Starting phenix.real_space_refine on Fri Jun 27 09:34:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zu8_60481/06_2025/8zu8_60481_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zu8_60481/06_2025/8zu8_60481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zu8_60481/06_2025/8zu8_60481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zu8_60481/06_2025/8zu8_60481.map" model { file = "/net/cci-nas-00/data/ceres_data/8zu8_60481/06_2025/8zu8_60481_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zu8_60481/06_2025/8zu8_60481_neut.cif" } resolution = 3.9 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= -0.001 sd= 0.013 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 3 5.49 5 S 183 5.16 5 C 20850 2.51 5 N 5163 2.21 5 O 5202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31401 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10418 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10418 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 10412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10412 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 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: 19.03, per 1000 atoms: 0.61 Number of scatterers: 31401 At special positions: 0 Unit cell: (224.985, 218.193, 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 3 15.00 O 5202 8.00 N 5163 7.00 C 20850 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: 7.20 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: 173 helices and 9 sheets defined 71.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 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: 3.556A 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 Processing helix chain 'A' and resid 679 through 701 Proline residue: A 687 - end of helix removed outlier: 3.533A 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: 3.522A 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: 3.717A pdb=" N ASN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A1008 " --> pdb=" O VAL A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.503A 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: 3.614A 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: 3.827A pdb=" N LEU A1187 " --> pdb=" O SER A1183 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.700A pdb=" N LEU A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1232 removed outlier: 3.641A pdb=" N TRP A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.517A 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: 4.011A 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: 3.526A 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: 3.546A 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: 4.170A 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: 3.551A 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: 3.583A pdb=" N PHE A2485 " --> pdb=" O CYS A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2505 removed outlier: 3.714A 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 625 Processing helix chain 'B' and resid 625 through 644 removed outlier: 3.834A pdb=" N PHE B 629 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP B 630 " --> pdb=" O LEU B 626 " (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: 3.717A pdb=" N ASN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B1008 " --> pdb=" O VAL B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1026 removed outlier: 3.503A 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: 3.614A 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: 3.827A pdb=" N LEU B1187 " --> pdb=" O SER B1183 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.700A pdb=" N LEU B1203 " --> pdb=" O PHE B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1232 removed outlier: 3.570A pdb=" N TYR B1221 " --> pdb=" O CYS B1217 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.991A pdb=" N VAL B1310 " --> pdb=" O TYR B1306 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.517A pdb=" N LEU B1549 " --> pdb=" O ALA B1545 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1568 removed outlier: 4.231A 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: 4.011A 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: 3.609A 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: 3.526A 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: 3.546A 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: 3.551A 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: 3.715A pdb=" N GLU B2497 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 3.635A 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 625 Processing helix chain 'C' and resid 626 through 644 Processing helix chain 'C' and resid 679 through 701 Proline residue: C 687 - end of helix removed outlier: 3.533A 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 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: 3.717A pdb=" N ASN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C1008 " --> pdb=" O VAL C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1026 removed outlier: 3.503A 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: 3.614A pdb=" N LEU C1037 " --> pdb=" O ALA C1033 " (cutoff:3.500A) Proline residue: C1039 - end of helix Processing helix chain 'C' and resid 1099 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: 3.827A pdb=" N LEU C1187 " --> pdb=" O SER C1183 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.700A pdb=" N LEU C1203 " --> pdb=" O PHE C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1232 removed outlier: 3.532A pdb=" N ARG C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C1230 " --> pdb=" O ILE C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1302 removed outlier: 3.668A 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: 3.518A 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: 4.011A 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: 3.526A 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: 3.551A 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: 3.595A 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 2227 removed outlier: 3.595A pdb=" N ASP B2209 " --> pdb=" O GLN B2308 " (cutoff:3.500A) removed outlier: 3.526A 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 2227 removed outlier: 3.595A pdb=" N ASP C2209 " --> pdb=" O GLN C2308 " (cutoff:3.500A) removed outlier: 3.525A 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) 2056 hydrogen bonds defined for protein. 6087 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: 11.37 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4670 1.28 - 1.42: 8943 1.42 - 1.55: 18261 1.55 - 1.69: 16 1.69 - 1.82: 288 Bond restraints: 32178 Sorted by residual: 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 9.14e+01 bond pdb=" C39 L9Q C2601 " pdb=" C40 L9Q C2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.12e+01 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=" C31 L9Q A2601 " pdb=" O2 L9Q A2601 " ideal model delta sigma weight residual 1.330 1.464 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C31 L9Q C2601 " pdb=" O2 L9Q C2601 " ideal model delta sigma weight residual 1.330 1.464 -0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 32173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 42033 3.30 - 6.60: 1355 6.60 - 9.90: 174 9.90 - 13.20: 33 13.20 - 16.50: 6 Bond angle restraints: 43601 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 111.90 103.39 8.51 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE B 684 " pdb=" CA ILE B 684 " pdb=" C ILE B 684 " ideal model delta sigma weight residual 111.90 103.41 8.49 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE A 684 " pdb=" CA ILE A 684 " pdb=" C ILE A 684 " ideal model delta sigma weight residual 111.90 103.42 8.48 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE A1025 " pdb=" CA ILE A1025 " pdb=" C ILE A1025 " ideal model delta sigma weight residual 111.90 103.60 8.30 8.10e-01 1.52e+00 1.05e+02 angle pdb=" N ILE C1025 " pdb=" CA ILE C1025 " pdb=" C ILE C1025 " ideal model delta sigma weight residual 111.90 103.62 8.28 8.10e-01 1.52e+00 1.05e+02 ... (remaining 43596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 16814 31.29 - 62.58: 1970 62.58 - 93.87: 81 93.87 - 125.16: 9 125.16 - 156.46: 9 Dihedral angle restraints: 18883 sinusoidal: 7603 harmonic: 11280 Sorted by residual: dihedral pdb=" C21 L9Q C2601 " pdb=" C22 L9Q C2601 " pdb=" C23 L9Q C2601 " pdb=" C24 L9Q C2601 " ideal model delta sinusoidal sigma weight residual 179.52 -24.02 -156.