Starting phenix.real_space_refine on Tue Aug 26 00:13:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yez_39205/08_2025/8yez_39205_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yez_39205/08_2025/8yez_39205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yez_39205/08_2025/8yez_39205_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yez_39205/08_2025/8yez_39205_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yez_39205/08_2025/8yez_39205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yez_39205/08_2025/8yez_39205.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 183 5.16 5 C 20988 2.51 5 N 5181 2.21 5 O 5241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10431 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10431 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10431 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'L9Q': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'L9Q': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.38, per 1000 atoms: 0.27 Number of scatterers: 31599 At special positions: 0 Unit cell: (226.683, 219.042, 156.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 183 16.00 P 6 15.00 O 5241 8.00 N 5181 7.00 C 20988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2411 " - pdb=" SG CYS A2415 " distance=2.04 Simple disulfide: pdb=" SG CYS B2411 " - pdb=" SG CYS B2415 " distance=2.04 Simple disulfide: pdb=" SG CYS C2411 " - pdb=" SG CYS C2415 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7314 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 9 sheets defined 71.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS A 584 " --> pdb=" O TRP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.554A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 626 through 644 removed outlier: 3.566A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 701 Proline residue: A 687 - end of helix removed outlier: 3.532A pdb=" N GLN A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 834 through 841 removed outlier: 3.521A pdb=" N VAL A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 930 through 956 Processing helix chain 'A' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP A 976 " --> pdb=" O ARG A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 995 through 1010 removed outlier: 3.718A pdb=" N ASN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A1008 " --> pdb=" O VAL A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.502A pdb=" N ALA A1024 " --> pdb=" O CYS A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1164 Processing helix chain 'A' and resid 1166 through 1179 Processing helix chain 'A' and resid 1183 through 1199 removed outlier: 3.826A pdb=" N LEU A1187 " --> pdb=" O SER A1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A1188 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A1189 " --> pdb=" O PHE A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 removed outlier: 3.701A pdb=" N LEU A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1232 removed outlier: 3.562A pdb=" N ASN A1222 " --> pdb=" O LEU A1218 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A1230 " --> pdb=" O ILE A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG A1300 " --> pdb=" O LEU A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1370 Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1514 through 1533 Processing helix chain 'A' and resid 1533 through 1557 removed outlier: 3.516A pdb=" N LEU A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU A1565 " --> pdb=" O HIS A1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A1568 " --> pdb=" O VAL A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1652 Processing helix chain 'A' and resid 1656 through 1668 removed outlier: 4.012A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1686 Processing helix chain 'A' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 Processing helix chain 'A' and resid 1726 through 1747 Processing helix chain 'A' and resid 1784 through 1803 Processing helix chain 'A' and resid 1941 through 1951 Processing helix chain 'A' and resid 1960 through 1978 Processing helix chain 'A' and resid 2002 through 2024 Processing helix chain 'A' and resid 2026 through 2045 removed outlier: 3.527A pdb=" N LYS A2030 " --> pdb=" O THR A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2084 Processing helix chain 'A' and resid 2100 through 2112 removed outlier: 3.547A pdb=" N VAL A2112 " --> pdb=" O GLY A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2114 through 2127 Processing helix chain 'A' and resid 2133 through 2159 Processing helix chain 'A' and resid 2168 through 2185 Processing helix chain 'A' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU A2191 " --> pdb=" O ILE A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2236 through 2248 Processing helix chain 'A' and resid 2250 through 2258 Processing helix chain 'A' and resid 2281 through 2295 Processing helix chain 'A' and resid 2311 through 2314 Processing helix chain 'A' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU A2342 " --> pdb=" O LEU A2338 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 Processing helix chain 'A' and resid 2437 through 2460 removed outlier: 3.550A pdb=" N MET A2441 " --> pdb=" O GLY A2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A2458 " --> pdb=" O PHE A2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A2459 " --> pdb=" O VAL A2455 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2490 removed outlier: 3.582A pdb=" N PHE A2485 " --> pdb=" O CYS A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2505 removed outlier: 3.715A pdb=" N GLU A2497 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A2502 " --> pdb=" O GLU A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2517 Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS B 584 " --> pdb=" O TRP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 618 removed outlier: 3.555A pdb=" N GLN B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 644 removed outlier: 5.642A pdb=" N LYS B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 Proline residue: B 687 - end of helix removed outlier: 3.532A pdb=" N GLN B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 829 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL B 838 " --> pdb=" O ASN B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 871 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 930 through 956 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP B 976 " --> pdb=" O ARG B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 995 through 1010 removed outlier: 3.718A pdb=" N ASN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B1008 " --> pdb=" O VAL B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1026 removed outlier: 3.502A pdb=" N ALA B1024 " --> pdb=" O CYS B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG B1036 " --> pdb=" O GLN B1032 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) Proline residue: B1039 - end of helix Processing helix chain 'B' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU B1105 " --> pdb=" O SER B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1164 Processing helix chain 'B' and resid 1166 through 1179 Processing helix chain 'B' and resid 1183 through 1199 removed outlier: 3.826A pdb=" N LEU B1187 " --> pdb=" O SER B1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B1188 " --> pdb=" O ILE B1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B1189 " --> pdb=" O PHE B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1199 through 1204 removed outlier: 3.701A pdb=" N LEU B1203 " --> pdb=" O PHE B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1232 removed outlier: 3.834A pdb=" N ASN B1230 " --> pdb=" O ILE B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG B1300 " --> pdb=" O LEU B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL B1310 " --> pdb=" O TYR B1306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B1318 " --> pdb=" O LEU B1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1320 through 1370 Processing helix chain 'B' and resid 1408 through 1412 Processing helix chain 'B' and resid 1514 through 1533 Processing helix chain 'B' and resid 1533 through 1557 removed outlier: 3.516A pdb=" N LEU B1549 " --> pdb=" O ALA B1545 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU B1565 " --> pdb=" O HIS B1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B1568 " --> pdb=" O VAL B1564 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1652 Processing helix chain 'B' and resid 1656 through 1668 removed outlier: 4.012A pdb=" N GLU B1660 " --> pdb=" O ILE B1656 " (cutoff:3.500A) Processing helix chain 'B' and resid 1670 through 1686 Processing helix chain 'B' and resid 1687 through 1702 removed outlier: 3.608A pdb=" N HIS B1699 " --> pdb=" O ILE B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1718 Processing helix chain 'B' and resid 1726 through 1747 Processing helix chain 'B' and resid 1784 through 1803 Processing helix chain 'B' and resid 1941 through 1951 Processing helix chain 'B' and resid 1960 through 1978 Processing helix chain 'B' and resid 2002 through 2024 Processing helix chain 'B' and resid 2026 through 2045 removed outlier: 3.527A pdb=" N LYS B2030 " --> pdb=" O THR B2026 " (cutoff:3.500A) Processing helix chain 'B' and resid 2061 through 2084 Processing helix chain 'B' and resid 2100 through 2112 removed outlier: 3.547A pdb=" N VAL B2112 " --> pdb=" O GLY B2108 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2127 Processing helix chain 'B' and resid 2133 through 2159 Processing helix chain 'B' and resid 2168 through 2185 Processing helix chain 'B' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU B2191 " --> pdb=" O ILE B2187 " (cutoff:3.500A) Processing helix chain 'B' and resid 2236 through 2248 Processing helix chain 'B' and resid 2250 through 2258 Processing helix chain 'B' and resid 2281 through 2295 Processing helix chain 'B' and resid 2311 through 2314 Processing helix chain 'B' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU B2342 " --> pdb=" O LEU B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2382 Processing helix chain 'B' and resid 2437 through 2460 removed outlier: 3.550A pdb=" N MET B2441 " --> pdb=" O GLY B2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B2458 " --> pdb=" O PHE