT: A 1562 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6168 (tpt-90) REVERT: A 1719 MET cc_start: 0.8913 (mtp) cc_final: 0.8696 (mtt) REVERT: A 1727 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.5761 (tptt) REVERT: A 2117 GLU cc_start: 0.8590 (mp0) cc_final: 0.8237 (mp0) REVERT: A 2420 MET cc_start: 0.6279 (tmm) cc_final: 0.6074 (tmm) REVERT: A 2504 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (tp) REVERT: A 2511 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: B 605 MET cc_start: 0.5552 (tpt) cc_final: 0.4185 (tmm) REVERT: B 702 HIS cc_start: 0.4586 (OUTLIER) cc_final: 0.3696 (t70) REVERT: B 710 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5663 (p0) REVERT: B 809 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5263 (mp) REVERT: B 834 ASN cc_start: 0.6507 (m-40) cc_final: 0.5655 (t0) REVERT: B 974 GLN cc_start: 0.7066 (tt0) cc_final: 0.6748 (tt0) REVERT: B 1057 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6758 (tp) REVERT: B 1156 ASP cc_start: 0.5086 (OUTLIER) cc_final: 0.4239 (t0) REVERT: B 1562 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6165 (tpt-90) REVERT: B 1696 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7505 (mp) REVERT: B 1727 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.5764 (tptp) REVERT: B 2027 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7965 (t) REVERT: B 2034 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: B 2117 GLU cc_start: 0.8516 (mp0) cc_final: 0.8022 (mp0) REVERT: B 2504 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 2511 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: C 605 MET cc_start: 0.5482 (tpt) cc_final: 0.4044 (tmm) REVERT: C 710 ASP cc_start: 0.6338 (OUTLIER) cc_final: 0.6068 (p0) REVERT: C 843 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: C 974 GLN cc_start: 0.7293 (tt0) cc_final: 0.6869 (tt0) REVERT: C 1011 MET cc_start: 0.7808 (mtt) cc_final: 0.7510 (mtp) REVERT: C 1156 ASP cc_start: 0.5173 (OUTLIER) cc_final: 0.4451 (t0) REVERT: C 1230 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7098 (t0) REVERT: C 1562 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6162 (tpt170) REVERT: C 1727 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.5753 (tptm) REVERT: C 2018 ASP cc_start: 0.8844 (t0) cc_final: 0.8592 (t0) REVERT: C 2034 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: C 2117 GLU cc_start: 0.8432 (mp0) cc_final: 0.8021 (mp0) REVERT: C 2462 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8896 (mp) REVERT: C 2504 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 2511 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7369 (mp0) outliers start: 174 outliers final: 96 residues processed: 425 average time/residue: 0.4379 time to fit residues: 316.4041 Evaluate side-chains 392 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 266 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2308 GLN Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1285 ILE Chi-restraints excluded: chain C residue 1535 HIS Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 357 optimal weight: 30.0000 chunk 344 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 213 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2034 GLN A2250 GLN A2308 GLN B1230 ASN B1535 HIS ** B1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2034 GLN ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1230 ASN C1535 HIS ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.187899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117319 restraints weight = 47895.388| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.29 r_work: 0.3274 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32373 Z= 0.153 Angle : 0.564 9.089 43815 Z= 0.284 Chirality : 0.039 0.190 4983 Planarity : 0.004 0.044 5325 Dihedral : 12.851 176.515 4586 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 5.44 % Allowed : 22.25 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3747 helix: 1.90 (0.10), residues: 2703 sheet: -0.92 (0.29), residues: 255 loop : -1.30 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2188 HIS 0.011 0.001 HIS C1535 PHE 0.021 0.001 PHE B 588 TYR 0.025 0.001 TYR B2219 ARG 0.008 0.000 ARG C1944 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 2059) hydrogen bonds : angle 4.05488 ( 6096) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.24228 ( 6) covalent geometry : bond 0.00357 (32370) covalent geometry : angle 0.56414 (43809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 275 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5574 (tpt) cc_final: 0.4029 (tmm) REVERT: A 702 HIS cc_start: 0.5034 (OUTLIER) cc_final: 0.4333 (t70) REVERT: A 710 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6396 (p0) REVERT: A 974 GLN cc_start: 0.7081 (tt0) cc_final: 0.6596 (tt0) REVERT: A 1156 ASP cc_start: 0.5017 (OUTLIER) cc_final: 0.4324 (t0) REVERT: A 1534 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7339 (mmt90) REVERT: A 1562 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6210 (tpt-90) REVERT: A 1716 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 1719 MET cc_start: 0.8927 (mtp) cc_final: 0.8714 (mtt) REVERT: A 1727 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6160 (tptm) REVERT: A 2005 LEU cc_start: 0.7857 (tt) cc_final: 0.7626 (mt) REVERT: A 2117 GLU cc_start: 0.8631 (mp0) cc_final: 0.8343 (mp0) REVERT: A 2420 MET cc_start: 0.6223 (tmm) cc_final: 0.5978 (tmm) REVERT: A 2467 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8959 (ptm) REVERT: A 2504 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8197 (tp) REVERT: A 2511 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: B 605 MET cc_start: 0.5553 (tpt) cc_final: 0.4164 (tmm) REVERT: B 710 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5404 (p0) REVERT: B 711 MET cc_start: 0.6450 (ttp) cc_final: 0.5889 (tpt) REVERT: B 809 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5255 (mp) REVERT: B 974 GLN cc_start: 0.7123 (tt0) cc_final: 0.6758 (tt0) REVERT: B 1156 ASP cc_start: 0.5116 (OUTLIER) cc_final: 0.4239 (t0) REVERT: B 1354 MET cc_start: 0.8484 (mmm) cc_final: 0.8059 (mmm) REVERT: B 1696 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7545 (mp) REVERT: B 1727 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6024 (tptm) REVERT: B 2117 GLU cc_start: 0.8525 (mp0) cc_final: 0.7995 (mp0) REVERT: B 2504 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8156 (tp) REVERT: C 605 MET cc_start: 0.5400 (tpt) cc_final: 0.3948 (tmm) REVERT: C 710 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.5937 (p0) REVERT: C 843 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: C 974 GLN cc_start: 0.7295 (tt0) cc_final: 0.6823 (tt0) REVERT: C 1156 ASP cc_start: 0.5194 (OUTLIER) cc_final: 0.4450 (t0) REVERT: C 1230 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6791 (t0) REVERT: C 1355 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7998 (tt0) REVERT: C 1527 ARG cc_start: 0.9046 (ptm-80) cc_final: 0.8623 (ptm-80) REVERT: C 1562 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6231 (tpt-90) REVERT: C 1727 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6122 (tptm) REVERT: C 2005 LEU cc_start: 0.7850 (tt) cc_final: 0.7600 (mt) REVERT: C 2018 ASP cc_start: 0.8937 (t0) cc_final: 0.8687 (t0) REVERT: C 2034 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: C 2117 GLU cc_start: 0.8508 (mp0) cc_final: 0.8129 (mp0) REVERT: C 2504 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8075 (tp) REVERT: C 2511 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.7450 (mp0) outliers start: 182 outliers final: 120 residues processed: 426 average time/residue: 0.3939 time to fit residues: 284.3513 Evaluate side-chains 408 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 264 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2308 GLN Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2195 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2513 MET Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 256 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 chunk 323 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 328 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN A2308 GLN B1535 HIS ** B1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2308 GLN C1018 HIS C1230 ASN C1535 HIS ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113564 restraints weight = 48083.938| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.12 r_work: 0.3234 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32373 Z= 0.206 Angle : 0.608 7.481 43815 Z= 0.306 Chirality : 0.041 0.215 4983 Planarity : 0.004 0.043 5325 Dihedral : 12.546 177.286 4576 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 6.12 % Allowed : 21.86 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.14), residues: 3747 helix: 1.78 (0.10), residues: 2700 sheet: -0.78 (0.29), residues: 261 loop : -1.36 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C2044 HIS 0.010 0.001 HIS C1535 PHE 0.022 0.002 PHE B 588 TYR 0.020 0.002 TYR B2219 ARG 0.004 0.000 ARG A1944 Details of bonding type rmsd hydrogen bonds : bond 0.05739 ( 2059) hydrogen bonds : angle 4.17282 ( 6096) SS BOND : bond 0.00122 ( 3) SS BOND : angle 0.27556 ( 6) covalent geometry : bond 0.00497 (32370) covalent geometry : angle 0.60799 (43809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 264 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5612 (tpt) cc_final: 0.4105 (tmm) REVERT: A 710 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6343 (p0) REVERT: A 974 GLN cc_start: 0.7201 (tt0) cc_final: 0.6749 (tt0) REVERT: A 1156 ASP cc_start: 0.5355 (OUTLIER) cc_final: 0.4534 (t0) REVERT: A 1531 GLU cc_start: 0.8608 (tp30) cc_final: 0.8401 (tp30) REVERT: A 1534 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7379 (mmt90) REVERT: A 1562 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6266 (tpt-90) REVERT: A 1716 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 1719 MET cc_start: 0.8939 (mtp) cc_final: 0.8732 (mtt) REVERT: A 1727 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6438 (tptm) REVERT: A 2005 LEU cc_start: 0.7926 (tt) cc_final: 0.7701 (mt) REVERT: A 2117 GLU cc_start: 0.8624 (mp0) cc_final: 0.8319 (mp0) REVERT: A 2420 MET cc_start: 0.6233 (tmm) cc_final: 0.5964 (tmm) REVERT: A 2467 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8960 (ptm) REVERT: A 2504 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 605 MET cc_start: 0.5556 (tpt) cc_final: 0.4062 (tmm) REVERT: B 710 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5328 (p0) REVERT: B 711 MET cc_start: 0.6593 (ttp) cc_final: 0.6047 (tpt) REVERT: B 809 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5308 (mp) REVERT: B 974 GLN cc_start: 0.7181 (tt0) cc_final: 0.6876 (tt0) REVERT: B 1156 ASP cc_start: 0.5124 (OUTLIER) cc_final: 0.4213 (t0) REVERT: B 1354 MET cc_start: 0.8500 (mmm) cc_final: 0.8299 (tpp) REVERT: B 1562 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6271 (tpt-90) REVERT: B 1696 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7558 (mp) REVERT: B 1727 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.6433 (tptp) REVERT: B 1791 MET cc_start: 0.8333 (mmt) cc_final: 0.8092 (mmt) REVERT: B 2117 GLU cc_start: 0.8562 (mp0) cc_final: 0.8028 (mp0) REVERT: B 2504 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8293 (tp) REVERT: C 605 MET cc_start: 0.5307 (tpt) cc_final: 0.3845 (tmm) REVERT: C 710 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6167 (p0) REVERT: C 843 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: C 974 GLN cc_start: 0.7155 (tt0) cc_final: 0.6706 (tt0) REVERT: C 1527 ARG cc_start: 0.9042 (ptm-80) cc_final: 0.8629 (ptm-80) REVERT: C 1716 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8288 (mp) REVERT: C 1727 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.6457 (tptp) REVERT: C 1952 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6602 (p) REVERT: C 2005 LEU cc_start: 0.7926 (tt) cc_final: 0.7689 (mt) REVERT: C 2034 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: C 2117 GLU cc_start: 0.8573 (mp0) cc_final: 0.8324 (mp0) REVERT: C 2193 PHE cc_start: 0.7402 (m-10) cc_final: 0.7160 (m-10) REVERT: C 2504 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8228 (tp) outliers start: 205 outliers final: 136 residues processed: 437 average time/residue: 0.3832 time to fit residues: 282.2751 Evaluate side-chains 409 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 252 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1950 LEU Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2195 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1535 HIS Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 230 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 318 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2100 HIS ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1535 HIS B1951 HIS C1230 ASN C1535 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115937 restraints weight = 47932.537| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.22 r_work: 0.3256 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32373 Z= 0.153 Angle : 0.567 7.785 43815 Z= 0.283 Chirality : 0.039 0.195 4983 Planarity : 0.004 0.043 5325 Dihedral : 12.240 176.726 4563 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 4.75 % Allowed : 