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C21 L9Q A2601 " pdb=" C22 L9Q A2601 " pdb=" C23 L9Q A2601 " pdb=" C24 L9Q A2601 " ideal model delta sinusoidal sigma weight residual 179.52 -24.05 -156.43 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C21 L9Q B2601 " pdb=" C22 L9Q B2601 " pdb=" C23 L9Q B2601 " pdb=" C24 L9Q B2601 " ideal model delta sinusoidal sigma weight residual 179.52 -24.12 -156.36 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 18880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3594 0.092 - 0.183: 1117 0.183 - 0.275: 223 0.275 - 0.366: 35 0.366 - 0.458: 14 Chirality restraints: 4983 Sorted by residual: chirality pdb=" CA LEU A2493 " pdb=" N LEU A2493 " pdb=" C LEU A2493 " pdb=" CB LEU A2493 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+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 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CA LEU B2493 " pdb=" N LEU B2493 " pdb=" C LEU B2493 " pdb=" CB LEU B2493 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 4980 not shown) Planarity restraints: 5303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B2601 " 0.146 2.00e-02 2.50e+03 2.47e-01 6.10e+02 pdb=" C39 L9Q B2601 " -0.318 2.00e-02 2.50e+03 pdb=" C40 L9Q B2601 " 0.317 2.00e-02 2.50e+03 pdb=" C41 L9Q B2601 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q C2601 " -0.146 2.00e-02 2.50e+03 2.47e-01 6.10e+02 pdb=" C39 L9Q C2601 " 0.318 2.00e-02 2.50e+03 pdb=" C40 L9Q C2601 " -0.317 2.00e-02 2.50e+03 pdb=" C41 L9Q C2601 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A2601 " 0.146 2.00e-02 2.50e+03 2.47e-01 6.10e+02 pdb=" C39 L9Q A2601 " -0.318 2.00e-02 2.50e+03 pdb=" C40 L9Q A2601 " 0.317 2.00e-02 2.50e+03 pdb=" C41 L9Q A2601 " -0.145 2.00e-02 2.50e+03 ... (remaining 5300 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 12 1.88 - 2.64: 734 2.64 - 3.39: 40858 3.39 - 4.15: 77074 4.15 - 4.90: 132360 Nonbonded interactions: 251038 Sorted by model distance: nonbonded pdb=" N GLU C 679 " pdb=" OE1 GLU C 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 A 679 " pdb=" OE1 GLU A 679 " model vdw 1.126 3.120 nonbonded pdb=" CB LYS C2157 " pdb=" NZ LYS C2157 " model vdw 1.702 3.520 nonbonded pdb=" CB LYS B2157 " pdb=" NZ LYS B2157 " model vdw 1.702 3.520 ... (remaining 251033 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 2335 or (resid 2336 and (name N or name CA or \ name C or name O or name CB )) or resid 2337 through 2521 or resid 2601)) selection = (chain 'B' and (resid 570 through 2335 or (resid 2336 and (name N or name CA or \ name C or name O or name CB )) or resid 2337 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.540 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: 1.430 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 68.830 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.130 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 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 32181 Z= 0.752 Angle : 1.438 16.500 43607 Z= 0.961 Chirality : 0.093 0.458 4983 Planarity : 0.010 0.247 5303 Dihedral : 23.150 156.455 11560 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.99 % Allowed : 8.78 % Favored : 90.23 % Rotamer: Outliers : 26.27 % Allowed : 13.21 % Favored : 60.52 % 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: -3.55 (0.11), residues: 3747 helix: -1.94 (0.08), residues: 2691 sheet: -1.85 (0.29), residues: 246 loop : -3.20 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP A2403 HIS 0.006 0.001 HIS B1947 PHE 0.037 0.003 PHE A2307 TYR 0.109 0.005 TYR B2319 ARG 0.008 0.001 ARG B2336 Details of bonding type rmsd hydrogen bonds : bond 0.23492 ( 2056) hydrogen bonds : angle 7.63812 ( 6087) SS BOND : bond 0.01029 ( 3) SS BOND : angle 0.75550 ( 6) covalent geometry : bond 0.01094 (32178) covalent geometry : angle 1.43827 (43601) *********************** 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 1871 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 877 poor density : 994 time to evaluate : 3.291 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.4626 (tp) REVERT: A 812 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5737 (mt) REVERT: A 816 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6133 (mttt) REVERT: A 929 ILE cc_start: 0.2074 (OUTLIER) cc_final: 0.1707 (mm) REVERT: A 976 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 989 PHE cc_start: 0.8048 (m-80) cc_final: 0.7835 (m-80) REVERT: A 993 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7766 (mmtt) REVERT: A 1037 LEU cc_start: 0.8215 (tp) cc_final: 0.8006 (tp) REVERT: A 1112 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7659 (tp-100) REVERT: A 1155 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 1203 LEU cc_start: 0.9293 (tp) cc_final: 0.8990 (tt) REVERT: A 1215 TRP cc_start: 0.7820 (OUTLIER) cc_final: 0.7466 (m-90) REVERT: A 1334 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8776 (tppt) REVERT: A 2033 PHE cc_start: 0.8365 (t80) cc_final: 0.8031 (t80) REVERT: A 2046 PHE cc_start: 0.7426 (m-80) cc_final: 0.6995 (m-80) REVERT: A 2064 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7746 (mm110) REVERT: A 2200 VAL cc_start: 0.3694 (OUTLIER) cc_final: 0.3313 (m) REVERT: A 2486 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8655 (tt) REVERT: A 2492 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7164 (tt0) REVERT: A 2496 GLU cc_start: 0.8732 (tt0) cc_final: 0.8384 (tt0) REVERT: A 2503 LEU cc_start: 0.9212 (tp) cc_final: 0.8654 (tt) REVERT: B 639 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.4478 (tp) REVERT: B 812 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5730 (mt) REVERT: B 816 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6242 (mttt) REVERT: B 929 ILE cc_start: 0.2124 (OUTLIER) cc_final: 0.1845 (mm) REVERT: B 976 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: B 993 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7804 (mmtt) REVERT: B 1034 ILE cc_start: 0.8856 (mt) cc_final: 0.8620 (mm) REVERT: B 1112 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7604 (tp-100) REVERT: B 1155 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 1203 LEU cc_start: 0.9302 (tp) cc_final: 0.9032 (tt) REVERT: B 1215 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7728 (m-90) REVERT: B 1317 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8498 (m) REVERT: B 1334 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8700 (tppt) REVERT: B 1342 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 1951 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6692 (m170) REVERT: B 2015 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6782 (mtt) REVERT: B 2033 PHE cc_start: 0.8396 (t80) cc_final: 0.8041 (t80) REVERT: B 2046 PHE cc_start: 0.7487 (m-80) cc_final: 0.6987 (m-80) REVERT: B 2200 VAL cc_start: 0.3825 (OUTLIER) cc_final: 0.3603 (m) REVERT: B 2486 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 2496 GLU cc_start: 0.8702 (tt0) cc_final: 0.8275 (tt0) REVERT: C 639 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.4825 (tp) REVERT: C 812 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5811 (mt) REVERT: C 816 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6471 (mttt) REVERT: C 869 LYS cc_start: 0.6224 (mttt) cc_final: 0.5891 (mttt) REVERT: C 976 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: C 989 PHE cc_start: 0.8029 (m-80) cc_final: 0.7797 (m-80) REVERT: C 993 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7783 (mmtt) REVERT: C 996 LEU cc_start: 0.8682 (mt) cc_final: 0.8427 (mp) REVERT: C 1112 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7520 (tp-100) REVERT: C 1155 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8204 (tt) REVERT: C 1317 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8536 (m) REVERT: C 1334 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8776 (tppt) REVERT: C 1354 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: C 2033 PHE cc_start: 0.8420 (t80) cc_final: 0.8103 (t80) REVERT: C 2046 PHE cc_start: 0.7366 (m-80) cc_final: 0.6886 (m-80) REVERT: C 2064 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7603 (mm-40) REVERT: C 2123 ASP cc_start: 0.8837 (m-30) cc_final: 0.8562 (m-30) outliers start: 877 outliers final: 113 residues processed: 1577 average time/residue: 0.4468 time to fit residues: 1088.4111 Evaluate side-chains 678 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 525 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1669 GLN Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2064 GLN Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2116 VAL Chi-restraints excluded: chain A residue 2161 GLN Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2192 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 2443 LEU Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 843 PHE Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE 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 1184 ILE Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1334 LYS Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1346 SER Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1650 LEU Chi-restraints excluded: chain B residue 1669 GLN Chi-restraints excluded: chain B residue 1682 CYS Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1949 ILE Chi-restraints excluded: chain B residue 1951 HIS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 2015 MET Chi-restraints excluded: chain B residue 2028 LEU Chi-restraints excluded: chain B residue 2062 VAL Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2122 MET Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2200 VAL Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2443 LEU 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 C residue 581 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 822 THR Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 