B2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B2459 " --> pdb=" O VAL B2455 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE B2485 " --> pdb=" O CYS B2481 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2505 removed outlier: 3.714A pdb=" N GLU B2497 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B2502 " --> pdb=" O GLU B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2517 Processing helix chain 'C' and resid 571 through 577 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS C 584 " --> pdb=" O TRP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 618 removed outlier: 3.555A pdb=" N GLN C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 644 removed outlier: 5.587A pdb=" N LYS C 627 " --> pdb=" O ARG C 623 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 628 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 701 Proline residue: C 687 - end of helix removed outlier: 3.532A pdb=" N GLN C 697 " --> pdb=" O ALA C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 709 Processing helix chain 'C' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 829 Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL C 838 " --> pdb=" O ASN C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 871 Processing helix chain 'C' and resid 924 through 929 Processing helix chain 'C' and resid 930 through 956 Processing helix chain 'C' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP C 976 " --> pdb=" O ARG C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.718A pdb=" N ASN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C1008 " --> pdb=" O VAL C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1026 removed outlier: 3.502A pdb=" N ALA C1024 " --> pdb=" O CYS C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG C1036 " --> pdb=" O GLN C1032 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C1037 " --> pdb=" O ALA C1033 " (cutoff:3.500A) Proline residue: C1039 - end of helix Processing helix chain 'C' and resid 1100 through 1116 removed outlier: 3.506A pdb=" N LEU C1105 " --> pdb=" O SER C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1155 through 1164 Processing helix chain 'C' and resid 1166 through 1179 Processing helix chain 'C' and resid 1183 through 1199 removed outlier: 3.826A pdb=" N LEU C1187 " --> pdb=" O SER C1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C1188 " --> pdb=" O ILE C1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C1189 " --> pdb=" O PHE C1185 " (cutoff:3.500A) Processing helix chain 'C' and resid 1199 through 1204 removed outlier: 3.701A pdb=" N LEU C1203 " --> pdb=" O PHE C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1232 removed outlier: 3.782A pdb=" N LEU C1218 " --> pdb=" O LEU C1214 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C1219 " --> pdb=" O TRP C1215 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1220 " --> pdb=" O ASP C1216 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C1230 " --> pdb=" O ILE C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1302 removed outlier: 3.669A pdb=" N ARG C1300 " --> pdb=" O LEU C1296 " (cutoff:3.500A) Processing helix chain 'C' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL C1310 " --> pdb=" O TYR C1306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1370 Processing helix chain 'C' and resid 1408 through 1412 Processing helix chain 'C' and resid 1514 through 1533 Processing helix chain 'C' and resid 1533 through 1557 removed outlier: 3.517A pdb=" N LEU C1549 " --> pdb=" O ALA C1545 " (cutoff:3.500A) Processing helix chain 'C' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU C1565 " --> pdb=" O HIS C1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU C1568 " --> pdb=" O VAL C1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 1646 through 1652 Processing helix chain 'C' and resid 1656 through 1668 removed outlier: 4.012A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) Processing helix chain 'C' and resid 1670 through 1686 Processing helix chain 'C' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 Processing helix chain 'C' and resid 1726 through 1747 Processing helix chain 'C' and resid 1784 through 1803 Processing helix chain 'C' and resid 1941 through 1951 Processing helix chain 'C' and resid 1960 through 1978 Processing helix chain 'C' and resid 2002 through 2024 Processing helix chain 'C' and resid 2026 through 2045 removed outlier: 3.527A pdb=" N LYS C2030 " --> pdb=" O THR C2026 " (cutoff:3.500A) Processing helix chain 'C' and resid 2061 through 2084 Processing helix chain 'C' and resid 2100 through 2112 removed outlier: 3.546A pdb=" N VAL C2112 " --> pdb=" O GLY C2108 " (cutoff:3.500A) Processing helix chain 'C' and resid 2114 through 2127 Processing helix chain 'C' and resid 2133 through 2159 Processing helix chain 'C' and resid 2168 through 2185 Processing helix chain 'C' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU C2191 " --> pdb=" O ILE C2187 " (cutoff:3.500A) Processing helix chain 'C' and resid 2236 through 2248 Processing helix chain 'C' and resid 2250 through 2258 Processing helix chain 'C' and resid 2281 through 2295 Processing helix chain 'C' and resid 2311 through 2314 Processing helix chain 'C' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU C2342 " --> pdb=" O LEU C2338 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2382 Processing helix chain 'C' and resid 2437 through 2460 removed outlier: 3.550A pdb=" N MET C2441 " --> pdb=" O GLY C2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C2458 " --> pdb=" O PHE C2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C2459 " --> pdb=" O VAL C2455 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE C2485 " --> pdb=" O CYS C2481 " (cutoff:3.500A) Processing helix chain 'C' and resid 2493 through 2505 removed outlier: 3.714A pdb=" N GLU C2497 " --> pdb=" O LEU C2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C2502 " --> pdb=" O GLU C2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2517 Processing sheet with id=AA1, first strand: chain 'A' and resid 2223 through 2228 removed outlier: 3.596A pdb=" N ASP A2209 " --> pdb=" O GLN A2308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A2299 " --> pdb=" O LEU A2328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2232 through 2234 Processing sheet with id=AA3, first strand: chain 'A' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN A2354 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A2383 " --> pdb=" O ASN A2354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2223 through 2228 removed outlier: 3.596A pdb=" N ASP B2209 " --> pdb=" O GLN B2308 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B2299 " --> pdb=" O LEU B2328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2232 through 2234 Processing sheet with id=AA6, first strand: chain 'B' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN B2354 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU B2383 " --> pdb=" O ASN B2354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2223 through 2228 removed outlier: 3.595A pdb=" N ASP C2209 " --> pdb=" O GLN C2308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C2299 " --> pdb=" O LEU C2328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2232 through 2234 Processing sheet with id=AA9, first strand: chain 'C' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN C2354 " --> pdb=" O LEU C2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C2383 " --> pdb=" O ASN C2354 " (cutoff:3.500A) 2059 hydrogen bonds defined for protein. 6096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4720 1.30 - 1.43: 9167 1.43 - 1.56: 18183 1.56 - 1.69: 12 1.69 - 1.82: 288 Bond restraints: 32370 Sorted by residual: bond pdb=" C39 L9Q A2601 " pdb=" C40 L9Q A2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C39 L9Q B2601 " pdb=" C40 L9Q B2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C39 L9Q A2603 " pdb=" C40 L9Q A2603 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C39 L9Q C2601 " pdb=" C40 L9Q C2601 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" C39 L9Q B2602 " pdb=" C40 L9Q B2602 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 ... (remaining 32365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 42246 3.40 - 6.80: 1354 6.80 - 10.21: 170 10.21 - 13.61: 27 13.61 - 17.01: 12 Bond angle restraints: 43809 Sorted by residual: angle pdb=" N ILE C 684 " pdb=" CA ILE C 684 " pdb=" C ILE C 684 " ideal model delta sigma weight residual 111.90 103.43 8.47 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE B 684 " pdb=" CA ILE B 684 " pdb=" C ILE B 684 " ideal model delta sigma weight residual 111.90 103.43 8.47 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE A 684 " pdb=" CA ILE A 684 " pdb=" C ILE A 684 " ideal model delta sigma weight residual 111.90 103.44 8.46 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE C1025 " pdb=" CA ILE C1025 " pdb=" C ILE C1025 " ideal model delta sigma weight residual 111.90 103.61 8.29 8.10e-01 1.52e+00 1.05e+02 angle pdb=" N ILE A1025 " pdb=" CA ILE A1025 " pdb=" C ILE A1025 " ideal model delta sigma weight residual 111.90 103.62 8.28 8.10e-01 1.52e+00 1.04e+02 ... (remaining 43804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 17260 35.45 - 70.91: 1713 70.91 - 106.36: 68 106.36 - 141.82: 0 141.82 - 177.27: 18 Dihedral angle restraints: 19059 sinusoidal: 7779 harmonic: 11280 Sorted by residual: dihedral pdb=" CA PHE A 923 " pdb=" C PHE A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" C ILE A1722 " pdb=" N ILE A1722 " pdb=" CA ILE A1722 " pdb=" CB ILE A1722 " ideal model delta harmonic sigma weight residual -122.00 -135.49 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" C ILE C1722 " pdb=" N ILE C1722 " pdb=" CA ILE C1722 " pdb=" CB ILE C1722 " ideal model delta harmonic sigma weight residual -122.00 -134.95 12.95 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 19056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3722 0.098 - 0.196: 1047 0.196 - 0.295: 174 0.295 - 0.393: 26 0.393 - 0.491: 14 Chirality restraints: 4983 Sorted by residual: chirality pdb=" CA ILE A1722 " pdb=" N ILE A1722 " pdb=" C ILE A1722 " pdb=" CB ILE A1722 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA ILE C1722 " pdb=" N ILE C1722 " pdb=" C ILE C1722 " pdb=" CB ILE C1722 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA LEU C2493 " pdb=" N LEU C2493 " pdb=" C