Starting phenix.real_space_refine on Mon Aug 25 23:34:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zu8_60481/08_2025/8zu8_60481_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zu8_60481/08_2025/8zu8_60481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zu8_60481/08_2025/8zu8_60481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zu8_60481/08_2025/8zu8_60481.map" model { file = "/net/cci-nas-00/data/ceres_data/8zu8_60481/08_2025/8zu8_60481_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zu8_60481/08_2025/8zu8_60481_neut.cif" } resolution = 3.9 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= -0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 183 5.16 5 C 20850 2.51 5 N 5163 2.21 5 O 5202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.02s 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: 31401 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10418 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 7, 'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10418 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 7, 'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 10412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1279, 10412 Classifications: {'peptide': 1279} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 41, 'TRANS': 1237} Chain breaks: 14 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 8, 'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.62, per 1000 atoms: 0.21 Number of scatterers: 31401 At special positions: 0 Unit cell: (224.985, 218.193, 156.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 183 16.00 P 3 15.00 O 5202 8.00 N 5163 7.00 C 20850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2411 " - pdb=" SG CYS A2415 " distance=2.04 Simple disulfide: pdb=" SG CYS B2411 " - pdb=" SG CYS B2415 " distance=2.04 Simple disulfide: pdb=" SG CYS C2411 " - pdb=" SG CYS C2415 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7314 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 9 sheets defined 71.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS A 584 " --> pdb=" O TRP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.556A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 626 through 644 Processing helix chain 'A' and resid 679 through 701 Proline residue: A 687 - end of helix removed outlier: 3.533A pdb=" N GLN A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 930 through 956 Processing helix chain 'A' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP A 976 " --> pdb=" O ARG A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 995 through 1010 removed outlier: 3.717A pdb=" N ASN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A1008 " --> pdb=" O VAL A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.503A pdb=" N ALA A1024 " --> pdb=" O CYS A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1164 Processing helix chain 'A' and resid 1166 through 1179 Processing helix chain 'A' and resid 1183 through 1199 removed outlier: 3.827A pdb=" N LEU A1187 " --> pdb=" O SER A1183 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A1188 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A1189 " --> pdb=" O PHE A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 removed outlier: 3.700A pdb=" N LEU A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1232 removed outlier: 3.641A pdb=" N TRP A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A1230 " --> pdb=" O ILE A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG A1300 " --> pdb=" O LEU A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1370 Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1514 through 1533 Processing helix chain 'A' and resid 1533 through 1557 removed outlier: 3.517A pdb=" N LEU A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU A1565 " --> pdb=" O HIS A1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A1568 " --> pdb=" O VAL A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1652 Processing helix chain 'A' and resid 1656 through 1668 removed outlier: 4.011A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1686 Processing helix chain 'A' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 Processing helix chain 'A' and resid 1726 through 1747 Processing helix chain 'A' and resid 1784 through 1803 Processing helix chain 'A' and resid 1941 through 1951 Processing helix chain 'A' and resid 1960 through 1978 Processing helix chain 'A' and resid 2002 through 2024 Processing