ARG Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1112 GLN Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1184 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1334 LYS Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1650 LEU Chi-restraints excluded: chain C residue 1652 ARG Chi-restraints excluded: chain C residue 1669 GLN Chi-restraints excluded: chain C residue 1682 CYS Chi-restraints excluded: chain C residue 1802 CYS Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 2028 LEU Chi-restraints excluded: chain C residue 2062 VAL Chi-restraints excluded: chain C residue 2064 GLN Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2443 LEU Chi-restraints excluded: chain C residue 2504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 7.9990 chunk 288 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 345 optimal weight: 0.0020 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 956 HIS A 977 GLN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1561 HIS A1567 GLN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2034 GLN A2064 GLN A2250 GLN ** A2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2369 ASN B 977 GLN B1012 ASN B1561 HIS B1567 GLN B1951 HIS ** B2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2369 ASN C 699 HIS C 873 GLN C 955 GLN C 956 HIS C 977 GLN ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1222 ASN C1414 HIS C1561 HIS C1567 GLN C1951 HIS C2034 GLN C2064 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2369 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.131816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.099054 restraints weight = 119735.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.100008 restraints weight = 59555.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.100758 restraints weight = 35204.297| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32181 Z= 0.180 Angle : 0.812 10.612 43607 Z= 0.402 Chirality : 0.045 0.241 4983 Planarity : 0.006 0.096 5303 Dihedral : 14.477 167.451 4641 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 8.39 % Allowed : 23.43 % Favored : 68.18 % 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: -0.45 (0.13), residues: 3747 helix: 0.46 (0.10), residues: 2691 sheet: -1.12 (0.30), residues: 249 loop : -2.39 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B2136 HIS 0.007 0.001 HIS C 956 PHE 0.026 0.002 PHE B1194 TYR 0.046 0.002 TYR C 604 ARG 0.012 0.001 ARG A 948 Details of bonding type rmsd hydrogen bonds : bond 0.06557 ( 2056) hydrogen bonds : angle 4.87143 ( 6087) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.54635 ( 6) covalent geometry : bond 0.00380 (32178) covalent geometry : angle 0.81210 (43601) *********************** 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 868 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 588 time to evaluate : 3.720 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.4898 (OUTLIER) cc_final: 0.4663 (tmm) REVERT: A 808 ARG cc_start: 0.8320 (tpt170) cc_final: 0.8047 (ttt180) REVERT: A 869 LYS cc_start: 0.6337 (mttt) cc_final: 0.5821 (mttt) REVERT: A 871 LEU cc_start: 0.7267 (tt) cc_final: 0.7049 (tp) REVERT: A 936 LEU cc_start: 0.8388 (tp) cc_final: 0.7858 (mp) REVERT: A 993 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7834 (mmmt) REVERT: A 1037 LEU cc_start: 0.8273 (tp) cc_final: 0.7848 (tp) REVERT: A 1052 GLN cc_start: 0.7194 (mt0) cc_final: 0.6961 (tp40) REVERT: A 1112 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8248 (tp-100) REVERT: A 1354 MET cc_start: 0.8413 (ttm) cc_final: 0.7901 (ttm) REVERT: A 1539 MET cc_start: 0.8946 (mtt) cc_final: 0.8583 (mtm) REVERT: A 1541 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8690 (m-30) REVERT: A 2033 PHE cc_start: 0.8567 (t80) cc_final: 0.8263 (t80) REVERT: A 2045 MET cc_start: 0.7463 (tmm) cc_final: 0.7007 (tmm) REVERT: A 2046 PHE cc_start: 0.7522 (m-80) cc_final: 0.5656 (m-80) REVERT: A 2459 PHE cc_start: 0.8118 (m-80) cc_final: 0.7832 (m-10) REVERT: A 2469 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6949 (tm-30) REVERT: A 2503 LEU cc_start: 0.9051 (tp) cc_final: 0.8703 (tt) REVERT: B 597 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6101 (mt) REVERT: B 807 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7075 (mtt-85) REVERT: B 833 MET cc_start: 0.7228 (mtp) cc_final: 0.6989 (mtp) REVERT: B 869 LYS cc_start: 0.5894 (mmtp) cc_final: 0.5488 (mmtp) REVERT: B 936 LEU cc_start: 0.8343 (tp) cc_final: 0.7920 (mp) REVERT: B 993 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7616 (mmtt) REVERT: B 1011 MET cc_start: 0.8225 (mmt) cc_final: 0.8004 (mmm) REVERT: B 1012 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7587 (p0) REVERT: B 1037 LEU cc_start: 0.8206 (tp) cc_final: 0.7716 (tp) REVERT: B 1674 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7570 (ptp90) REVERT: B 1731 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8081 (mpp) REVERT: B 1782 TYR cc_start: 0.6889 (p90) cc_final: 0.6589 (p90) REVERT: B 1952 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7298 (m) REVERT: B 2033 PHE cc_start: 0.8580 (t80) cc_final: 0.8163 (t80) REVERT: B 2045 MET cc_start: 0.7570 (tmm) cc_final: 0.7149 (tmm) REVERT: B 2046 PHE cc_start: 0.7623 (m-80) cc_final: 0.6727 (m-80) REVERT: B 2170 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 2469 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 2486 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8760 (tt) REVERT: B 2503 LEU cc_start: 0.9076 (tp) cc_final: 0.8621 (tt) REVERT: C 706 MET cc_start: 0.5898 (tpt) cc_final: 0.5693 (tpp) REVERT: C 833 MET cc_start: 0.7216 (mtp) cc_final: 0.6872 (mtp) REVERT: C 871 LEU cc_start: 0.7296 (tt) cc_final: 0.6985 (tp) REVERT: C 928 TYR cc_start: 0.3635 (t80) cc_final: 0.3365 (t80) REVERT: C 936 LEU cc_start: 0.8414 (tp) cc_final: 0.7972 (mp) REVERT: C 989 PHE cc_start: 0.8574 (m-80) cc_final: 0.8255 (m-80) REVERT: C 993 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7945 (mmmt) REVERT: C 1037 LEU cc_start: 0.8126 (tp) cc_final: 0.7646 (tp) REVERT: C 1337 ASP cc_start: 0.8932 (m-30) cc_final: 0.8596 (m-30) REVERT: C 1354 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7817 (ttm) REVERT: C 1724 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8208 (mtm180) REVERT: C 2005 LEU cc_start: 0.8807 (tp) cc_final: 0.8585 (mp) REVERT: C 2033 PHE cc_start: 0.8541 (t80) cc_final: 0.8282 (t80) REVERT: C 2045 MET cc_start: 0.7702 (tmm) cc_final: 0.7287 (tmm) REVERT: C 2046 PHE cc_start: 0.7554 (m-80) cc_final: 0.6345 (m-80) REVERT: C 2122 MET cc_start: 0.8749 (mmm) cc_final: 0.8531 (mmm) REVERT: C 2137 MET cc_start: 0.8122 (mtm) cc_final: 0.7766 (mtm) REVERT: C 2170 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8403 (mm) REVERT: C 2469 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 2503 LEU cc_start: 0.9088 (tp) cc_final: 0.8630 (tt) outliers start: 280 outliers final: 129 residues processed: 810 average time/residue: 0.4429 time to fit residues: 582.8920 Evaluate side-chains 611 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 466 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 805 PHE 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 930 GLN Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1310 VAL Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1541 ASP Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1958 THR Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2512 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 807 ARG Chi-restraints excluded: chain B residue 817 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 929 ILE Chi-restraints excluded: chain B residue 930 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1012 ASN Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1113 TRP Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2443 LEU Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2512 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1228 SER Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1310 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1724 ARG Chi-restraints excluded: chain C residue 1802 CYS Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2443 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2512 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 320 optimal weight: 0.8980 chunk 309 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 313 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 HIS A 973 GLN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 HIS A2011 GLN A2034 GLN A2042 HIS A2228 GLN A2321 ASN A2375 GLN B 925 ASN B 955 GLN B 956 HIS ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN B1230 ASN B2011 GLN B2228 GLN ** B2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2375 GLN C 973 GLN C1012 ASN ** C1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2011 GLN C2034 GLN C2228 GLN C2321 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.123266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.089894 restraints weight = 121350.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.088626 restraints weight = 64689.