LEU C2493 " pdb=" CB LEU C2493 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 ... (remaining 4980 not shown) Planarity restraints: 5325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q C2601 " 0.184 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C39 L9Q C2601 " -0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q C2601 " -0.183 2.00e-02 2.50e+03 pdb=" C41 L9Q C2601 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B2602 " 0.184 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C39 L9Q B2602 " -0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q B2602 " -0.183 2.00e-02 2.50e+03 pdb=" C41 L9Q B2602 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A2602 " 0.184 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C39 L9Q A2602 " -0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q A2602 " -0.183 2.00e-02 2.50e+03 pdb=" C41 L9Q A2602 " 0.184 2.00e-02 2.50e+03 ... (remaining 5322 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 9 1.88 - 2.64: 716 2.64 - 3.39: 40880 3.39 - 4.15: 77631 4.15 - 4.90: 133557 Nonbonded interactions: 252793 Sorted by model distance: nonbonded pdb=" N GLU A 679 " pdb=" OE1 GLU A 679 " model vdw 1.126 3.120 nonbonded pdb=" N GLU B 679 " pdb=" OE1 GLU B 679 " model vdw 1.126 3.120 nonbonded pdb=" N GLU C 679 " pdb=" OE1 GLU C 679 " model vdw 1.126 3.120 nonbonded pdb=" CB LYS A2157 " pdb=" NZ LYS A2157 " model vdw 1.702 3.520 nonbonded pdb=" CB LYS C2157 " pdb=" NZ LYS C2157 " model vdw 1.702 3.520 ... (remaining 252788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 570 through 2601) selection = (chain 'B' and resid 570 through 2601) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.960 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.191 32373 Z= 0.765 Angle : 1.476 17.008 43815 Z= 0.969 Chirality : 0.094 0.491 4983 Planarity : 0.010 0.184 5325 Dihedral : 23.842 177.270 11736 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.62 % Favored : 90.26 % Rotamer: Outliers : 25.90 % Allowed : 12.93 % Favored : 61.17 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.11), residues: 3747 helix: -2.00 (0.08), residues: 2688 sheet: -1.85 (0.29), residues: 246 loop : -3.10 (0.18), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2336 TYR 0.109 0.005 TYR A2319 PHE 0.037 0.003 PHE B2307 TRP 0.071 0.005 TRP B2403 HIS 0.004 0.001 HIS A2324 Details of bonding type rmsd covalent geometry : bond 0.01129 (32370) covalent geometry : angle 1.47633 (43809) SS BOND : bond 0.01094 ( 3) SS BOND : angle 0.75212 ( 6) hydrogen bonds : bond 0.23562 ( 2059) hydrogen bonds : angle 7.70177 ( 6096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 867 poor density : 516 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.6211 (tpt) cc_final: 0.4236 (tmm) REVERT: A 699 HIS cc_start: 0.6193 (OUTLIER) cc_final: 0.5376 (m-70) REVERT: A 702 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6279 (t70) REVERT: A 820 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.4835 (tt) REVERT: A 877 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.7010 (m) REVERT: A 929 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6839 (mt) REVERT: A 972 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.4242 (mmt90) REVERT: A 984 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7341 (mmtt) REVERT: A 997 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: A 998 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 1011 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: A 1156 ASP cc_start: 0.5570 (OUTLIER) cc_final: 0.5118 (t0) REVERT: A 1523 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7524 (t0) REVERT: A 1694 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 1719 MET cc_start: 0.8611 (mtp) cc_final: 0.8332 (mtt) REVERT: A 1727 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.6893 (tptm) REVERT: A 2027 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8155 (t) REVERT: A 2045 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7940 (ttt) REVERT: A 2134 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7175 (p) REVERT: A 2169 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7889 (mmtm) REVERT: A 2181 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 2476 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: A 2511 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: A 2515 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: A 2516 TRP cc_start: 0.8331 (t-100) cc_final: 0.7868 (t-100) REVERT: B 605 MET cc_start: 0.6268 (tpt) cc_final: 0.4502 (tmm) REVERT: B 699 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.5333 (m-70) REVERT: B 877 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6816 (m) REVERT: B 929 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6830 (mt) REVERT: B 972 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.4257 (mmt90) REVERT: B 984 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7391 (mmtt) REVERT: B 997 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: B 998 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6553 (tp) REVERT: B 1156 ASP cc_start: 0.5563 (OUTLIER) cc_final: 0.5172 (t0) REVERT: B 1523 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7562 (t0) REVERT: B 1719 MET cc_start: 0.8677 (mtp) cc_final: 0.8387 (mtt) REVERT: B 1727 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.6868 (tptp) REVERT: B 1797 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6625 (ttt-90) REVERT: B 2027 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8312 (t) REVERT: B 2045 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7906 (ttt) REVERT: B 2064 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: B 2100 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7349 (t-90) REVERT: B 2117 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 2134 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7325 (p) REVERT: B 2166 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8619 (mtmm) REVERT: B 2169 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7724 (mtpp) REVERT: B 2181 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8729 (mm) REVERT: B 2200 VAL cc_start: 0.1761 (OUTLIER) cc_final: 0.1531 (p) REVERT: B 2456 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7565 (tpp-160) REVERT: B 2467 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (mtm) REVERT: B 2511 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: B 2515 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: B 2516 TRP cc_start: 0.8337 (t-100) cc_final: 0.7928 (t-100) REVERT: C 605 MET cc_start: 0.6198 (tpt) cc_final: 0.4338 (tmm) REVERT: C 699 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5358 (m-70) REVERT: C 820 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.4887 (tt) REVERT: C 843 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: C 877 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6782 (m) REVERT: C 972 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.4283 (mmt90) REVERT: C 984 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7349 (mmtt) REVERT: C 997 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6220 (tt0) REVERT: C 998 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6509 (tp) REVERT: C 1156 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.5052 (t0) REVERT: C 1523 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7636 (t0) REVERT: C 1694 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7779 (mp) REVERT: C 1696 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 1719 MET cc_start: 0.8660 (mtp) cc_final: 0.8351 (mtt) REVERT: C 1727 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.6937 (tptm) REVERT: C 1797 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6969 (ttt-90) REVERT: C 1971 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7900 (t0) REVERT: C 2122 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: C 2134 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7252 (p) REVERT: C 2169 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7773 (mmtm) REVERT: C 2181 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8718 (mm) REVERT: C 2200 VAL cc_start: 0.1745 (OUTLIER) cc_final: 0.1501 (p) REVERT: C 2231 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6556 (p) REVERT: C 2476 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6394 (mtm180) REVERT: C 2511 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: C 2515 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8089 (ttmt) REVERT: C 2516 TRP cc_start: 0.8326 (t-100) cc_final: 0.7325 (t-100) outliers start: 867 outliers final: 225 residues processed: 1178 average time/residue: 0.2426 time to fit residues: 433.0866 Evaluate side-chains 582 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 286 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1053 TYR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1682 CYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1728 ARG Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1958 THR Chi-restraints excluded: chain A residue 2024 ARG Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2045 MET Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2169 LYS Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2186 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2193 PHE Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2476 ARG Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2515 LYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 843 PHE Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 984 LYS Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 998 ILE Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1053 TYR Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1112 GLN Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1180 THR Chi-restraints excluded: chain B residue 1198 LEU Chi-restraints excluded: chain B residue 1212 LEU Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1304 SER Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1338 PHE Chi-restraints excluded: chain B residue 1346 SER Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1646 SER Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1682 CYS Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1728 ARG Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1797 ARG Chi-restraints excluded: chain B residue 1798 SER Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1963 