helix chain 'A' and resid 2026 through 2045 removed outlier: 3.526A pdb=" N LYS A2030 " --> pdb=" O THR A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2084 Processing helix chain 'A' and resid 2100 through 2112 removed outlier: 3.546A pdb=" N VAL A2112 " --> pdb=" O GLY A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2114 through 2127 Processing helix chain 'A' and resid 2133 through 2159 Processing helix chain 'A' and resid 2168 through 2185 Processing helix chain 'A' and resid 2187 through 2198 removed outlier: 4.170A pdb=" N LEU A2191 " --> pdb=" O ILE A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2236 through 2248 Processing helix chain 'A' and resid 2250 through 2258 Processing helix chain 'A' and resid 2281 through 2295 Processing helix chain 'A' and resid 2311 through 2314 Processing helix chain 'A' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU A2342 " --> pdb=" O LEU A2338 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 Processing helix chain 'A' and resid 2437 through 2460 removed outlier: 3.551A pdb=" N MET A2441 " --> pdb=" O GLY A2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A2458 " --> pdb=" O PHE A2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A2459 " --> pdb=" O VAL A2455 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE A2485 " --> pdb=" O CYS A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2505 removed outlier: 3.714A pdb=" N GLU A2497 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A2502 " --> pdb=" O GLU A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2517 Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS B 584 " --> pdb=" O TRP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 618 removed outlier: 3.555A pdb=" N GLN B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 625 through 644 removed outlier: 3.834A pdb=" N PHE B 629 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 Proline residue: B 687 - end of helix removed outlier: 3.532A pdb=" N GLN B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 829 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL B 838 " --> pdb=" O ASN B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 871 Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 930 through 956 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP B 976 " --> pdb=" O ARG B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 995 through 1010 removed outlier: 3.717A pdb=" N ASN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B1008 " --> pdb=" O VAL B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1026 removed outlier: 3.503A pdb=" N ALA B1024 " --> pdb=" O CYS B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG B1036 " --> pdb=" O GLN B1032 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) Proline residue: B1039 - end of helix Processing helix chain 'B' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU B1105 " --> pdb=" O SER B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1164 Processing helix chain 'B' and resid 1166 through 1179 Processing helix chain 'B' and resid 1183 through 1199 removed outlier: 3.827A pdb=" N LEU B1187 " --> pdb=" O SER B1183 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B1188 " --> pdb=" O ILE B1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B1189 " --> pdb=" O PHE B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1199 through 1204 removed outlier: 3.700A pdb=" N LEU B1203 " --> pdb=" O PHE B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1232 removed outlier: 3.570A pdb=" N TYR B1221 " --> pdb=" O CYS B1217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B1230 " --> pdb=" O ILE B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG B1300 " --> pdb=" O LEU B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1320 removed outlier: 3.991A pdb=" N VAL B1310 " --> pdb=" O TYR B1306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B1318 " --> pdb=" O LEU B1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1320 through 1370 Processing helix chain 'B' and resid 1408 through 1412 Processing helix chain 'B' and resid 1514 through 1533 Processing helix chain 'B' and resid 1533 through 1557 removed outlier: 3.517A pdb=" N LEU B1549 " --> pdb=" O ALA B1545 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1568 removed outlier: 4.231A pdb=" N LEU B1565 " --> pdb=" O HIS B1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B1568 " --> pdb=" O VAL B1564 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1652 