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089696 restraints weight = 44041.679| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 32181 Z= 0.279 Angle : 0.823 11.670 43607 Z= 0.413 Chirality : 0.045 0.286 4983 Planarity : 0.005 0.054 5303 Dihedral : 11.173 152.217 4437 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 8.33 % Allowed : 24.42 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.14), residues: 3747 helix: 1.07 (0.10), residues: 2667 sheet: -1.10 (0.29), residues: 255 loop : -1.77 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 841 HIS 0.010 0.002 HIS A1309 PHE 0.046 0.002 PHE A1194 TYR 0.052 0.002 TYR C 604 ARG 0.006 0.001 ARG C1036 Details of bonding type rmsd hydrogen bonds : bond 0.06263 ( 2056) hydrogen bonds : angle 4.97725 ( 6087) SS BOND : bond 0.00034 ( 3) SS BOND : angle 0.18064 ( 6) covalent geometry : bond 0.00617 (32178) covalent geometry : angle 0.82299 (43601) *********************** 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 721 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 443 time to evaluate : 4.781 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 839 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8326 (t) REVERT: A 936 LEU cc_start: 0.8484 (tp) cc_final: 0.8084 (mp) REVERT: A 993 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8060 (mmmt) REVERT: A 1112 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8237 (tp-100) REVERT: A 1215 TRP cc_start: 0.8394 (OUTLIER) cc_final: 0.7695 (m-90) REVERT: A 1310 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 1355 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 2033 PHE cc_start: 0.8723 (t80) cc_final: 0.8392 (t80) REVERT: A 2469 GLU cc_start: 0.7796 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 2504 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9301 (tp) REVERT: B 597 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6176 (tp) REVERT: B 839 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 870 MET cc_start: 0.6895 (tpt) cc_final: 0.6591 (tpt) REVERT: B 993 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7895 (mmtt) REVERT: B 1215 TRP cc_start: 0.8592 (OUTLIER) cc_final: 0.7490 (m-90) REVERT: B 1355 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8631 (tm-30) REVERT: B 1546 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8958 (tp30) REVERT: B 1549 LEU cc_start: 0.8968 (mt) cc_final: 0.8705 (mt) REVERT: B 1674 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7531 (ptp90) REVERT: B 1954 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6958 (p90) REVERT: B 2033 PHE cc_start: 0.8720 (t80) cc_final: 0.8327 (t80) REVERT: B 2044 TRP cc_start: 0.8250 (t-100) cc_final: 0.8013 (t-100) REVERT: B 2045 MET cc_start: 0.7748 (tmm) cc_final: 0.7517 (tmm) REVERT: B 2046 PHE cc_start: 0.8091 (m-80) cc_final: 0.7751 (m-80) REVERT: B 2288 MET cc_start: 0.6503 (ptm) cc_final: 0.6211 (ptm) REVERT: B 2469 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 2486 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8822 (tt) REVERT: C 833 MET cc_start: 0.7624 (mtp) cc_final: 0.7321 (mtp) REVERT: C 839 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8484 (t) REVERT: C 843 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7169 (m-10) REVERT: C 936 LEU cc_start: 0.8723 (tp) cc_final: 0.8367 (mp) REVERT: C 993 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8003 (mmtt) REVERT: C 1215 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7664 (m-90) REVERT: C 1310 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8277 (p) REVERT: C 1355 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8638 (tm-30) REVERT: C 1724 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8387 (mtm180) REVERT: C 1954 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7003 (p90) REVERT: C 2033 PHE cc_start: 0.8701 (t80) cc_final: 0.8302 (t80) REVERT: C 2122 MET cc_start: 0.8821 (mmm) cc_final: 0.8507 (mmm) REVERT: C 2469 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 2496 GLU cc_start: 0.8713 (tt0) cc_final: 0.8479 (tt0) outliers start: 278 outliers final: 166 residues processed: 652 average time/residue: 0.5612 time to fit residues: 617.8007 Evaluate side-chains 563 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 378 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1310 VAL Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1975 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2184 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2219 TYR Chi-restraints excluded: chain A residue 2401 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2487 VAL Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1357 ILE Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1649 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1739 ILE Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1955 ARG Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2184 ILE Chi-restraints excluded: chain B residue 2401 LEU Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 584 CYS Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1184 ILE Chi-restraints excluded: chain C residue 1187 LEU Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1310 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1547 ARG Chi-restraints excluded: chain C residue 1649 LEU Chi-restraints excluded: chain C residue 1652 ARG Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1724 ARG Chi-restraints excluded: chain C residue 1739 ILE Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1955 ARG Chi-restraints excluded: chain C residue 1969 VAL Chi-restraints excluded: chain C residue 1975 ILE Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2062 VAL Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2184 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2401 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2512 THR 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 219 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 363 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 372 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 ASN A2321 ASN ** B2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 HIS C2375 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.126030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089137 restraints weight = 120707.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.091588 restraints weight = 51120.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.093032 restraints weight = 31591.141| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32181 Z= 0.135 Angle : 0.687 11.150 43607 Z= 0.328 Chirality : 0.042 0.397 4983 Planarity : 0.004 0.048 5303 Dihedral : 10.285 145.478 4390 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 4.64 % Allowed : 27.35 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.98 (0.14), residues: 3747 helix: 1.52 (0.10), residues: 2688 sheet: -1.12 (0.29), residues: 255 loop : -1.71 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 580 HIS 0.007 0.001 HIS B1951 PHE 0.026 0.001 PHE B1194 TYR 0.027 0.001 TYR C 604 ARG 0.005 0.000 ARG B 953 Details of bonding type rmsd hydrogen bonds : bond 0.05052 ( 2056) hydrogen bonds : angle 4.38611 ( 6087) SS BOND : bond 0.00121 ( 3) SS BOND : angle 0.20103 ( 6) covalent geometry : bond 0.00289 (32178) covalent geometry : angle 0.68689 (43601) *********************** 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 635 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 480 time to evaluate : 3.707 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 866 ILE cc_start: 0.6777 (mt) cc_final: 0.6568 (mt) REVERT: A 936 LEU cc_start: 0.8462 (tp) cc_final: 0.8123 (mp) REVERT: A 989 PHE cc_start: 0.8509 (m-80) cc_final: 0.8141 (m-80) REVERT: A 993 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7775 (mmtt) REVERT: A 1112 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8084 (tp-100) REVERT: A 1355 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8567 (tm-30) REVERT: A 1708 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8391 (tp) REVERT: A 1974 ILE cc_start: 0.9095 (mm) cc_final: 0.8771 (tt) REVERT: A 2033 PHE cc_start: 0.8637 (t80) cc_final: 0.8408 (t80) REVERT: A 2097 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8805 (mtmm) REVERT: A 2288 MET cc_start: 0.6267 (ptm) cc_final: 0.6005 (tmm) REVERT: A 2459 PHE cc_start: 0.7864 (m-80) cc_final: 0.7528 (m-80) REVERT: A 2469 GLU cc_start: 0.7836 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 2470 GLU cc_start: 0.8793 (tp30) cc_final: 0.8477 (tp30) REVERT: A 2503 LEU cc_start: 0.9245 (tp) cc_final: 0.8903 (tp) REVERT: A 2504 ILE cc_start: 0.9605 (OUTLIER) cc_final: 0.9283 (tp) REVERT: B 597 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6202 (mt) REVERT: B 870 MET cc_start: 0.6756 (tpt) cc_final: 0.6495 (tpt) REVERT: B 993 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7607 (mmtt) REVERT: B 1215 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.7375 (m-90) REVERT: B 1310 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 1355 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8591 (tm-30) REVERT: B 1546 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8791 (tp30) REVERT: B 1654 