23.18 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.14), residues: 3747 helix: 1.92 (0.10), residues: 2694 sheet: -0.70 (0.29), residues: 261 loop : -1.26 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C2044 HIS 0.018 0.001 HIS C1535 PHE 0.019 0.001 PHE B1977 TYR 0.015 0.001 TYR B2219 ARG 0.003 0.000 ARG B1944 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 2059) hydrogen bonds : angle 4.02787 ( 6096) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.24419 ( 6) covalent geometry : bond 0.00358 (32370) covalent geometry : angle 0.56739 (43809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 271 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5551 (tpt) cc_final: 0.4109 (tmm) REVERT: A 710 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6360 (p0) REVERT: A 974 GLN cc_start: 0.7231 (tt0) cc_final: 0.6805 (tt0) REVERT: A 1156 ASP cc_start: 0.5353 (OUTLIER) cc_final: 0.4555 (t0) REVERT: A 1534 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7392 (mmt90) REVERT: A 1716 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 1719 MET cc_start: 0.8915 (mtp) cc_final: 0.8708 (mtt) REVERT: A 1727 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6311 (tptm) REVERT: A 1968 ASP cc_start: 0.7756 (m-30) cc_final: 0.7448 (t0) REVERT: A 2005 LEU cc_start: 0.7889 (tt) cc_final: 0.7685 (mt) REVERT: A 2420 MET cc_start: 0.6231 (tmm) cc_final: 0.5950 (tmm) REVERT: A 2467 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8898 (ptm) REVERT: A 2504 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8103 (tp) REVERT: B 605 MET cc_start: 0.5531 (tpt) cc_final: 0.4068 (tmm) REVERT: B 710 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5357 (p0) REVERT: B 711 MET cc_start: 0.6519 (ttp) cc_final: 0.5996 (tpt) REVERT: B 809 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.5219 (mp) REVERT: B 974 GLN cc_start: 0.7119 (tt0) cc_final: 0.6818 (tt0) REVERT: B 1156 ASP cc_start: 0.5104 (OUTLIER) cc_final: 0.4165 (t0) REVERT: B 1354 MET cc_start: 0.8448 (mmm) cc_final: 0.8085 (mmm) REVERT: B 1562 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6308 (tpt170) REVERT: B 1696 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 1727 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6313 (tptm) REVERT: B 2117 GLU cc_start: 0.8543 (mp0) cc_final: 0.7982 (mp0) REVERT: B 2504 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8189 (tp) REVERT: C 605 MET cc_start: 0.5405 (tpt) cc_final: 0.3964 (tmm) REVERT: C 710 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6496 (p0) REVERT: C 843 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: C 974 GLN cc_start: 0.7101 (tt0) cc_final: 0.6640 (tt0) REVERT: C 1158 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6054 (tt) REVERT: C 1355 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7978 (tt0) REVERT: C 1527 ARG cc_start: 0.9042 (ptm-80) cc_final: 0.8643 (ptm-80) REVERT: C 1562 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6273 (tpt170) REVERT: C 1716 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (mp) REVERT: C 1727 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.6379 (tptm) REVERT: C 1952 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6539 (p) REVERT: C 2005 LEU cc_start: 0.7885 (tt) cc_final: 0.7680 (mt) REVERT: C 2034 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: C 2504 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8137 (tp) REVERT: C 2511 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.7413 (tt0) outliers start: 159 outliers final: 119 residues processed: 406 average time/residue: 0.3912 time to fit residues: 269.6992 Evaluate side-chains 399 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 257 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1700 MET Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 230 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 335 optimal weight: 0.0770 chunk 362 optimal weight: 9.9990 chunk 291 optimal weight: 0.5980 chunk 343 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 ASN B1535 HIS ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS C1535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122366 restraints weight = 48215.741| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.45 r_work: 0.3290 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.119 Angle : 0.527 8.324 43815 Z= 0.261 Chirality : 0.038 0.198 4983 Planarity : 0.004 0.044 5325 Dihedral : 11.853 177.450 4551 