LEU Chi-restraints excluded: chain B residue 1966 LEU Chi-restraints excluded: chain B residue 1971 ASP Chi-restraints excluded: chain B residue 2024 ARG Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2028 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2062 VAL Chi-restraints excluded: chain B residue 2064 GLN Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2117 GLU Chi-restraints excluded: chain B residue 2122 MET Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2166 LYS Chi-restraints excluded: chain B residue 2169 LYS Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2186 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2200 VAL Chi-restraints excluded: chain B residue 2456 ARG Chi-restraints excluded: chain B residue 2460 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2467 MET Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2515 LYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 703 ARG Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 855 SER Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 982 CYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 984 LYS Chi-restraints excluded: chain C residue 997 GLU Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1053 TYR Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1180 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1228 SER Chi-restraints excluded: chain C residue 1304 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1336 ILE Chi-restraints excluded: chain C residue 1338 PHE Chi-restraints excluded: chain C residue 1417 ASP Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1523 ASP Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1646 SER Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1682 CYS Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1701 VAL Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1728 ARG Chi-restraints excluded: chain C residue 1797 ARG Chi-restraints excluded: chain C residue 1802 CYS Chi-restraints excluded: chain C residue 1949 ILE Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 1971 ASP Chi-restraints excluded: chain C residue 2026 THR Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2028 LEU Chi-restraints excluded: chain C residue 2045 MET Chi-restraints excluded: chain C residue 2062 VAL Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2119 ARG Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2131 LEU Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2166 LYS Chi-restraints excluded: chain C residue 2169 LYS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2175 MET Chi-restraints excluded: chain C residue 2181 LEU Chi-restraints excluded: chain C residue 2186 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2193 PHE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2460 SER Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2476 ARG Chi-restraints excluded: chain C residue 2486 LEU Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2515 LYS Chi-restraints excluded: chain C residue 2518 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN A1556 GLN A2099 ASN ** A2250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1222 ASN B1230 ASN B1535 HIS B2064 GLN B2099 ASN ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1230 ASN C1535 HIS C1556 GLN C2099 ASN ** C2228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.191358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127308 restraints weight = 47602.446| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.10 r_work: 0.3293 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32373 Z= 0.170 Angle : 0.693 15.110 43815 Z= 0.363 Chirality : 0.041 0.183 4983 Planarity : 0.006 0.060 5325 Dihedral : 18.076 178.322 5083 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 8.93 % Allowed : 18.70 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.13), residues: 3747 helix: 0.43 (0.10), residues: 2691 sheet: -1.01 (0.30), residues: 249 loop : -2.32 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1028 TYR 0.026 0.002 TYR B2219 PHE 0.044 0.002 PHE C2193 TRP 0.015 0.002 TRP C2136 HIS 0.008 0.001 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00353 (32370) covalent geometry : angle 0.69327 (43809) SS BOND : bond 0.00159 ( 3) SS BOND : angle 0.65305 ( 6) hydrogen bonds : bond 0.06779 ( 2059) hydrogen bonds : angle 4.80799 ( 6096) *********************** 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 663 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 364 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5766 (tpt) cc_final: 0.4100 (tmm) REVERT: A 702 HIS cc_start: 0.5579 (OUTLIER) cc_final: 0.4843 (t70) REVERT: A 972 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.3964 (mmt90) REVERT: A 1011 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: A 1057 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6752 (tp) REVERT: A 1230 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7269 (t0) REVERT: A 1304 SER cc_start: 0.8371 (t) cc_final: 0.8163 (t) REVERT: A 1727 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6097 (tptm) REVERT: A 1948 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7965 (t0) REVERT: A 2034 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: A 2045 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8535 (tpt) REVERT: A 2122 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (mtp) REVERT: A 2166 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8844 (ptpp) REVERT: A 2169 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7458 (mmtm) REVERT: A 2181 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8506 (mm) REVERT: A 2254 MET cc_start: 0.1670 (OUTLIER) cc_final: 0.1327 (mmm) REVERT: A 2504 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 2516 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.6954 (m-90) REVERT: B 587 MET cc_start: 0.5330 (mmp) cc_final: 0.5050 (mmp) REVERT: B 605 MET cc_start: 0.5748 (tpt) cc_final: 0.4309 (tmm) REVERT: B 702 HIS cc_start: 0.5279 (OUTLIER) cc_final: 0.4214 (t70) REVERT: B 710 ASP cc_start: 0.5850 (OUTLIER) cc_final: 0.5584 (p0) REVERT: B 972 ARG cc_start: 0.5324 (OUTLIER) cc_final: 0.3769 (mmt90) REVERT: B 974 GLN cc_start: 0.7161 (tt0) cc_final: 0.6863 (tt0) REVERT: B 1057 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6773 (tp) REVERT: B 1156 ASP cc_start: 0.5455 (OUTLIER) cc_final: 0.4888 (t0) REVERT: B 1230 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7182 (t0) REVERT: B 1696 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 1727 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6156 (tptm) REVERT: B 1948 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7630 (t0) REVERT: B 2027 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8276 (t) REVERT: B 2117 GLU cc_start: 0.8532 (mp0) cc_final: 0.8061 (mp0) REVERT: B 2122 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8381 (mtp) REVERT: B 2166 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8747 (ptpp) REVERT: B 2169 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7269 (mmtm) REVERT: B 2181 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (mm) REVERT: B 2254 MET cc_start: 0.1268 (mmp) cc_final: 0.1031 (mmm) REVERT: B 2486 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 2504 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8432 (tp) REVERT: C 605 MET cc_start: 0.5696 (tpt) cc_final: 0.4120 (tmm) REVERT: C 702 HIS cc_start: 0.4730 (OUTLIER) cc_final: 0.4022 (t70) REVERT: C 703 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7461 (mtt90) REVERT: C 710 ASP cc_start: 0.5777 (OUTLIER) cc_final: 0.5520 (p0) REVERT: C 843 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: C 942 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: C 972 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.3735 (mmt90) REVERT: C 974 GLN cc_start: 0.7053 (tt0) cc_final: 0.6691 (tt0) REVERT: C 998 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7127 (tp) REVERT: C 1011 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7831 (mtt) REVERT: C 1057 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6243 (tp) REVERT: C 1156 ASP cc_start: 0.5095 (OUTLIER) cc_final: 0.4749 (t0) REVERT: C 1230 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7146 (t0) REVERT: C 1528 TRP cc_start: 0.8555 (t-100) cc_final: 0.8323 (t-100) REVERT: C 1719 MET cc_start: 0.8889 (mtp) cc_final: 0.8526 (mtt) REVERT: C 1727 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6246 (tptm) REVERT: C 1948 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7597 (t70) REVERT: C 2034 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: C 2045 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8482 (tpt) REVERT: C 2122 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: C 2169 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7411 (mmtm) REVERT: C 2181 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (mm) REVERT: C 2486 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7932 (tt) REVERT: C 2504 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8290 (tp) outliers start: 299 outliers final: 134 residues processed: 608 average time/residue: 0.1890 time to fit residues: 189.2459 Evaluate side-chains 473 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 287 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1360 LYS Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1682 CYS Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2045 MET Chi-restraints excluded: chain A residue 2065 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2169 LYS Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2181 LEU Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2254 MET Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 982 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1198 LEU Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1535 HIS Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1682 CYS Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2122 MET Chi-restraints excluded: chain B residue 2166 LYS Chi-restraints excluded: chain B residue 2169 LYS Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2181 LEU Chi-restraints excluded: chain B residue 2193 PHE Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2435 LEU Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2487 VAL Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 