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (mm) REVERT: B 1700 MET cc_start: 0.8375 (tpp) cc_final: 0.8126 (tpp) REVERT: B 1708 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8472 (tp) REVERT: B 1954 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6767 (p90) REVERT: B 1974 ILE cc_start: 0.9028 (mm) cc_final: 0.8708 (tt) REVERT: B 2033 PHE cc_start: 0.8661 (t80) cc_final: 0.8400 (t80) REVERT: B 2044 TRP cc_start: 0.8029 (t-100) cc_final: 0.7800 (t-100) REVERT: B 2097 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8791 (mtmm) REVERT: B 2290 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7837 (tpt90) REVERT: B 2467 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8558 (ptm) REVERT: B 2469 GLU cc_start: 0.7702 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 2486 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 2503 LEU cc_start: 0.9282 (tp) cc_final: 0.8547 (tt) REVERT: C 833 MET cc_start: 0.7586 (mtp) cc_final: 0.7264 (mtp) REVERT: C 866 ILE cc_start: 0.6483 (mm) cc_final: 0.6031 (mt) REVERT: C 993 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7835 (mmtt) REVERT: C 1196 LEU cc_start: 0.9578 (tp) cc_final: 0.9377 (tp) REVERT: C 1215 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7476 (m-90) REVERT: C 1355 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8684 (tm-30) REVERT: C 1954 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6716 (p90) REVERT: C 1974 ILE cc_start: 0.8999 (mm) cc_final: 0.8676 (tt) REVERT: C 2033 PHE cc_start: 0.8622 (t80) cc_final: 0.8329 (t80) REVERT: C 2137 MET cc_start: 0.8150 (mtm) cc_final: 0.7744 (mtm) REVERT: C 2290 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7874 (tpt90) REVERT: C 2469 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7139 (tm-30) REVERT: C 2503 LEU cc_start: 0.9324 (tp) cc_final: 0.8603 (tt) outliers start: 155 outliers final: 93 residues processed: 583 average time/residue: 0.3982 time to fit residues: 388.5231 Evaluate side-chains 528 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 419 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1791 MET Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2183 LEU Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2467 MET Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1310 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2512 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 379 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 349 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 973 GLN ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2321 ASN C 873 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.125459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090612 restraints weight = 121272.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.091642 restraints weight = 62502.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.091324 restraints weight = 40648.090| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32181 Z= 0.155 Angle : 0.675 10.608 43607 Z= 0.326 Chirality : 0.042 0.228 4983 Planarity : 0.004 0.051 5303 Dihedral : 9.629 135.017 4377 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 5.84 % Allowed : 27.50 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.14), residues: 3747 helix: 1.72 (0.10), residues: 2670 sheet: -1.10 (0.29), residues: 255 loop : -1.34 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 841 HIS 0.008 0.001 HIS B1951 PHE 0.025 0.001 PHE A2012 TYR 0.025 0.001 TYR C 604 ARG 0.004 0.000 ARG B2302 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 2056) hydrogen bonds : angle 4.34428 ( 6087) SS BOND : bond 0.00059 ( 3) SS BOND : angle 0.11257 ( 6) covalent geometry : bond 0.00345 (32178) covalent geometry : angle 0.67518 (43601) *********************** 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 636 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 441 time to evaluate : 3.981 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: 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 638 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.4374 (tmm) REVERT: A 866 ILE cc_start: 0.6792 (mt) cc_final: 0.6583 (mt) REVERT: A 936 LEU cc_start: 0.8571 (tp) cc_final: 0.8221 (mp) REVERT: A 993 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7791 (mmtt) REVERT: A 1112 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8217 (tp-100) REVERT: A 1215 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.7883 (m-90) REVERT: A 2033 PHE cc_start: 0.8625 (t80) cc_final: 0.8372 (t80) REVERT: A 2045 MET cc_start: 0.7597 (tmm) cc_final: 0.7254 (tmm) REVERT: A 2288 MET cc_start: 0.6252 (ptm) cc_final: 0.5887 (ptm) REVERT: A 2469 GLU cc_start: 0.7900 (tm-30) cc_final: 0.6913 (tm-30) REVERT: B 597 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5951 (tt) REVERT: B 833 MET cc_start: 0.7696 (mtt) cc_final: 0.7317 (mmm) REVERT: B 870 MET cc_start: 0.7167 (tpt) cc_final: 0.6782 (tpt) REVERT: B 993 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7735 (mmtt) REVERT: B 1215 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.7406 (m-90) REVERT: B 1546 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9066 (tp30) REVERT: B 1708 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 1731 MET cc_start: 0.8578 (mpp) cc_final: 0.8259 (mmp) REVERT: B 1954 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7027 (p90) REVERT: B 1974 ILE cc_start: 0.8982 (mm) cc_final: 0.8701 (tt) REVERT: B 2043 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 2045 MET cc_start: 0.7686 (tmm) cc_final: 0.7343 (tmm) REVERT: B 2288 MET cc_start: 0.6478 (ptm) cc_final: 0.6085 (ptm) REVERT: B 2467 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8553 (ptm) REVERT: B 2469 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6966 (tm-30) REVERT: B 2486 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8804 (tt) REVERT: C 833 MET cc_start: 0.7732 (mtp) cc_final: 0.7392 (mmm) REVERT: C 866 ILE cc_start: 0.6671 (mm) cc_final: 0.6344 (mt) REVERT: C 993 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7865 (mmtt) REVERT: C 1011 MET cc_start: 0.8358 (mmm) cc_final: 0.8068 (tpp) REVERT: C 1215 TRP cc_start: 0.8409 (OUTLIER) cc_final: 0.7758 (m-90) REVERT: C 1954 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7122 (p90) REVERT: C 1974 ILE cc_start: 0.8964 (mm) cc_final: 0.8673 (tt) REVERT: C 2097 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8768 (mtmm) REVERT: C 2290 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7885 (ttp80) REVERT: C 2469 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7217 (tm-30) outliers start: 195 outliers final: 127 residues processed: 578 average time/residue: 0.3908 time to fit residues: 380.7651 Evaluate side-chains 546 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 404 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1310 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1664 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1975 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2401 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1664 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1739 ILE Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2183 LEU Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2467 MET Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1969 VAL Chi-restraints excluded: chain C residue 1970 VAL Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2512 THR Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 300 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 ASN B 803 GLN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.119785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.084335 restraints weight = 124508.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.085042 restraints weight = 66974.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.084789 restraints weight = 44316.413| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.7789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 32181 Z= 0.325 Angle : 0.876 12.790 43607 Z= 0.438 Chirality : 0.049 0.405 4983 Planarity : 0.005 0.056 5303 Dihedral : 9.535 120.084 4370 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 7.55 % Allowed : 26.90 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.59 (0.14), residues: 3747 helix: 1.17 (0.10), residues: 2676 sheet: -1.39 (0.28), residues: 255 loop : -1.46 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 841 HIS 0.010 0.002 HIS A1309 PHE 0.048 0.003 PHE B1194 TYR 0.030 0.003 TYR B1418 ARG 0.007 0.001 ARG C2285 Details of bonding type rmsd hydrogen bonds : bond 0.06257 ( 2056) hydrogen bonds : angle 5.11994 ( 6087) SS BOND : bond 0.00136 ( 3) SS BOND : angle 0.15786 ( 6) covalent geometry : bond 0.00719 (32178) covalent geometry : angle 0.87624 (43601) *********************** 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 649 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 397 time to evaluate : 3.345 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: 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: symmetry clash REVERT: A 638 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4995 (tmm) REVERT: A 993 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7971 (mmtt) REVERT: A 1112 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (tp-100) REVERT: A 1215 TRP cc_start: 0.8599 (OUTLIER) cc_final: 0.7766 (m-90) REVERT: A 2033 PHE cc_start: 0.8741 (t80) cc_final: 0.8473 (t80) REVERT: A 2045 MET cc_start: 0.7967 (tmm) cc_final: 0.7749 (tmm) REVERT: A 2129 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9328 (p) REVERT: A 2178 LEU cc_start: 0.9316 (mm) cc_final: 0.8857 (tt) REVERT: A 2288 MET cc_start: 0.6298 (ptm) cc_final: 0.5951 (ptm) REVERT: A 2469 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7013 (tm-30) REVERT: B 597 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6111 (mp) REVERT: B 843 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: B 993 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7957 (mmtt) REVERT: B 1103 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 1215 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.7348 (m-90) REVERT: B 1731 MET cc_start: 0.8655 (mpp) cc_final: 0.8278 (mmp) REVERT: B 1954 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7151 (p90) REVERT: B 2033 PHE cc_start: 0.8658 (t80) cc_final: 0.8383 (t80) REVERT: B 2178 LEU cc_start: 0.9287 (mm) cc_final: 0.8846 (tp) REVERT: B 2288 MET cc_start: 0.6578 (ptm) cc_final: 0.6154 (ptm) REVERT: B 2290 ARG cc_start: 0.8298 (mtt180) cc_final: 0.8006 (ttp-110) REVERT: B 2469 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 2486 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8896 (tt) REVERT: C 833 MET cc_start: 0.8067 (mtp) cc_final: 0.7533 (mmm) REVERT: C 866 ILE cc_start: 0.6620 (mm) cc_final: 0.6419 (mm) REVERT: C 931 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7619 (p0) REVERT: C 993 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.7929 (mmtt) REVERT: C 1011 MET cc_start: 0.8649 (mmm) cc_final: 0.8309 (tpp) REVERT: C 1215 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.7437 (m-90) REVERT: C 1731 MET cc_start: 0.8976 (mmp) cc_final: 0.8688 (mmp) REVERT: C 1954 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7229 (p90) REVERT: C 2004 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5309 (m-80) REVERT: C 2178 LEU cc_start: 0.9311 (mm) cc_final: 0.8932 (tt) REVERT: C 2469 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7218 (tm-30) outliers start: 252 outliers final: 184 residues processed: 564 average time/residue: 0.3753 time to fit residues: 354.8030 Evaluate side-chains 571 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 369 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1296 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1664 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1964 MET Chi-restraints excluded: chain A residue 1970 VAL 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 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2219 TYR Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2401 LEU Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 843 PHE Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1211 ARG Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1226 ILE Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1357 ILE Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1513 PHE Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1649 LEU Chi-restraints excluded: chain B residue 1664 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1714 VAL Chi-restraints excluded: chain B residue 1739 ILE Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2062 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2219 TYR Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2401 LEU Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 931 ASN Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1184 ILE Chi-restraints excluded: chain C residue 1193 CYS Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1649 LEU Chi-restraints excluded: chain C residue 1652 ARG Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1710 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1948 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1969 VAL Chi-restraints excluded: chain C residue 1970 VAL Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2005 LEU Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2111 LEU Chi-restraints excluded: chain C residue 2155 THR Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2401 LEU Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 51 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 293 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 chunk 274 optimal weight: 0.0980 chunk 233 optimal weight: 20.0000 chunk 368 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 GLN B1789 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.123421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086097 restraints weight = 121750.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.088475 restraints weight = 52775.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.089874 restraints weight = 32825.960| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32181 Z= 0.132 Angle : 0.697 11.943 43607 Z= 0.331 Chirality : 0.042 0.360 4983 Planarity : 0.004 0.057 5303 Dihedral : 9.093 117.215 4368 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.03 % Allowed : 29.39 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.29 (0.14), residues: 3747 helix: 1.71 (0.10), residues: 2685 sheet: -1.27 (0.29), residues: 264 loop : -1.29 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B2188 HIS 0.007 0.001 HIS B1951 PHE 0.047 0.002 PHE B1194 TYR 0.029 0.001 TYR A 872 ARG 0.006 0.000 ARG A2119 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 2056) hydrogen bonds : angle 4.29998 ( 6087) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.23924 ( 6) covalent geometry : bond 0.00284 (32178) covalent geometry : angle 0.69752 (43601) *********************** 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 620 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 452 time to evaluate : 3.298 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: 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: symmetry clash REVERT: A 638 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.5065 (tmm) REVERT: A 993 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7659 (mmtt) REVERT: A 1215 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7969 (t-100) REVERT: A 1342 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9343 (tp) REVERT: A 1708 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 2043 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 2045 MET cc_start: 0.7896 (tmm) cc_final: 0.7572 (tmm) REVERT: A 2118 LEU cc_start: 0.9647 (mm) cc_final: 0.8393 (mm) REVERT: A 2137 MET cc_start: 0.8419 (mmm) cc_final: 0.8076 (mmm) REVERT: A 2178 LEU cc_start: 0.9302 (mm) cc_final: 0.8987 (tt) REVERT: A 2288 MET cc_start: 0.6367 (ptm) cc_final: 0.6048 (ptm) REVERT: A 2469 GLU cc_start: 0.7892 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 2470 GLU cc_start: 0.8729 (tp30) cc_final: 0.8097 (tp30) REVERT: B 597 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6172 (tt) REVERT: B 606 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 993 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7719 (mmtt) REVERT: B 1215 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.7452 (m-90) REVERT: B 1547 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8319 (mtm110) REVERT: B 1653 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7626 (tpm170) REVERT: B 1708 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8620 (tp) REVERT: B 1731 MET cc_start: 0.8537 (mpp) cc_final: 0.8111 (mmp) REVERT: B 1738 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8149 (tt0) REVERT: B 1954 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6809 (p90) REVERT: B 2033 PHE cc_start: 0.8636 (t80) cc_final: 0.8350 (t80) REVERT: B 2043 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8843 (mt) REVERT: B 2178 LEU cc_start: 0.9281 (mm) cc_final: 0.9010 (tt) REVERT: B 2288 MET cc_start: 0.6564 (ptm) cc_final: 0.6224 (ptm) REVERT: B 2469 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6861 (tm-30) REVERT: B 2486 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8855 (tt) REVERT: B 2503 LEU cc_start: 0.9268 (tp) cc_final: 0.8620 (tt) REVERT: C 606 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6845 (t80) REVERT: C 833 MET cc_start: 0.7893 (mtp) cc_final: 0.7413 (mmm) REVERT: C 866 ILE cc_start: 0.6644 (mm) cc_final: 0.6205 (mt) REVERT: C 931 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7749 (p0) REVERT: C 947 ARG cc_start: 0.8279 (mmt180) cc_final: 0.7804 (mmm-85) REVERT: C 993 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7700 (mmtt) REVERT: C 1215 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7731 (m-90) REVERT: C 1708 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8720 (tp) REVERT: C 1954 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6895 (p90) REVERT: C 2043 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8807 (mt) REVERT: C 2178 LEU cc_start: 0.9290 (mm) cc_final: 0.9028 (tt) REVERT: C 2469 GLU cc_start: 0.7797 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 2503 LEU cc_start: 0.9301 (tp) cc_final: 0.9052 (tp) REVERT: C 2504 ILE cc_start: 0.9565 (tp) cc_final: 0.9317 (tp) outliers start: 168 outliers final: 111 residues processed: 561 average time/residue: 0.3803 time to fit residues: 357.0386 Evaluate side-chains 535 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 401 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 606 PHE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1513 PHE Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1653 ARG Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 606 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 931 ASN Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1710 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2512 THR Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 110 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 251 optimal weight: 0.4980 chunk 182 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 345 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 878 ASN A1112 GLN ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 GLN ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 878 ASN C1230 ASN C1789 GLN ** C2321 ASN ** 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 = 0.4164 r_free = 0.4164 target = 0.122109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.084283 restraints weight = 122877.