Processing helix chain 'B' and resid 1656 through 1668 removed outlier: 4.011A pdb=" N GLU B1660 " --> pdb=" O ILE B1656 " (cutoff:3.500A) Processing helix chain 'B' and resid 1670 through 1686 Processing helix chain 'B' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS B1699 " --> pdb=" O ILE B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1718 Processing helix chain 'B' and resid 1726 through 1747 Processing helix chain 'B' and resid 1784 through 1803 Processing helix chain 'B' and resid 1941 through 1951 Processing helix chain 'B' and resid 1960 through 1978 Processing helix chain 'B' and resid 2002 through 2024 Processing helix chain 'B' and resid 2026 through 2045 removed outlier: 3.526A pdb=" N LYS B2030 " --> pdb=" O THR B2026 " (cutoff:3.500A) Processing helix chain 'B' and resid 2061 through 2084 Processing helix chain 'B' and resid 2100 through 2112 removed outlier: 3.546A pdb=" N VAL B2112 " --> pdb=" O GLY B2108 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2127 Processing helix chain 'B' and resid 2133 through 2159 Processing helix chain 'B' and resid 2168 through 2185 Processing helix chain 'B' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU B2191 " --> pdb=" O ILE B2187 " (cutoff:3.500A) Processing helix chain 'B' and resid 2236 through 2248 Processing helix chain 'B' and resid 2250 through 2258 Processing helix chain 'B' and resid 2281 through 2295 Processing helix chain 'B' and resid 2311 through 2314 Processing helix chain 'B' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU B2342 " --> pdb=" O LEU B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2382 Processing helix chain 'B' and resid 2437 through 2460 removed outlier: 3.551A pdb=" N MET B2441 " --> pdb=" O GLY B2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B2458 " --> pdb=" O PHE B2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B2459 " --> pdb=" O VAL B2455 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE B2485 " --> pdb=" O CYS B2481 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2505 removed outlier: 3.715A pdb=" N GLU B2497 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B2502 " --> pdb=" O GLU B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2517 Processing helix chain 'C' and resid 571 through 577 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.920A pdb=" N CYS C 584 " --> pdb=" O TRP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 618 removed outlier: 3.555A pdb=" N GLN C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 626 through 644 Processing helix chain 'C' and resid 679 through 701 Proline residue: C 687 - end of helix removed outlier: 3.533A pdb=" N GLN C 697 " --> pdb=" O ALA C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 709 Processing helix chain 'C' and resid 790 through 813 removed outlier: 3.561A pdb=" N LEU C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 829 Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.522A pdb=" N VAL C 838 " --> pdb=" O ASN C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 871 Processing helix chain 'C' and resid 930 through 956 Processing helix chain 'C' and resid 971 through 976 removed outlier: 3.963A pdb=" N ASP C 976 " --> pdb=" O ARG C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.717A pdb=" N ASN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C1008 " --> pdb=" O VAL C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1026 removed outlier: 3.503A pdb=" N ALA C1024 " --> pdb=" O CYS C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 3.621A pdb=" N ARG C1036 " --> pdb=" O GLN C1032 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C1037 " --> pdb=" O ALA C1033 " (cutoff:3.500A) Proline residue: C1039 - end of helix Processing helix chain 'C' and resid 1099 through 1116 removed outlier: 3.506A pdb=" N LEU C1105 " --> pdb=" O SER C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1155 through 1164 Processing helix chain 'C' and resid 1166 through 1179 Processing helix chain 'C' and resid 1183 through 1199 removed outlier: 3.827A pdb=" N LEU C1187 " --> pdb=" O SER C1183 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C1188 " --> pdb=" O ILE C1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C1189 " --> pdb=" O PHE C1185 " (cutoff:3.500A) Processing helix chain 'C' and resid 1199 through 1204 removed outlier: 3.700A pdb=" N LEU C1203 " --> pdb=" O PHE C1199 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1232 removed