703 ARG Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 982 CYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1360 LYS Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1682 CYS Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1942 LEU Chi-restraints excluded: chain C residue 1948 ASP Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2045 MET Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2169 LYS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2181 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2435 LEU Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2486 LEU Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 281 optimal weight: 0.2980 chunk 118 optimal weight: 0.0170 chunk 116 optimal weight: 5.9990 chunk 364 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 284 optimal weight: 0.5980 chunk 295 optimal weight: 0.8980 chunk 319 optimal weight: 0.5980 chunk 351 optimal weight: 10.0000 chunk 366 optimal weight: 50.0000 chunk 65 optimal weight: 0.0370 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 GLN A1040 ASN A2034 GLN ** A2250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2308 GLN B 930 GLN B1040 ASN B1222 ASN B2034 GLN B2308 GLN C1040 ASN C1114 GLN ** C2228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2308 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.191918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125331 restraints weight = 48045.382| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.41 r_work: 0.3359 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32373 Z= 0.125 Angle : 0.569 8.910 43815 Z= 0.291 Chirality : 0.038 0.184 4983 Planarity : 0.005 0.050 5325 Dihedral : 14.947 179.260 4747 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 6.30 % Allowed : 20.82 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3747 helix: 1.50 (0.10), residues: 2700 sheet: -0.94 (0.31), residues: 252 loop : -1.86 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1341 TYR 0.014 0.001 TYR B1782 PHE 0.028 0.001 PHE B 588 TRP 0.015 0.001 TRP A2188 HIS 0.016 0.001 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00257 (32370) covalent geometry : angle 0.56901 (43809) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.33339 ( 6) hydrogen bonds : bond 0.05233 ( 2059) hydrogen bonds : angle 4.21765 ( 6096) *********************** 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 506 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 295 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5695 (tpt) cc_final: 0.4177 (tmm) REVERT: A 702 HIS cc_start: 0.5266 (OUTLIER) cc_final: 0.4453 (t70) REVERT: A 710 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5758 (p0) REVERT: A 974 GLN cc_start: 0.6948 (tt0) cc_final: 0.6497 (tt0) REVERT: A 979 LEU cc_start: 0.7598 (mp) cc_final: 0.7350 (mt) REVERT: A 983 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 1708 LEU cc_start: 0.7430 (tp) cc_final: 0.7107 (mt) REVERT: A 1719 MET cc_start: 0.8889 (mtp) cc_final: 0.8668 (mtt) REVERT: A 1727 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.5664 (tptt) REVERT: A 2122 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: A 2254 MET cc_start: 0.1375 (mmp) cc_final: 0.1104 (mmm) REVERT: A 2420 MET cc_start: 0.6278 (tmm) cc_final: 0.6057 (tmm) REVERT: A 2462 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 2511 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: B 587 MET cc_start: 0.5468 (mmp) cc_final: 0.5228 (mmp) REVERT: B 605 MET cc_start: 0.5581 (tpt) cc_final: 0.4175 (tmm) REVERT: B 702 HIS cc_start: 0.4703 (OUTLIER) cc_final: 0.3792 (t70) REVERT: B 708 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6562 (mt) REVERT: B 710 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5726 (p0) REVERT: B 974 GLN cc_start: 0.7087 (tt0) cc_final: 0.6766 (tt0) REVERT: B 1156 ASP cc_start: 0.5107 (OUTLIER) cc_final: 0.4333 (t0) REVERT: B 1354 MET cc_start: 0.8236 (mmm) cc_final: 0.8015 (tpp) REVERT: B 1562 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6121 (tpt-90) REVERT: B 1696 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7637 (mt) REVERT: B 1727 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.5653 (tptp) REVERT: B 2027 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7918 (t) REVERT: B 2117 GLU cc_start: 0.8490 (mp0) cc_final: 0.7986 (mp0) REVERT: B 2194 MET cc_start: 0.7271 (mtp) cc_final: 0.7040 (mtp) REVERT: B 2462 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9046 (mp) REVERT: B 2504 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 2511 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: C 587 MET cc_start: 0.5484 (mmp) cc_final: 0.5189 (mmp) REVERT: C 605 MET cc_start: 0.5470 (tpt) cc_final: 0.4036 (tmm) REVERT: C 710 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5976 (p0) REVERT: C 843 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: C 974 GLN cc_start: 0.7196 (tt0) cc_final: 0.6748 (tt0) REVERT: C 1011 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7545 (mtp) REVERT: C 1156 ASP cc_start: 0.5144 (OUTLIER) cc_final: 0.4550 (t0) REVERT: C 1158 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.5969 (tt) REVERT: C 1355 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8181 (mm-30) REVERT: C 1422 GLU cc_start: 0.8745 (tp30) cc_final: 0.8491 (mm-30) REVERT: C 1727 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.5682 (tptm) REVERT: C 2117 GLU cc_start: 0.8419 (mp0) cc_final: 0.7965 (mp0) REVERT: C 2462 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8908 (mp) REVERT: C 2504 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7904 (tp) outliers start: 211 outliers final: 112 residues processed: 465 average time/residue: 0.1723 time to fit residues: 136.0293 Evaluate side-chains 400 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 262 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2034 GLN Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2308 GLN Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2195 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1304 SER Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 173 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN A2308 GLN B1230 ASN ** B1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1230 ASN ** C2228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2308 GLN ** 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 = 0.4343 r_free = 0.4343 target = 0.187626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119823 restraints weight = 47818.271| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.58 r_work: 0.3265 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32373 Z= 0.164 Angle : 0.578 9.233 43815 Z= 0.294 Chirality : 0.039 0.165 4983 Planarity : 0.004 0.046 5325 Dihedral : 13.379 177.420 4607 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Rotamer: Outliers : 5.50 % Allowed : 21.27 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.14), residues: 3747 helix: 1.74 (0.10), residues: 2703 sheet: -1.03 (0.29), residues: 255 loop : -1.60 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1341 TYR 0.018 0.001 TYR B1328 PHE 0.022 0.001 PHE B 588 TRP 0.015 0.001 TRP A2188 HIS 0.007 0.001 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00374 (32370) covalent geometry : angle 0.57798 (43809) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.30271 ( 6) hydrogen bonds : bond 0.05493 ( 2059) hydrogen bonds : angle 4.15490 ( 6096) *********************** 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 469 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 285 time to evaluate : 1.069 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: A 605 MET cc_start: 0.5664 (tpt) cc_final: 0.4103 (tmm) REVERT: A 702 HIS cc_start: 0.5160 (OUTLIER) cc_final: 0.4320 (t70) REVERT: A 710 ASP cc_start: 0.6390 (OUTLIER) cc_final: 0.5942 (p0) REVERT: A 974 GLN cc_start: 0.7113 (tt0) cc_final: 0.6580 (tt0) REVERT: A 1534 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7348 (mmt90) REVERT: A 1562 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6199 (tpt-90) REVERT: A 1719 MET cc_start: 0.8926 (mtp) cc_final: 0.8705 (mtt) REVERT: A 1727 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6133 (tptm) REVERT: A 2005 LEU cc_start: 0.7883 (tt) cc_final: 0.7650 (mt) REVERT: A 2117 GLU cc_start: 0.8465 (mp0) cc_final: 0.8176 (mp0) REVERT: A 2122 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8377 (mtp) REVERT: A 2420 MET cc_start: 0.6298 (tmm) cc_final: 0.6085 (tmm) REVERT: A 2504 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7787 (tp) REVERT: A 2511 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: B 605 MET cc_start: 0.5557 (tpt) cc_final: 0.4152 (tmm) REVERT: B 702 HIS cc_start: 0.4669 (OUTLIER) cc_final: 0.3759 (t70) REVERT: B 710 ASP cc_start: 0.6035 (OUTLIER) cc_final: 0.5782 (p0) REVERT: B 809 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5298 (mp) REVERT: B 974 GLN cc_start: 0.6988 (tt0) cc_final: 0.6678 (tt0) REVERT: B 1011 MET cc_start: 0.8100 (mtt) cc_final: 0.7877 (mtp) REVERT: B 1156 ASP cc_start: 0.5284 (OUTLIER) cc_final: 0.4426 (t0) REVERT: B 1562 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6213 (tpt-90) REVERT: B 1696 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 1727 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6063 (tptm) REVERT: B 2034 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7140 (tp40) REVERT: B 2117 GLU cc_start: 0.8558 (mp0) cc_final: 0.8086 (mp0) REVERT: B 2504 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 587 MET cc_start: 0.5600 (mmp) cc_final: 0.5357 (mmp) REVERT: C 605 MET cc_start: 0.5386 (tpt) cc_final: 0.3909 (tmm) REVERT: C 710 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.6083 (p0) REVERT: C 843 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: C 974 GLN cc_start: 0.7251 (tt0) cc_final: 0.6805 (tt0) REVERT: C 1156 ASP cc_start: 0.5288 (OUTLIER) cc_final: 0.4563 (t0) REVERT: C 1158 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6045 (tt) REVERT: C 1562 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6153 (tpt170) REVERT: C 1727 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6142 (tptm) REVERT: C 2005 LEU cc_start: 0.7855 (tt) cc_final: 0.7648 (mt) REVERT: C 2018 ASP cc_start: 0.8887 (t0) cc_final: 0.8623 (t0) REVERT: C 2034 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: C 2117 GLU