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 4.15 % Allowed : 23.72 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.14), residues: 3747 helix: 2.23 (0.10), residues: 2685 sheet: -0.65 (0.30), residues: 261 loop : -1.20 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1168 HIS 0.011 0.001 HIS B1535 PHE 0.025 0.001 PHE B1977 TYR 0.019 0.001 TYR B 952 ARG 0.002 0.000 ARG C 947 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 2059) hydrogen bonds : angle 3.84298 ( 6096) SS BOND : bond 0.00131 ( 3) SS BOND : angle 0.19794 ( 6) covalent geometry : bond 0.00266 (32370) covalent geometry : angle 0.52730 (43809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 283 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5525 (tpt) cc_final: 0.4067 (tmm) REVERT: A 710 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6364 (p0) REVERT: A 974 GLN cc_start: 0.7203 (tt0) cc_final: 0.6815 (tt0) REVERT: A 1156 ASP cc_start: 0.5288 (OUTLIER) cc_final: 0.4538 (t0) REVERT: A 1716 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8354 (mp) REVERT: A 1727 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6141 (tptm) REVERT: A 1968 ASP cc_start: 0.7756 (m-30) cc_final: 0.7489 (t0) REVERT: A 2420 MET cc_start: 0.6232 (tmm) cc_final: 0.5941 (tmm) REVERT: A 2467 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8936 (ptm) REVERT: A 2504 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8100 (tp) REVERT: B 605 MET cc_start: 0.5536 (tpt) cc_final: 0.4083 (tmm) REVERT: B 710 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5463 (p0) REVERT: B 711 MET cc_start: 0.6562 (ttp) cc_final: 0.6044 (tpt) REVERT: B 809 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5190 (mp) REVERT: B 974 GLN cc_start: 0.7165 (tt0) cc_final: 0.6851 (tt0) REVERT: B 1156 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.4431 (t0) REVERT: B 1354 MET cc_start: 0.8539 (mmm) cc_final: 0.8179 (mmm) REVERT: B 1562 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6395 (tpt170) REVERT: B 1696 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7577 (mp) REVERT: B 1727 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6130 (tptm) REVERT: B 1968 ASP cc_start: 0.7947 (m-30) cc_final: 0.7538 (t0) REVERT: B 2117 GLU cc_start: 0.8537 (mp0) cc_final: 0.7996 (mp0) REVERT: B 2504 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8187 (tp) REVERT: B 2511 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 605 MET cc_start: 0.5337 (tpt) cc_final: 0.3871 (tmm) REVERT: C 843 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: C 974 GLN cc_start: 0.7150 (tt0) cc_final: 0.6709 (tt0) REVERT: C 1158 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6122 (tt) REVERT: C 1355 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7974 (tt0) REVERT: C 1527 ARG cc_start: 0.9032 (ptm-80) cc_final: 0.8629 (ptm-80) REVERT: C 1562 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6366 (tpt170) REVERT: C 1716 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8113 (mp) REVERT: C 1727 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6111 (tptm) REVERT: C 1952 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6579 (p) REVERT: C 2034 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 2504 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8064 (tp) REVERT: C 2511 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.7383 (tt0) outliers start: 139 outliers final: 98 residues processed: 397 average time/residue: 0.3798 time to fit residues: 256.8070 Evaluate side-chains 384 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 263 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2447 ILE Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2513 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1535 HIS Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 350 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 298 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.188113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118214 restraints weight = 47942.570| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.20 r_work: 0.3285 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.132 Angle : 0.542 7.745 43815 Z= 0.269 Chirality : 0.038 0.195 4983 Planarity : 0.004 0.044 5325 Dihedral : 11.746 178.409 4543 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 4.18 % Allowed : 23.95 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.14), residues: 3747 helix: 2.25 (0.10), residues: 2679 sheet: -0.62 (0.30), residues: 261 loop : -1.19 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1168 HIS 0.032 0.001 HIS C1535 PHE 0.025 0.001 PHE B1977 TYR 0.021 0.001 TYR B1328 ARG 0.004 0.000 ARG C1534 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 2059) hydrogen bonds : angle 3.86343 ( 6096) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.21758 ( 6) covalent geometry : bond 0.00303 (32370) covalent geometry : angle 0.54210 (43809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 266 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5444 (tpt) cc_final: 0.3970 (tmm) REVERT: A 974 GLN cc_start: 0.7182 (tt0) cc_final: 0.6792 (tt0) REVERT: A 1156 ASP cc_start: 0.5244 (OUTLIER) cc_final: 0.4413 (t0) REVERT: A 1716 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 1727 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6258 (tptm) REVERT: A 1968 ASP cc_start: 0.7777 (m-30) cc_final: 0.7346 (t0) REVERT: A 2467 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8909 (ptm) REVERT: A 2504 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8072 (tp) REVERT: B 587 MET cc_start: 0.5795 (mmp) cc_final: 0.5595 (mmp) REVERT: B 605 MET cc_start: 0.5555 (tpt) cc_final: 0.4096 (tmm) REVERT: B 710 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5621 (p0) REVERT: B 974 GLN cc_start: 0.7115 (tt0) cc_final: 0.6789 (tt0) REVERT: B 1156 ASP cc_start: 0.5107 (OUTLIER) cc_final: 0.4242 (t0) REVERT: B 1516 MET cc_start: 0.5861 (ppp) cc_final: 0.5610 (ptt) REVERT: B 1562 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6393 (tpt170) REVERT: B 1696 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7505 (mp) REVERT: B 1727 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6164 (tptm) REVERT: B 2117 GLU cc_start: 0.8535 (mp0) cc_final: 0.7989 (mp0) REVERT: B 2504 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 2511 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: C 605 MET cc_start: 0.5317 (tpt) cc_final: 0.3841 (tmm) REVERT: C 843 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: C 974 GLN cc_start: 0.7152 (tt0) cc_final: 0.6709 (tt0) REVERT: C 1158 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6068 (tt) REVERT: C 1355 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7935 (tt0) REVERT: C 1516 MET cc_start: 0.5713 (ppp) cc_final: 0.5415 (mmt) REVERT: C 1527 ARG cc_start: 0.9040 (ptm-80) cc_final: 0.8635 (ptm-80) REVERT: C 1562 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6362 (tpt170) REVERT: C 1716 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8053 (mp) REVERT: C 1727 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6199 (tptm) REVERT: C 1952 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6569 (p) REVERT: C 2034 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.6474 (tt0) REVERT: C 2504 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8033 (tp) REVERT: C 2511 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.7352 (tt0) outliers start: 140 outliers final: 105 residues processed: 380 average time/residue: 0.3858 time to fit residues: 249.4670 Evaluate side-chains 384 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 258 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1719 MET Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2513 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1535 HIS Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 170 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 123 optimal weight: 0.0000 chunk 248 optimal weight: 0.6980 chunk 324 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 288 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS C1535 HIS C2250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118949 restraints weight = 48026.536| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.15 r_work: 0.3301 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.117 Angle : 0.530 9.127 43815 Z= 0.262 Chirality : 0.038 0.199 4983 Planarity : 0.004 0.044 5325 Dihedral : 11.589 178.518 4540 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 3.73 % Allowed : 24.46 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.14), residues: 3747 helix: 2.35 (0.10), residues: 2679 sheet: -0.60 (0.30), residues: 261 loop : -1.11 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1168 HIS 0.028 0.001 HIS C1535 PHE 0.025 0.001 PHE B1977 TYR 0.022 0.001 TYR B1328 ARG 0.005 0.000 ARG A1944 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 