outlier: 3.532A pdb=" N ARG C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C1230 " --> pdb=" O ILE C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1302 removed outlier: 3.668A pdb=" N ARG C1300 " --> pdb=" O LEU C1296 " (cutoff:3.500A) Processing helix chain 'C' and resid 1306 through 1320 removed outlier: 3.990A pdb=" N VAL C1310 " --> pdb=" O TYR C1306 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1370 Processing helix chain 'C' and resid 1408 through 1412 Processing helix chain 'C' and resid 1514 through 1533 Processing helix chain 'C' and resid 1533 through 1557 removed outlier: 3.518A pdb=" N LEU C1549 " --> pdb=" O ALA C1545 " (cutoff:3.500A) Processing helix chain 'C' and resid 1561 through 1568 removed outlier: 4.230A pdb=" N LEU C1565 " --> pdb=" O HIS C1561 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU C1568 " --> pdb=" O VAL C1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 1646 through 1652 Processing helix chain 'C' and resid 1656 through 1668 removed outlier: 4.011A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) Processing helix chain 'C' and resid 1670 through 1686 Processing helix chain 'C' and resid 1687 through 1702 removed outlier: 3.609A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 Processing helix chain 'C' and resid 1726 through 1747 Processing helix chain 'C' and resid 1784 through 1803 Processing helix chain 'C' and resid 1941 through 1951 Processing helix chain 'C' and resid 1960 through 1978 Processing helix chain 'C' and resid 2002 through 2024 Processing helix chain 'C' and resid 2026 through 2045 removed outlier: 3.526A pdb=" N LYS C2030 " --> pdb=" O THR C2026 " (cutoff:3.500A) Processing helix chain 'C' and resid 2061 through 2084 Processing helix chain 'C' and resid 2100 through 2112 removed outlier: 3.546A pdb=" N VAL C2112 " --> pdb=" O GLY C2108 " (cutoff:3.500A) Processing helix chain 'C' and resid 2114 through 2127 Processing helix chain 'C' and resid 2133 through 2159 Processing helix chain 'C' and resid 2168 through 2185 Processing helix chain 'C' and resid 2187 through 2198 removed outlier: 4.169A pdb=" N LEU C2191 " --> pdb=" O ILE C2187 " (cutoff:3.500A) Processing helix chain 'C' and resid 2236 through 2248 Processing helix chain 'C' and resid 2250 through 2258 Processing helix chain 'C' and resid 2281 through 2295 Processing helix chain 'C' and resid 2311 through 2314 Processing helix chain 'C' and resid 2332 through 2342 removed outlier: 3.607A pdb=" N LEU C2342 " --> pdb=" O LEU C2338 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2382 Processing helix chain 'C' and resid 2437 through 2460 removed outlier: 3.551A pdb=" N MET C2441 " --> pdb=" O GLY C2437 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C2458 " --> pdb=" O PHE C2454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C2459 " --> pdb=" O VAL C2455 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2490 removed outlier: 3.583A pdb=" N PHE C2485 " --> pdb=" O CYS C2481 " (cutoff:3.500A) Processing helix chain 'C' and resid 2493 through 2505 removed outlier: 3.714A pdb=" N GLU C2497 " --> pdb=" O LEU C2493 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C2502 " --> pdb=" O GLU C2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2517 Processing sheet with id=AA1, first strand: chain 'A' and resid 2223 through 2228 removed outlier: 3.595A pdb=" N ASP A2209 " --> pdb=" O GLN A2308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A2299 " --> pdb=" O LEU A2328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2232 through 2234 Processing sheet with id=AA3, first strand: chain 'A' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN A2354 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A2383 " --> pdb=" O ASN A2354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2223 through 2227 removed outlier: 3.595A pdb=" N ASP B2209 " --> pdb=" O GLN B2308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B2299 " --> pdb=" O LEU B2328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2232 through 2234 Processing sheet with id=AA6, first strand: chain 'B' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN B2354 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU B2383 " --> pdb=" O ASN B2354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2223 through 2227 removed outlier: 3.595A pdb=" N ASP C2209 " --> pdb=" O GLN C2308 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C2299 " --> pdb=" O LEU C2328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2232 through 2234 Processing sheet with id=AA9, first strand: chain 'C' and resid 2350 through 2356 removed outlier: 3.964A pdb=" N ASN C2354 " --> pdb=" O LEU C2383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C2383 " --> pdb=" O ASN C2354 " (cutoff:3.500A) 2056 hydrogen bonds defined for protein. 