cc_start: 0.8523 (mp0) cc_final: 0.8098 (mp0) REVERT: C 2504 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8089 (tp) REVERT: C 2511 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8462 (mm-30) outliers start: 184 outliers final: 111 residues processed: 439 average time/residue: 0.1693 time to fit residues: 124.7035 Evaluate side-chains 407 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 271 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2122 MET Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2308 GLN Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2516 TRP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1285 ILE Chi-restraints excluded: chain C residue 1304 SER Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1335 SER Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 64 optimal weight: 1.9990 chunk 291 optimal weight: 0.6980 chunk 192 optimal weight: 0.0980 chunk 252 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 181 optimal weight: 0.4980 chunk 355 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 157 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2308 GLN B1230 ASN ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 GLN C2100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.190413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123684 restraints weight = 48018.273| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.67 r_work: 0.3315 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32373 Z= 0.114 Angle : 0.527 8.969 43815 Z= 0.263 Chirality : 0.037 0.178 4983 Planarity : 0.004 0.045 5325 Dihedral : 12.659 176.401 4587 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.54 % Allowed : 22.61 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.14), residues: 3747 helix: 2.11 (0.10), residues: 2688 sheet: -0.92 (0.29), residues: 255 loop : -1.28 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1341 TYR 0.019 0.001 TYR B2219 PHE 0.022 0.001 PHE A2093 TRP 0.014 0.001 TRP A2188 HIS 0.006 0.001 HIS B 702 Details of bonding type rmsd covalent geometry : bond 0.00243 (32370) covalent geometry : angle 0.52698 (43809) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.24245 ( 6) hydrogen bonds : bond 0.04558 ( 2059) hydrogen bonds : angle 3.89791 ( 6096) *********************** 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 434 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 282 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5668 (tpt) cc_final: 0.4153 (tmm) REVERT: A 702 HIS cc_start: 0.5001 (OUTLIER) cc_final: 0.4334 (t70) REVERT: A 710 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6394 (p0) REVERT: A 974 GLN cc_start: 0.7111 (tt0) cc_final: 0.6625 (tt0) REVERT: A 1562 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6218 (tpt-90) REVERT: A 1716 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8361 (mp) REVERT: A 1719 MET cc_start: 0.8914 (mtp) cc_final: 0.8702 (mtt) REVERT: A 1727 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.5835 (tptp) REVERT: A 2420 MET cc_start: 0.6305 (tmm) cc_final: 0.6054 (tmm) REVERT: A 2504 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7637 (tp) REVERT: A 2511 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: B 605 MET cc_start: 0.5535 (tpt) cc_final: 0.4184 (tmm) REVERT: B 710 ASP cc_start: 0.6021 (OUTLIER) cc_final: 0.5645 (p0) REVERT: B 809 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5255 (mp) REVERT: B 974 GLN cc_start: 0.6996 (tt0) cc_final: 0.6651 (tt0) REVERT: B 1156 ASP cc_start: 0.5257 (OUTLIER) cc_final: 0.4431 (t0) REVERT: B 1230 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6795 (t0) REVERT: B 1354 MET cc_start: 0.8312 (tpp) cc_final: 0.7836 (mmm) REVERT: B 1674 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7189 (mtt90) REVERT: B 1696 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 1716 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 1727 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.5800 (tptm) REVERT: B 2117 GLU cc_start: 0.8517 (mp0) cc_final: 0.8052 (mp0) REVERT: B 2504 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8061 (tp) REVERT: B 2511 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: C 587 MET cc_start: 0.5617 (mmp) cc_final: 0.5347 (mmp) REVERT: C 605 MET cc_start: 0.5443 (tpt) cc_final: 0.4031 (tmm) REVERT: C 710 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6218 (p0) REVERT: C 843 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: C 974 GLN cc_start: 0.7236 (tt0) cc_final: 0.6773 (tt0) REVERT: C 1156 ASP cc_start: 0.5231 (OUTLIER) cc_final: 0.4505 (t0) REVERT: C 1230 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7057 (t0) REVERT: C 1355 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8017 (tt0) REVERT: C 1527 ARG cc_start: 0.9044 (ptm-80) cc_final: 0.8603 (ptm-80) REVERT: C 1562 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6259 (tpt170) REVERT: C 1727 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.5871 (tptt) REVERT: C 2018 ASP cc_start: 0.8907 (t0) cc_final: 0.8665 (t0) REVERT: C 2034 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: C 2117 GLU cc_start: 0.8442 (mp0) cc_final: 0.8034 (mp0) REVERT: C 2504 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7995 (tp) REVERT: C 2511 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.7977 (mp0) outliers start: 152 outliers final: 94 residues processed: 404 average time/residue: 0.1679 time to fit residues: 114.4437 Evaluate side-chains 380 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 261 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 HIS Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2195 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1562 ARG Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 307 optimal weight: 1.9990 chunk 296 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 365 optimal weight: 30.0000 chunk 376 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 344 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN A1535 HIS A2100 HIS A2250 GLN ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 HIS ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.188724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122487 restraints weight = 47826.467| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.77 r_work: 0.3273 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.133 Angle : 0.533 7.614 43815 Z= 0.266 Chirality : 0.038 0.205 4983 Planarity : 0.004 0.044 5325 Dihedral : 12.283 176.821 4572 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 4.81 % Allowed : 22.85 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.14), residues: 3747 helix: 2.17 (0.10), residues: 2688 sheet: -0.77 (0.29), residues: 261 loop : -1.30 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 947 TYR 0.022 0.001 TYR B2219 PHE 0.021 0.001 PHE B 588 TRP 0.011 0.001 TRP A2188 HIS 0.012 0.001 HIS A1535 Details of bonding type rmsd covalent geometry : bond 0.00298 (32370) covalent geometry : angle 0.53340 (43809) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.21347 ( 6) hydrogen bonds : bond 0.04700 ( 2059) hydrogen bonds : angle 3.89244 ( 6096) *********************** 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 435 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 274 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5578 (tpt) cc_final: 0.4061 (tmm) REVERT: A 710 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6391 (p0) REVERT: A 974 GLN cc_start: 0.7165 (tt0) cc_final: 0.6723 (tt0) REVERT: A 1534 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7354 (mmt90) REVERT: A 1716 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 1719 MET cc_start: 0.8936 (mtp) cc_final: 0.8710 (mtt) REVERT: A 1727 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6131 (tptm) REVERT: A 2420 MET cc_start: 0.6210 (tmm) cc_final: 0.5975 (tmm) REVERT: A 2467 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8890 (ptm) REVERT: A 2504 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7702 (tp) REVERT: A 2511 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8470 (mm-30) REVERT: A 2513 MET cc_start: 0.8684 (ttm) cc_final: 0.8393 (ttp) REVERT: B 605 MET cc_start: 0.5456 (tpt) cc_final: 0.4102 (tmm) REVERT: B 710 ASP cc_start: 0.6224 (OUTLIER) cc_final: 0.5642 (p0) REVERT: B 809 LEU cc_start: 0.5474 (OUTLIER) cc_final: 0.5220 (mp) REVERT: B 974 GLN cc_start: 0.7037 (tt0) cc_final: 0.6722 (tt0) REVERT: B 1156 ASP cc_start: 0.5311 (OUTLIER) cc_final: 0.4426 (t0) REVERT: B 1354 MET cc_start: 0.8175 (tpp) cc_final: 0.7815 (mmm) REVERT: B 1674 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7190 (mtt90) REVERT: B 1696 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7551 (mp) REVERT: B 1716 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8256 (mt) REVERT: B 1727 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6008 (tptm) REVERT: B 1791 MET cc_start: 0.8313 (mmt) cc_final: 0.8070 (mmt) REVERT: B 2117 GLU cc_start: 0.8564 (mp0) cc_final: 0.8077 (mp0) REVERT: B 2504 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8098 (tp) REVERT: B 2511 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: C 587 MET cc_start: 0.5668 (mmp) cc_final: 0.5463 (mmp) REVERT: C 605 MET cc_start: 0.5365 (tpt) cc_final: 0.3979 (tmm) REVERT: C 710 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6564 (p0) REVERT: C 843 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: C 974 GLN cc_start: 0.7134 (tt0) cc_final: 0.6650 (tt0) REVERT: C 1156 ASP cc_start: 0.5195 (OUTLIER) cc_final: 0.4413 (t0) REVERT: C 1230 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7082 (t0) REVERT: C 1527 ARG cc_start: 0.9041 (ptm-80) cc_final: 0.8635 (ptm-80) REVERT: C 1716 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8229 (mp) REVERT: C 1727 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6095 (tptp) REVERT: C 2018 ASP cc_start: 0.8937 (t0) cc_final: 0.8708 (t0) REVERT: C 2034 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: C 2117 GLU cc_start: 0.8481 (mp0) cc_final: 0.8088 (mp0) REVERT: C 2504 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8045 (tp) outliers start: 161 outliers final: 109 residues processed: 405 average time/residue: 0.1748 time to fit residues: 120.3064 Evaluate side-chains 389 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 258 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1230 