2059) hydrogen bonds : angle 3.81262 ( 6096) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.20116 ( 6) covalent geometry : bond 0.00259 (32370) covalent geometry : angle 0.52961 (43809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 265 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5453 (tpt) cc_final: 0.4004 (tmm) REVERT: A 974 GLN cc_start: 0.7226 (tt0) cc_final: 0.6843 (tt0) REVERT: A 1156 ASP cc_start: 0.5257 (OUTLIER) cc_final: 0.4440 (t0) REVERT: A 1716 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 1727 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6240 (tptm) REVERT: A 1968 ASP cc_start: 0.7756 (m-30) cc_final: 0.7359 (t0) REVERT: A 2175 MET cc_start: 0.7604 (mtp) cc_final: 0.7392 (mtm) REVERT: A 2467 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8939 (ptm) REVERT: A 2504 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 587 MET cc_start: 0.5877 (mmp) cc_final: 0.5649 (mmp) REVERT: B 605 MET cc_start: 0.5545 (tpt) cc_final: 0.4090 (tmm) REVERT: B 710 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5984 (p0) REVERT: B 809 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5195 (mp) REVERT: B 974 GLN cc_start: 0.7152 (tt0) cc_final: 0.6861 (tt0) REVERT: B 1156 ASP cc_start: 0.5068 (OUTLIER) cc_final: 0.4209 (t0) REVERT: B 1516 MET cc_start: 0.5832 (ppp) cc_final: 0.5567 (ptt) REVERT: B 1534 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7320 (mmt90) REVERT: B 1562 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6383 (tpt170) REVERT: B 1674 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7097 (mtt90) REVERT: B 1696 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 1727 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6127 (tptm) REVERT: B 2117 GLU cc_start: 0.8528 (mp0) cc_final: 0.7987 (mp0) REVERT: B 2504 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 2511 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: C 587 MET cc_start: 0.6272 (mmp) cc_final: 0.6072 (mmp) REVERT: C 605 MET cc_start: 0.5365 (tpt) cc_final: 0.3893 (tmm) REVERT: C 974 GLN cc_start: 0.7200 (tt0) cc_final: 0.6809 (tt0) REVERT: C 1158 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6152 (tt) REVERT: C 1355 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7955 (tt0) REVERT: C 1516 MET cc_start: 0.5698 (ppp) cc_final: 0.5409 (ptt) REVERT: C 1527 ARG cc_start: 0.9041 (ptm-80) cc_final: 0.8706 (ptt90) REVERT: C 1562 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6393 (tpt170) REVERT: C 1716 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8121 (mp) REVERT: C 1727 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6228 (tptm) REVERT: C 2034 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6456 (tt0) REVERT: C 2504 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8036 (tp) REVERT: C 2511 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.7374 (tt0) outliers start: 125 outliers final: 94 residues processed: 369 average time/residue: 0.3813 time to fit residues: 238.0641 Evaluate side-chains 373 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 259 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1719 MET Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 368 optimal weight: 20.0000 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 GLN C1535 HIS C2034 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119429 restraints weight = 48055.253| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.51 r_work: 0.3265 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.139 Angle : 0.545 9.026 43815 Z= 0.270 Chirality : 0.039 0.201 4983 Planarity : 0.004 0.044 5325 Dihedral : 11.467 179.308 4535 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 3.91 % Allowed : 24.34 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.14), residues: 3747 helix: 2.30 (0.10), residues: 2679 sheet: -0.58 (0.30), residues: 261 loop : -0.99 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2044 HIS 0.015 0.001 HIS C1535 PHE 0.025 0.001 PHE B1977 TYR 0.022 0.001 TYR B1328 ARG 0.003 0.000 ARG A1944 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 2059) hydrogen bonds : angle 3.87150 ( 6096) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.21979 ( 6) covalent geometry : bond 0.00325 (32370) covalent geometry : angle 0.54489 (43809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23793.10 seconds wall clock time: 414 minutes 37.89 seconds (24877.89 seconds total)