6087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4670 1.28 - 1.42: 8943 1.42 - 1.55: 18261 1.55 - 1.69: 16 1.69 - 1.82: 288 Bond restraints: 32178 Sorted by residual: bond pdb=" C39 L9Q B2601 " pdb=" C40 L9Q B2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.14e+01 bond pdb=" C39 L9Q C2601 " pdb=" C40 L9Q C2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.12e+01 bond pdb=" C39 L9Q A2601 " pdb=" C40 L9Q A2601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C31 L9Q A2601 " pdb=" O2 L9Q A2601 " ideal model delta sigma weight residual 1.330 1.464 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C31 L9Q C2601 " pdb=" O2 L9Q C2601 " ideal model delta sigma weight residual 1.330 1.464 -0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 32173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 42033 3.30 - 6.60: 1355 6.60 - 9.90: 174 9.90 - 13.20: 33 13.20 - 16.50: 6 Bond angle restraints: 43601 Sorted by residual: angle pdb=" N ILE C 684 " pdb=" CA ILE C 684 " pdb=" C ILE C 684 " ideal model delta sigma weight residual 111.90 103.39 8.51 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE B 684 " pdb=" CA ILE B 684 " pdb=" C ILE B 684 " ideal model delta sigma weight residual 111.90 103.41 8.49 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE A 684 " pdb=" CA ILE A 684 " pdb=" C ILE A 684 " ideal model delta sigma weight residual 111.90 103.42 8.48 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE A1025 " pdb=" CA ILE A1025 " pdb=" C ILE A1025 " ideal model delta sigma weight residual 111.90 103.60 8.30 8.10e-01 1.52e+00 1.05e+02 angle pdb=" N ILE C1025 " pdb=" CA ILE C1025 " pdb=" C ILE C1025 " ideal model delta sigma weight residual 111.90 103.62 8.28 8.10e-01 1.52e+00 1.05e+02 ... (remaining 43596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 16814 31.29 - 62.58: 1970 62.58 - 93.87: 81 93.87 - 125.16: 9 125.16 - 156.46: 9 Dihedral angle restraints: 18883 sinusoidal: 7603 harmonic: 11280 Sorted by residual: dihedral pdb=" C21 L9Q C2601 " pdb=" C22 L9Q C2601 " pdb=" C23 L9Q C2601 " pdb=" C24 L9Q C2601 " ideal model delta sinusoidal sigma weight residual 179.52 -24.02 -156.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C21 L9Q A2601 " pdb=" C22 L9Q A2601 " pdb=" C23 L9Q A2601 " pdb=" C24 L9Q A2601 " ideal model delta sinusoidal sigma weight residual 179.52 -24.05 -156.43 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C21 L9Q B2601 " pdb=" C22 L9Q B2601 " pdb=" C23 L9Q B2601 " pdb=" C24 L9Q B2601 " ideal model delta sinusoidal sigma weight residual 179.52 -24.12 -156.36 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 18880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3594 0.092 - 0.183: 1117 0.183 - 0.275: 223 0.275 - 0.366: 35 0.366 - 0.458: 14 Chirality restraints: 4983 Sorted by residual: chirality pdb=" CA LEU A2493 " pdb=" N LEU A2493 " pdb=" C LEU A2493 " pdb=" CB LEU A2493 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU C2493 " pdb=" N LEU C2493 " pdb=" C LEU C2493 " pdb=" CB LEU C2493 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CA LEU B2493 " pdb=" N LEU B2493 " pdb=" C LEU B2493 " pdb=" CB LEU B2493 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 4980 not shown) Planarity restraints: 5303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B2601 " 0.146 2.00e-02 2.50e+03 2.47e-01 6.10e+02 pdb=" C39 L9Q B2601 " -0.318 2.00e-02 2.50e+03 pdb=" C40 L9Q B2601 " 0.317 2.00e-02 2.50e+03 pdb=" C41 L9Q B2601 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q C2601 " -0.146 2.00e-02 2.50e+03 2.47e-01 6.10e+02 pdb=" C39 L9Q C2601 " 0.318 2.00e-02 2.50e+03 pdb=" C40 L9Q C2601 " -0.317 2.00e-02 2.50e+03 pdb=" C41 L9Q C2601 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A2601 " 0.146 2.00e-02 2.50e+03 2.47e-01 6.10e+02 pdb=" C39 L9Q A2601 " -0.318 2.00e-02 2.50e+03 pdb=" C40 L9Q A2601 " 0.317 2.00e-02 2.50e+03 pdb=" C41 L9Q A2601 " -0.145 2.00e-02 2.50e+03 ... (remaining 5300 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 12 1.88 - 2.64: 734 2.64 - 3.39: 40858 3.39 - 4.15: 77074 4.15 - 4.90: 132360 Nonbonded interactions: 251038 Sorted