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086565 restraints weight = 54265.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087948 restraints weight = 34224.605| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32181 Z= 0.145 Angle : 0.710 13.670 43607 Z= 0.335 Chirality : 0.042 0.235 4983 Planarity : 0.004 0.056 5303 Dihedral : 8.662 105.835 4363 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.12 % Allowed : 29.63 % Favored : 65.25 % 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: 1.34 (0.14), residues: 3747 helix: 1.71 (0.10), residues: 2703 sheet: -1.31 (0.28), residues: 264 loop : -1.16 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 841 HIS 0.012 0.001 HIS B1951 PHE 0.026 0.001 PHE A1194 TYR 0.017 0.001 TYR C 604 ARG 0.007 0.000 ARG A1341 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 2056) hydrogen bonds : angle 4.26585 ( 6087) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.20164 ( 6) covalent geometry : bond 0.00324 (32178) covalent geometry : angle 0.71016 (43601) *********************** 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 592 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 421 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: 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: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5247 (OUTLIER) cc_final: 0.4991 (tmm) REVERT: A 833 MET cc_start: 0.8068 (mtt) cc_final: 0.7504 (mmp) REVERT: A 993 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7584 (mmtt) REVERT: A 1007 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7470 (tp) REVERT: A 1215 TRP cc_start: 0.8231 (OUTLIER) cc_final: 0.7968 (m-90) REVERT: A 1708 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 1731 MET cc_start: 0.9014 (mmp) cc_final: 0.8274 (ptt) REVERT: A 2043 LEU cc_start: 0.9160 (pp) cc_final: 0.8858 (mt) REVERT: A 2045 MET cc_start: 0.8042 (tmm) cc_final: 0.7767 (tmm) REVERT: A 2137 MET cc_start: 0.8492 (mmm) cc_final: 0.8278 (mmm) REVERT: A 2178 LEU cc_start: 0.9331 (mm) cc_final: 0.9010 (tt) REVERT: A 2288 MET cc_start: 0.6410 (ptm) cc_final: 0.6055 (ptm) REVERT: A 2469 GLU cc_start: 0.7979 (tm-30) cc_final: 0.6890 (tm-30) REVERT: B 597 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6315 (tt) REVERT: B 606 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 993 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7737 (mmtt) REVERT: B 1215 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7420 (m-90) REVERT: B 1547 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8310 (mtm110) REVERT: B 1731 MET cc_start: 0.8521 (mpp) cc_final: 0.8122 (mmp) REVERT: B 1954 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6868 (p90) REVERT: B 2033 PHE cc_start: 0.8671 (t80) cc_final: 0.8441 (t80) REVERT: B 2178 LEU cc_start: 0.9308 (mm) cc_final: 0.9036 (tt) REVERT: B 2288 MET cc_start: 0.6492 (ptm) cc_final: 0.6148 (ptm) REVERT: B 2469 GLU cc_start: 0.7879 (tm-30) cc_final: 0.6926 (tm-30) REVERT: B 2486 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8857 (tt) REVERT: C 606 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6908 (t80) REVERT: C 833 MET cc_start: 0.7939 (mtp) cc_final: 0.7483 (mmm) REVERT: C 866 ILE cc_start: 0.6702 (mm) cc_final: 0.6458 (mm) REVERT: C 947 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7881 (mmm-85) REVERT: C 993 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7581 (mmtt) REVERT: C 1011 MET cc_start: 0.8572 (tpp) cc_final: 0.7893 (tpp) REVERT: C 1215 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.7877 (m-90) REVERT: C 1739 ILE cc_start: 0.9447 (mm) cc_final: 0.8920 (mm) REVERT: C 1954 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6992 (p90) REVERT: C 2043 LEU cc_start: 0.9107 (pp) cc_final: 0.8857 (mt) REVERT: C 2178 LEU cc_start: 0.9335 (mm) cc_final: 0.9119 (tt) REVERT: C 2469 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6877 (tm-30) outliers start: 171 outliers final: 131 residues processed: 536 average time/residue: 0.3971 time to fit residues: 356.6842 Evaluate side-chains 544 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 396 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1710 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 606 PHE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1513 PHE Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2111 LEU Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2458 PHE Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 606 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1539 MET Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1652 ARG Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1710 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2111 LEU Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2512 THR Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 335 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 162 optimal weight: 0.0980 chunk 199 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 329 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN B1205 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.122283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.084650 restraints weight = 122923.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086949 restraints weight = 54025.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.088300 restraints weight = 34043.219| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.8267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32181 Z= 0.139 Angle : 0.709 12.567 43607 Z= 0.334 Chirality : 0.042 0.292 4983 Planarity : 0.004 0.056 5303 Dihedral : 8.365 92.746 4363 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.70 % Allowed : 30.23 % Favored : 65.07 % 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: 1.44 (0.14), residues: 3747 helix: 1.78 (0.10), residues: 2700 sheet: -1.30 (0.28), residues: 264 loop : -1.09 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B2188 HIS 0.007 0.001 HIS B1951 PHE 0.030 0.001 PHE C 588 TYR 0.012 0.001 TYR C 604 ARG 0.009 0.000 ARG B1653 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 2056) hydrogen bonds : angle 4.20240 ( 6087) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.18423 ( 6) covalent geometry : bond 0.00313 (32178) covalent geometry : angle 0.70865 (43601) *********************** 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 569 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 412 time to evaluate : 7.965 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.4931 (tmm) REVERT: A 833 MET cc_start: 0.8077 (mtt) cc_final: 0.7553 (mmp) REVERT: A 993 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7411 (mmtt) REVERT: A 1708 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 1731 MET cc_start: 0.8971 (mmp) cc_final: 0.8706 (mmp) REVERT: A 2043 LEU cc_start: 0.9154 (pp) cc_final: 0.8826 (mt) REVERT: A 2045 MET cc_start: 0.8064 (tmm) cc_final: 0.7761 (tmm) REVERT: A 2178 LEU cc_start: 0.9342 (mm) cc_final: 0.9011 (tt) REVERT: A 2288 MET cc_start: 0.6420 (ptm) cc_final: 0.6079 (ptm) REVERT: A 2469 GLU cc_start: 0.7970 (tm-30) cc_final: 0.6862 (tm-30) REVERT: B 597 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6237 (tt) REVERT: B 606 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 993 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7703 (mmtt) REVERT: B 1103 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: B 1215 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.7510 (m-90) REVERT: B 1547 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8334 (mtm110) REVERT: B 1731 MET cc_start: 0.8505 (mpp) cc_final: 0.8111 (mmp) REVERT: B 1738 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 1954 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6837 (p90) REVERT: B 2178 LEU cc_start: 0.9323 (mm) cc_final: 0.9040 (tt) REVERT: B 2288 MET