ASN Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1230 ASN Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1951 HIS Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 356 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 205 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 280 optimal weight: 0.1980 chunk 238 optimal weight: 2.9990 chunk 197 optimal weight: 0.0030 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 ASN B1951 HIS ** B2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.189674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119459 restraints weight = 48110.798| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.21 r_work: 0.3311 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.115 Angle : 0.522 7.708 43815 Z= 0.259 Chirality : 0.038 0.183 4983 Planarity : 0.004 0.044 5325 Dihedral : 11.965 176.787 4552 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 4.57 % Allowed : 23.33 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.14), residues: 3747 helix: 2.32 (0.10), residues: 2682 sheet: -0.65 (0.29), residues: 261 loop : -1.22 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 947 TYR 0.018 0.001 TYR B1782 PHE 0.022 0.001 PHE B1977 TRP 0.010 0.001 TRP A2188 HIS 0.019 0.001 HIS A1535 Details of bonding type rmsd covalent geometry : bond 0.00256 (32370) covalent geometry : angle 0.52211 (43809) SS BOND : bond 0.00124 ( 3) SS BOND : angle 0.20587 ( 6) hydrogen bonds : bond 0.04460 ( 2059) hydrogen bonds : angle 3.81943 ( 6096) *********************** 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 434 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 281 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5525 (tpt) cc_final: 0.4033 (tmm) REVERT: A 710 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6268 (p0) REVERT: A 974 GLN cc_start: 0.7191 (tt0) cc_final: 0.6763 (tt0) REVERT: A 1716 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 1719 MET cc_start: 0.8924 (mtp) cc_final: 0.8715 (mtt) REVERT: A 1727 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6097 (tptm) REVERT: A 2420 MET cc_start: 0.6229 (tmm) cc_final: 0.5966 (tmm) REVERT: A 2467 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8940 (ptm) REVERT: A 2504 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7676 (tp) REVERT: A 2511 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: A 2513 MET cc_start: 0.8654 (ttm) cc_final: 0.8380 (ttp) REVERT: B 605 MET cc_start: 0.5480 (tpt) cc_final: 0.4104 (tmm) REVERT: B 710 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.5724 (p0) REVERT: B 809 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5200 (mp) REVERT: B 974 GLN cc_start: 0.7037 (tt0) cc_final: 0.6733 (tt0) REVERT: B 1156 ASP cc_start: 0.5130 (OUTLIER) cc_final: 0.4224 (t0) REVERT: B 1354 MET cc_start: 0.8199 (tpp) cc_final: 0.7953 (mmm) REVERT: B 1562 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6387 (tpt170) REVERT: B 1674 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7186 (mtt90) REVERT: B 1696 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7565 (mp) REVERT: B 1716 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 1727 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.5973 (tptm) REVERT: B 1968 ASP cc_start: 0.7952 (m-30) cc_final: 0.7550 (t0) REVERT: B 2034 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: B 2117 GLU cc_start: 0.8545 (mp0) cc_final: 0.8042 (mp0) REVERT: B 2504 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8099 (tp) REVERT: B 2511 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: C 587 MET cc_start: 0.5800 (mmp) cc_final: 0.5600 (mmp) REVERT: C 605 MET cc_start: 0.5324 (tpt) cc_final: 0.3915 (tmm) REVERT: C 843 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: C 974 GLN cc_start: 0.7163 (tt0) cc_final: 0.6693 (tt0) REVERT: C 1156 ASP cc_start: 0.5195 (OUTLIER) cc_final: 0.4432 (t0) REVERT: C 1214 LEU cc_start: 0.8563 (tp) cc_final: 0.8297 (tt) REVERT: C 1230 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7118 (t0) REVERT: C 1355 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8010 (tt0) REVERT: C 1527 ARG cc_start: 0.9042 (ptm-80) cc_final: 0.8631 (ptm-80) REVERT: C 1716 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8117 (mp) REVERT: C 1727 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6077 (tptp) REVERT: C 1952 THR cc_start: 0.6536 (OUTLIER) cc_final: 0.6301 (p) REVERT: C 2018 ASP cc_start: 0.8927 (t0) cc_final: 0.8716 (t0) REVERT: C 2034 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: C 2117 GLU cc_start: 0.8447 (mp0) cc_final: 0.8091 (mp0) REVERT: C 2504 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8039 (tp) REVERT: C 2511 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.7988 (mp0) outliers start: 153 outliers final: 107 residues processed: 405 average time/residue: 0.1668 time to fit residues: 114.6493 Evaluate side-chains 397 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 265 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2447 ILE Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 314 optimal weight: 7.9990 chunk 370 optimal weight: 8.9990 chunk 308 optimal weight: 0.2980 chunk 242 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 333 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.188567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120515 restraints weight = 48170.838| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.50 r_work: 0.3290 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.133 Angle : 0.531 8.340 43815 Z= 0.264 Chirality : 0.038 0.182 4983 Planarity : 0.004 0.044 5325 Dihedral : 11.795 177.387 4545 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 4.39 % Allowed : 23.54 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.14), residues: 3747 helix: 2.30 (0.10), residues: 2685 sheet: -0.60 (0.30), residues: 261 loop : -1.16 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 703 TYR 0.023 0.001 TYR B1782 PHE 0.025 0.001 PHE C2182 TRP 0.009 0.001 TRP C2044 HIS 0.017 0.001 HIS C 702 Details of bonding type rmsd covalent geometry : bond 0.00305 (32370) covalent geometry : angle 0.53090 (43809) SS BOND : bond 0.00116 ( 3) SS BOND : angle 0.21377 ( 6) hydrogen bonds : bond 0.04614 ( 2059) hydrogen bonds : angle 3.85272 ( 6096) *********************** 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 418 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 271 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5534 (tpt) cc_final: 0.4047 (tmm) REVERT: A 710 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6114 (p0) REVERT: A 974 GLN cc_start: 0.7133 (tt0) cc_final: 0.6718 (tt0) REVERT: A 1516 MET cc_start: 0.5601 (ppp) cc_final: 0.5386 (mmt) REVERT: A 1562 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6302 (tpt170) REVERT: A 1716 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 1719 MET cc_start: 0.8953 (mtp) cc_final: 0.8730 (mtt) REVERT: A 1727 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6207 (tptp) REVERT: A 1968 ASP cc_start: 0.7775 (m-30) cc_final: 0.7378 (t0) REVERT: A 2005 LEU cc_start: 0.7960 (tt) cc_final: 0.7742 (mt) REVERT: A 2467 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8978 (ptm) REVERT: A 2504 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7750 (tp) REVERT: B 605 MET cc_start: 0.5513 (tpt) cc_final: 0.4057 (tmm) REVERT: B 710 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5923 (p0) REVERT: B 974 GLN cc_start: 0.7074 (tt0) cc_final: 0.6747 (tt0) REVERT: B 1156 ASP cc_start: 0.5144 (OUTLIER) cc_final: 0.4237 (t0) REVERT: B 1354 MET cc_start: 0.8229 (tpp) cc_final: 0.8029 (mmm) REVERT: B 1562 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6379 (tpt170) REVERT: B 1674 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7186 (mtt90) REVERT: B 1696 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 1716 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 1727 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6120 (tptm) REVERT: B 1968 ASP cc_start: 0.7944 (m-30) cc_final: 0.7527 (t0) REVERT: B 2034 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: B 2117 GLU cc_start: 0.8527 (mp0) cc_final: 0.8040 (mp0) REVERT: B 2420 MET cc_start: 0.6168 (tmm) cc_final: 0.5959 (tmm) REVERT: B 2504 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 2511 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: C 605 MET cc_start: 0.5320 (tpt) cc_final: 0.3876 (tmm) REVERT: C 974 GLN cc_start: 0.7165 (tt0) cc_final: 0.6696 (tt0) REVERT: C 1230 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7086 (t0) REVERT: C 1355 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8001 (tt0) REVERT: C 1527 ARG cc_start: 0.9042 (ptm-80) cc_final: 0.8630 (ptm-80) REVERT: C 1716 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8147 (mp) REVERT: C 1727 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6164 (tptp) REVERT: C 1952 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6456 (p) REVERT: C 2018 ASP cc_start: 0.8947 (t0) cc_final: 0.8740 (t0) REVERT: C 2034 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: C 2504 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8082 (tp) REVERT: C 2511 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.7982 (mp0) outliers start: 147 outliers final: 112 residues processed: 391 average time/residue: 0.1577 time to fit residues: 104.6630 Evaluate side-chains 394 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 260 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 231 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 347 optimal weight: 0.9990 chunk 70 optimal weight: 0.0270 chunk 193 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS C1230 ASN C2250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.188617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119398 restraints weight = 47929.653| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.57 r_work: 0.3279 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.128 Angle : 0.530 8.703 43815 Z= 0.262 Chirality : 0.038 0.182 4983 Planarity : 0.004 0.045 5325 Dihedral : 11.563 177.405 4537 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 4.21 % Allowed : 23.63 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.14), residues: 3747 helix: 2.35 (0.10), residues: 2688 sheet: -0.54 (0.30), residues: 261 loop : -1.07 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1944 