by model distance: nonbonded pdb=" N GLU C 679 " pdb=" OE1 GLU C 679 " model vdw 1.126 3.120 nonbonded pdb=" N GLU B 679 " pdb=" OE1 GLU B 679 " model vdw 1.126 3.120 nonbonded pdb=" N GLU A 679 " pdb=" OE1 GLU A 679 " model vdw 1.126 3.120 nonbonded pdb=" CB LYS C2157 " pdb=" NZ LYS C2157 " model vdw 1.702 3.520 nonbonded pdb=" CB LYS B2157 " pdb=" NZ LYS B2157 " model vdw 1.702 3.520 ... (remaining 251033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 570 through 2335 or (resid 2336 and (name N or name CA or \ name C or name O or name CB )) or resid 2337 through 2601)) selection = (chain 'B' and (resid 570 through 2335 or (resid 2336 and (name N or name CA or \ name C or name O or name CB )) or resid 2337 through 2601)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.990 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.191 32181 Z= 0.752 Angle : 1.438 16.500 43607 Z= 0.961 Chirality : 0.093 0.458 4983 Planarity : 0.010 0.247 5303 Dihedral : 23.150 156.455 11560 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.99 % Allowed : 8.78 % Favored : 90.23 % Rotamer: Outliers : 26.27 % Allowed : 13.21 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.55 (0.11), residues: 3747 helix: -1.94 (0.08), residues: 2691 sheet: -1.85 (0.29), residues: 246 loop : -3.20 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2336 TYR 0.109 0.005 TYR B2319 PHE 0.037 0.003 PHE A2307 TRP 0.071 0.005 TRP A2403 HIS 0.006 0.001 HIS B1947 Details of bonding type rmsd covalent geometry : bond 0.01094 (32178) covalent geometry : angle 1.43827 (43601) SS BOND : bond 0.01029 ( 3) SS BOND : angle 0.75550 ( 6) hydrogen bonds : bond 0.23492 ( 2056) hydrogen bonds : angle 7.63812 ( 6087) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1871 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 877 poor density : 994 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.4626 (tp) REVERT: A 812 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5738 (mt) REVERT: A 816 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6134 (mttt) REVERT: A 929 ILE cc_start: 0.2074 (OUTLIER) cc_final: 0.1704 (mm) REVERT: A 976 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: A 989 PHE cc_start: 0.8048 (m-80) cc_final: 0.7835 (m-80) REVERT: A 993 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7767 (mmtt) REVERT: A 1037 LEU cc_start: 0.8215 (tp) cc_final: 0.8005 (tp) REVERT: A 1112 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7659 (tp-100) REVERT: A 1155 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8099 (tt) REVERT: A 1203 LEU cc_start: 0.9293 (tp) cc_final: 0.8990 (tt) REVERT: A 1215 TRP cc_start: 0.7820 (OUTLIER) cc_final: 0.7469 (m-90) REVERT: A 1334 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8777 (tppt) REVERT: A 2033 PHE cc_start: 0.8365 (t80) cc_final: 0.8031 (t80) REVERT: A 2046 PHE cc_start: 0.7426 (m-80) cc_final: 0.6996 (m-80) REVERT: A 2064 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7746 (mm110) REVERT: A 2200 VAL cc_start: 0.3694 (OUTLIER) cc_final: 0.3314 (m) REVERT: A 2486 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8653 (tt) REVERT: A 2492 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7164 (tt0) REVERT: A 2496 GLU cc_start: 0.8732 (tt0) cc_final: 0.8362 (tt0) REVERT: A 2503 LEU cc_start: 0.9212 (tp) cc_final: 0.8654 (tt) REVERT: B 639 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.4479 (tp) REVERT: B 812 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5728 (mt) REVERT: B 816 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6243 (mttt) REVERT: B 929 ILE cc_start: 0.2124 (OUTLIER) cc_final: 0.1837 (mm) REVERT: B 976 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: B 993 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7806 (mmtt) REVERT: B 1034 ILE cc_start: 0.8856 (mt) cc_final: 0.8622 (mm) REVERT: B 1112 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7606 (tp-100) REVERT: B 1155 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 1203 LEU cc_start: 0.9302 (tp) cc_final: 0.9031 (tt) REVERT: B 1215 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7730 (m-90) REVERT: B 1317 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 1334 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8700 (tppt) REVERT: B 1342 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8855 (tp) REVERT: B 1951 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6692 (m170) REVERT: B 2015 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6784 (mtt) REVERT: B 2033 PHE cc_start: 0.8396 (t80) cc_final: 0.8040 (t80) REVERT: B 2046 PHE cc_start: 0.7487 (m-80) cc_final: 0.6988 (m-80) REVERT: B 2200 VAL cc_start: 0.3825 (OUTLIER) cc_final: 0.3603 (m) REVERT: B 2486 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8663 (tt) REVERT: B 2496 GLU cc_start: 0.8702 (tt0) cc_final: 0.8365 (tt0) REVERT: C 639 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.4825 (tp) REVERT: C 812 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5813 (mt) REVERT: C 816 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6471 (mttt) REVERT: C 869 LYS cc_start: 0.6224 (mttt) cc_final: 0.5888 (mttt) REVERT: C 976 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: C 989 PHE cc_start: 0.8029 (m-80) cc_final: 0.7797 (m-80) REVERT: C 993 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7783 (mmtt) REVERT: C 996 LEU cc_start: 0.8682 (mt) cc_final: 0.8428 (mp) REVERT: C 1112 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7520 (tp-100) REVERT: C 1155 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 1317 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8537 (m) REVERT: C 1334 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8777 (tppt) REVERT: C 1354 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: C 2033 PHE cc_start: 0.8420 (t80) cc_final: 0.8102 (t80) REVERT: C 2046 PHE cc_start: 0.7366 (m-80) cc_final: 0.6886 (m-80) REVERT: C 2064 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7604 (mm-40) REVERT: C 2123 ASP cc_start: 0.8837 (m-30) cc_final: 0.8561 (m-30) outliers start: 877 outliers final: 116 residues processed: 1577 average time/residue: 0.1806 time to fit residues: 442.3459 Evaluate side-chains 684 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 528 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1222 ASN Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1652 ARG Chi-restraints excluded: chain A residue 1669 GLN Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2064 GLN Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2116 VAL Chi-restraints excluded: chain A residue 2161 GLN Chi-restraints excluded: chain A residue 2170 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2203 VAL Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 843 PHE Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 920 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1112 GLN Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1317 THR Chi-restraints excluded: chain B residue 1334 LYS Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1346 SER Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1650 LEU Chi-restraints excluded: chain B residue 1652 ARG Chi-restraints excluded: chain B residue 1669 GLN Chi-restraints excluded: chain B residue 1682 CYS Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1949 ILE Chi-restraints excluded: chain B residue 1951 HIS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 2015 MET Chi-restraints excluded: chain B residue 2028 LEU Chi-restraints excluded: chain B residue 2062 VAL Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2122 MET Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2200 VAL Chi-restraints excluded: chain B residue 2203 VAL Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2443 LEU Chi-restraints excluded: chain B residue 2467 MET Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 822 THR Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 ARG Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1112 GLN Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1184 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1334 LYS Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1650 LEU Chi-restraints excluded: chain C residue 1652 ARG Chi-restraints excluded: chain C residue 1669 GLN Chi-restraints excluded: chain C residue 1682 CYS Chi-restraints excluded: chain C residue 1802 CYS Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 2028 LEU Chi-restraints excluded: chain C residue 2062 VAL Chi-restraints excluded: chain C residue 2064 GLN Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2203 VAL Chi-restraints excluded: chain C residue 2231 SER Chi-restraints excluded: chain C residue 2443 LEU Chi-restraints excluded: chain C residue 2504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 HIS A 956 HIS A 977 GLN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1561 HIS ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2064 GLN A2250 GLN ** A2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2369 ASN B 955 GLN B 956 HIS B 977 GLN ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1414 HIS B1561 HIS B1951 HIS ** B2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2369 ASN C 699 HIS C 873 GLN C 955 GLN C 956 HIS C 977 GLN ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1222 ASN C1414 HIS C1561 HIS C1951 HIS C2064 GLN ** C2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2369 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.094843 restraints weight = 120094.