cc_start: 0.6508 (ptm) cc_final: 0.6174 (ptm) REVERT: B 2361 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8305 (ptm-80) REVERT: B 2469 GLU cc_start: 0.7862 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 2486 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8844 (tt) REVERT: B 2503 LEU cc_start: 0.9273 (tp) cc_final: 0.8610 (tt) REVERT: C 606 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6656 (t80) REVERT: C 827 LEU cc_start: 0.8360 (mt) cc_final: 0.8147 (mt) REVERT: C 833 MET cc_start: 0.7970 (mtp) cc_final: 0.7521 (mmm) REVERT: C 866 ILE cc_start: 0.6677 (mm) cc_final: 0.6172 (mt) REVERT: C 993 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7336 (mmtt) REVERT: C 1011 MET cc_start: 0.8633 (tpp) cc_final: 0.7949 (tpp) REVERT: C 1215 TRP cc_start: 0.8350 (OUTLIER) cc_final: 0.7814 (m-90) REVERT: C 1731 MET cc_start: 0.8926 (mmp) cc_final: 0.8174 (ptm) REVERT: C 1954 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7002 (p90) REVERT: C 2043 LEU cc_start: 0.9091 (pp) cc_final: 0.8872 (mt) REVERT: C 2178 LEU cc_start: 0.9314 (mm) cc_final: 0.9101 (tt) REVERT: C 2194 MET cc_start: 0.8722 (ttm) cc_final: 0.8113 (tmm) REVERT: C 2290 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7780 (ttp80) REVERT: C 2469 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6871 (tm-30) outliers start: 157 outliers final: 128 residues processed: 514 average time/residue: 0.4509 time to fit residues: 390.2804 Evaluate side-chains 539 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 395 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 PHE Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1710 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2451 ILE Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 606 PHE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1513 PHE Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2111 LEU Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2458 PHE Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 606 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1193 CYS Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1289 SER Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1710 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 2008 LEU Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2111 LEU Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 357 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 380 optimal weight: 0.6980 chunk 268 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A1205 GLN B 988 ASN B1205 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.122393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.084831 restraints weight = 122515.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.087116 restraints weight = 54141.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088454 restraints weight = 34137.624| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32181 Z= 0.134 Angle : 0.711 13.127 43607 Z= 0.331 Chirality : 0.041 0.275 4983 Planarity : 0.004 0.056 5303 Dihedral : 8.117 90.126 4361 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.37 % Allowed : 30.44 % Favored : 65.19 % 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: 1.54 (0.14), residues: 3747 helix: 1.85 (0.10), residues: 2703 sheet: -1.28 (0.28), residues: 264 loop : -1.04 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B2188 HIS 0.007 0.001 HIS B1951 PHE 0.033 0.001 PHE C1103 TYR 0.026 0.001 TYR B 604 ARG 0.007 0.000 ARG A1341 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 2056) hydrogen bonds : angle 4.15089 ( 6087) SS BOND : bond 0.00082 ( 3) SS BOND : angle 0.18517 ( 6) covalent geometry : bond 0.00300 (32178) covalent geometry : angle 0.71102 (43601) ********************** 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 557 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 411 time to evaluate : 3.284 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 833 MET cc_start: 0.8083 (mtt) cc_final: 0.7571 (mmp) REVERT: A 1011 MET cc_start: 0.8893 (tpp) cc_final: 0.8184 (tpp) REVERT: A 1700 MET cc_start: 0.8581 (tpp) cc_final: 0.8143 (mmm) REVERT: A 1708 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 2007 MET cc_start: 0.9090 (mmp) cc_final: 0.8609 (mmt) REVERT: A 2043 LEU cc_start: 0.9126 (pp) cc_final: 0.8824 (mt) REVERT: A 2044 TRP cc_start: 0.7940 (t-100) cc_final: 0.7301 (t-100) REVERT: A 2178 LEU cc_start: 0.9359 (mm) cc_final: 0.9039 (tt) REVERT: A 2194 MET cc_start: 0.8705 (ttm) cc_final: 0.8112 (tmm) REVERT: A 2288 MET cc_start: 0.6516 (ptm) cc_final: 0.6175 (ptm) REVERT: A 2451 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8914 (tp) REVERT: A 2469 GLU cc_start: 0.7942 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 2486 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8719 (tt) REVERT: B 597 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6333 (tt) REVERT: B 989 PHE cc_start: 0.8461 (m-80) cc_final: 0.8157 (m-10) REVERT: B 993 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7662 (mmtt) REVERT: B 1103 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: B 1215 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7516 (m-90) REVERT: B 1547 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8268 (mtm110) REVERT: B 1731 MET cc_start: 0.8499 (mpp) cc_final: 0.8079 (mmp) REVERT: B 1954 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7282 (p90) REVERT: B 2178 LEU cc_start: 0.9322 (mm) cc_final: 0.9087 (tt) REVERT: B 2288 MET cc_start: 0.6529 (ptm) cc_final: 0.6218 (ptm) REVERT: B 2469 GLU cc_start: 0.7861 (tm-30) cc_final: 0.6897 (tm-30) REVERT: B 2486 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8806 (tt) REVERT: B 2503 LEU cc_start: 0.9264 (tp) cc_final: 0.8595 (tt) REVERT: C 606 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 833 MET cc_start: 0.7974 (mtp) cc_final: 0.7675 (mmp) REVERT: C 866 ILE cc_start: 0.6721 (mm) cc_final: 0.6448 (mm) REVERT: C 1215 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.7831 (m-90) REVERT: C 1731 MET cc_start: 0.8912 (mmp) cc_final: 0.8109 (ptm) REVERT: C 1954 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6992 (p90) REVERT: C 2043 LEU cc_start: 0.9086 (pp) cc_final: 0.8875 (mt) REVERT: C 2194 MET cc_start: 0.8720 (ttm) cc_final: 0.8129 (tmm) REVERT: C 2290 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7722 (ttp80) REVERT: C 2469 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6869 (tm-30) outliers start: 146 outliers final: 120 residues processed: 507 average time/residue: 0.4532 time to fit residues: 389.6627 Evaluate side-chains 522 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 388 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1710 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2451 ILE Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 606 PHE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1513 PHE Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1790 LEU Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 606 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1193 CYS Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1342 ILE Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1514 LEU Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1539 MET Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1710 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1955 ARG Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 2008 LEU Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 346 optimal weight: 0.0050 chunk 144 optimal weight: 10.0000 chunk 361 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 254 optimal weight: 30.0000 chunk 349 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 313 optimal weight: 8.9990 chunk 333 optimal weight: 0.7980 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A1205 GLN B1205 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.122434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084875 restraints weight = 122731.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.087135 restraints weight = 54438.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.088519 restraints weight = 34487.338| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.8522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32181 Z= 0.135 Angle : 0.723 12.934 43607 Z= 0.335 Chirality : 0.041 0.237 4983 Planarity : 0.004 0.057 5303 Dihedral : 7.965 89.445 4359 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.46 % Allowed : 30.26 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.14), residues: 3747 helix: 1.92 (0.10), residues: 2697 sheet: -1.23 (0.29), residues: 255 loop : -0.98 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C2188 HIS 0.006 0.001 HIS A1699 PHE 0.030 0.001 PHE B2033 TYR 0.020 0.001 TYR B 604 ARG 0.011 0.000 ARG A1341 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 2056) hydrogen bonds : angle 4.14763 ( 6087) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.17620 ( 6) covalent geometry : bond 0.00305 (32178) covalent geometry : angle 0.72286 (43601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16341.41 seconds wall clock time: 288 minutes 27.88 seconds (17307.88 seconds total)