TYR 0.021 0.001 TYR B1782 PHE 0.025 0.001 PHE B1977 TRP 0.011 0.001 TRP A2188 HIS 0.011 0.001 HIS C 702 Details of bonding type rmsd covalent geometry : bond 0.00292 (32370) covalent geometry : angle 0.53008 (43809) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.21556 ( 6) hydrogen bonds : bond 0.04535 ( 2059) hydrogen bonds : angle 3.80729 ( 6096) *********************** 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 416 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 275 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5412 (tpt) cc_final: 0.3956 (tmm) REVERT: A 974 GLN cc_start: 0.7138 (tt0) cc_final: 0.6730 (tt0) REVERT: A 1562 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6295 (tpt170) REVERT: A 1716 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 1719 MET cc_start: 0.8939 (mtp) cc_final: 0.8716 (mtt) REVERT: A 1727 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6192 (tptm) REVERT: A 1968 ASP cc_start: 0.7741 (m-30) cc_final: 0.7288 (t0) REVERT: A 2467 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8934 (ptm) REVERT: A 2504 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7712 (tp) REVERT: B 605 MET cc_start: 0.5462 (tpt) cc_final: 0.4028 (tmm) REVERT: B 809 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5153 (mp) REVERT: B 974 GLN cc_start: 0.7058 (tt0) cc_final: 0.6735 (tt0) REVERT: B 1156 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4358 (t0) REVERT: B 1562 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6376 (tpt170) REVERT: B 1696 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 1727 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6163 (tptp) REVERT: B 2034 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: B 2117 GLU cc_start: 0.8537 (mp0) cc_final: 0.8034 (mp0) REVERT: B 2420 MET cc_start: 0.6320 (tmm) cc_final: 0.6098 (tmm) REVERT: B 2504 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8164 (tp) REVERT: B 2511 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: C 605 MET cc_start: 0.5343 (tpt) cc_final: 0.3911 (tmm) REVERT: C 974 GLN cc_start: 0.7132 (tt0) cc_final: 0.6694 (tt0) REVERT: C 1214 LEU cc_start: 0.8561 (tp) cc_final: 0.8298 (tt) REVERT: C 1355 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7949 (tt0) REVERT: C 1516 MET cc_start: 0.5891 (ppp) cc_final: 0.5583 (ptt) REVERT: C 1527 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8661 (ptm-80) REVERT: C 1727 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6150 (tptp) REVERT: C 1952 THR cc_start: 0.6713 (OUTLIER) cc_final: 0.6480 (p) REVERT: C 2034 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: C 2504 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8044 (tp) REVERT: C 2511 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8010 (mp0) outliers start: 141 outliers final: 107 residues processed: 394 average time/residue: 0.1866 time to fit residues: 124.6697 Evaluate side-chains 393 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 268 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2167 LYS Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2134 SER Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Chi-restraints excluded: chain C residue 2516 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 98 optimal weight: 20.0000 chunk 229 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 chunk 327 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.188257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116965 restraints weight = 47959.545| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.14 r_work: 0.3288 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32373 Z= 0.133 Angle : 0.536 10.666 43815 Z= 0.266 Chirality : 0.038 0.203 4983 Planarity : 0.004 0.045 5325 Dihedral : 11.408 177.785 4531 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 3.70 % Allowed : 23.95 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.14), residues: 3747 helix: 2.35 (0.10), residues: 2688 sheet: -0.56 (0.30), residues: 261 loop : -1.03 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1944 TYR 0.020 0.001 TYR B1782 PHE 0.026 0.001 PHE B1977 TRP 0.010 0.001 TRP A1515 HIS 0.007 0.001 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00309 (32370) covalent geometry : angle 0.53603 (43809) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.22382 ( 6) hydrogen bonds : bond 0.04613 ( 2059) hydrogen bonds : angle 3.82335 ( 6096) ********************** 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 392 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 268 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 MET cc_start: 0.5365 (tpt) cc_final: 0.3931 (tmm) REVERT: A 974 GLN cc_start: 0.7190 (tt0) cc_final: 0.6776 (tt0) REVERT: A 1562 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6304 (tpt170) REVERT: A 1716 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 1719 MET cc_start: 0.8945 (mtp) cc_final: 0.8730 (mtt) REVERT: A 1727 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6260 (tptm) REVERT: A 1968 ASP cc_start: 0.7672 (m-30) cc_final: 0.7293 (t0) REVERT: A 2467 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8964 (ptm) REVERT: A 2504 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7766 (tp) REVERT: B 605 MET cc_start: 0.5508 (tpt) cc_final: 0.4037 (tmm) REVERT: B 809 LEU cc_start: 0.5477 (OUTLIER) cc_final: 0.5136 (mp) REVERT: B 974 GLN cc_start: 0.7106 (tt0) cc_final: 0.6772 (tt0) REVERT: B 1156 ASP cc_start: 0.5253 (OUTLIER) cc_final: 0.4372 (t0) REVERT: B 1534 ARG cc_start: 0.7654 (tpp80) cc_final: 0.7340 (mmt90) REVERT: B 1562 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6378 (tpt170) REVERT: B 1696 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7532 (mp) REVERT: B 1727 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6261 (tptm) REVERT: B 2034 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: B 2117 GLU cc_start: 0.8532 (mp0) cc_final: 0.8029 (mp0) REVERT: B 2420 MET cc_start: 0.6298 (tmm) cc_final: 0.6072 (tmm) REVERT: B 2504 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8183 (tp) REVERT: B 2511 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 605 MET cc_start: 0.5354 (tpt) cc_final: 0.3895 (tmm) REVERT: C 974 GLN cc_start: 0.7169 (tt0) cc_final: 0.6711 (tt0) REVERT: C 1214 LEU cc_start: 0.8583 (tp) cc_final: 0.8317 (tt) REVERT: C 1230 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7026 (t0) REVERT: C 1355 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7943 (tt0) REVERT: C 1516 MET cc_start: 0.5746 (ppp) cc_final: 0.5418 (ptt) REVERT: C 1527 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8657 (ptm-80) REVERT: C 1727 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6185 (tptp) REVERT: C 1952 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6591 (p) REVERT: C 2034 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.6498 (tt0) REVERT: C 2504 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8043 (tp) REVERT: C 2511 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.7991 (mp0) outliers start: 124 outliers final: 98 residues processed: 374 average time/residue: 0.1912 time to fit residues: 120.5180 Evaluate side-chains 376 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 259 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1562 ARG Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1716 LEU Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1948 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2044 TRP Chi-restraints excluded: chain A residue 2167 LYS Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2467 MET Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1562 ARG Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1727 LYS Chi-restraints excluded: chain B residue 1948 ASP Chi-restraints excluded: chain B residue 1952 THR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2004 PHE Chi-restraints excluded: chain B residue 2034 GLN Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2044 TRP Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2448 VAL Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2511 GLU Chi-restraints excluded: chain B residue 2516 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 685 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1230 ASN Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1719 MET Chi-restraints excluded: chain C residue 1727 LYS Chi-restraints excluded: chain C residue 1952 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2034 GLN Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2044 TRP Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2122 MET Chi-restraints excluded: chain C residue 2134 SER Chi-restraints excluded: chain C residue 2200 VAL Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2447 ILE Chi-restraints excluded: chain C residue 2448 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2467 MET Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2511 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 320 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 319 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 296 optimal weight: 0.5980 chunk 265 optimal weight: 0.4980 chunk 287 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.189259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118088 restraints weight = 48242.784| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.16 r_work: 0.3308 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32373 Z= 0.116 Angle : 0.526 9.496 43815 Z= 0.259 Chirality : 0.038 0.195 4983 Planarity : 0.004 0.045 5325 Dihedral : 11.264 177.780 4531 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 3.58 % Allowed : 24.19 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.14), residues: 3747 helix: 2.47 (0.10), residues: 2685 sheet: -0.53 (0.30), residues: 261 loop : -0.90 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1944 TYR 0.020 0.001 TYR B1782 PHE 0.027 0.001 PHE A2182 TRP 0.010 0.001 TRP C1168 HIS 0.007 0.001 HIS B1535 Details of bonding type rmsd covalent geometry : bond 0.00262 (32370) covalent geometry : angle 0.52635 (43809) SS BOND : bond 0.00097 ( 3) SS BOND : angle 0.17858 ( 6) hydrogen bonds : bond 0.04312 ( 2059) hydrogen bonds : angle 3.73031 ( 6096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11241.20 seconds wall clock time: 192 minutes 10.95 seconds (11530.95 seconds total)