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097497 restraints weight = 48491.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.099028 restraints weight = 28925.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.099900 restraints weight = 21755.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.100329 restraints weight = 18714.992| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32181 Z= 0.187 Angle : 0.800 10.736 43607 Z= 0.400 Chirality : 0.045 0.241 4983 Planarity : 0.006 0.099 5303 Dihedral : 14.557 165.528 4651 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 8.39 % Allowed : 23.61 % Favored : 68.00 % 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: -0.40 (0.13), residues: 3747 helix: 0.51 (0.10), residues: 2688 sheet: -1.13 (0.30), residues: 249 loop : -2.40 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 948 TYR 0.045 0.002 TYR C 604 PHE 0.025 0.002 PHE B1194 TRP 0.022 0.002 TRP C2136 HIS 0.009 0.001 HIS C 956 Details of bonding type rmsd covalent geometry : bond 0.00396 (32178) covalent geometry : angle 0.80040 (43601) SS BOND : bond 0.00108 ( 3) SS BOND : angle 0.52938 ( 6) hydrogen bonds : bond 0.06788 ( 2056) hydrogen bonds : angle 4.93481 ( 6087) *********************** 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 845 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 565 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4761 (tmm) REVERT: A 808 ARG cc_start: 0.8226 (tpt170) cc_final: 0.8023 (ttt180) REVERT: A 869 LYS cc_start: 0.6479 (mttt) cc_final: 0.5923 (mttt) REVERT: A 871 LEU cc_start: 0.7214 (tt) cc_final: 0.6976 (tp) REVERT: A 936 LEU cc_start: 0.8363 (tp) cc_final: 0.7855 (mp) REVERT: A 993 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7725 (mmtt) REVERT: A 1037 LEU cc_start: 0.8331 (tp) cc_final: 0.7921 (tp) REVERT: A 1052 GLN cc_start: 0.7215 (mt0) cc_final: 0.6959 (tp40) REVERT: A 1112 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8275 (tp-100) REVERT: A 1354 MET cc_start: 0.8349 (ttm) cc_final: 0.7822 (ttm) REVERT: A 1539 MET cc_start: 0.8990 (mtt) cc_final: 0.8691 (mtm) REVERT: A 1541 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: A 2033 PHE cc_start: 0.8522 (t80) cc_final: 0.8220 (t80) REVERT: A 2045 MET cc_start: 0.7428 (tmm) cc_final: 0.7189 (tmm) REVERT: A 2288 MET cc_start: 0.7032 (ptm) cc_final: 0.6654 (ptm) REVERT: A 2459 PHE cc_start: 0.8172 (m-80) cc_final: 0.7846 (m-10) REVERT: A 2469 GLU cc_start: 0.7617 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 2503 LEU cc_start: 0.9310 (tp) cc_final: 0.8592 (tt) REVERT: B 597 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6174 (mt) REVERT: B 833 MET cc_start: 0.7133 (mtp) cc_final: 0.6923 (mtp) REVERT: B 869 LYS cc_start: 0.5913 (mmtp) cc_final: 0.5442 (mmtp) REVERT: B 936 LEU cc_start: 0.8275 (tp) cc_final: 0.7899 (mp) REVERT: B 993 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7627 (mmtt) REVERT: B 1011 MET cc_start: 0.8304 (mmt) cc_final: 0.8086 (mmm) REVERT: B 1037 LEU cc_start: 0.8194 (tp) cc_final: 0.7668 (tp) REVERT: B 1052 GLN cc_start: 0.7266 (mt0) cc_final: 0.7043 (tp40) REVERT: B 1197 LEU cc_start: 0.9540 (tp) cc_final: 0.9328 (tp) REVERT: B 1674 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7642 (ptp90) REVERT: B 1786 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: B 2033 PHE cc_start: 0.8556 (t80) cc_final: 0.8121 (t80) REVERT: B 2045 MET cc_start: 0.7502 (tmm) cc_final: 0.7151 (tmm) REVERT: B 2046 PHE cc_start: 0.7524 (m-80) cc_final: 0.6601 (m-80) REVERT: B 2170 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8323 (mm) REVERT: B 2469 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7202 (tm-30) REVERT: B 2486 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8781 (tt) REVERT: B 2503 LEU cc_start: 0.9339 (tp) cc_final: 0.8636 (tt) REVERT: B 2504 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9433 (tp) REVERT: C 706 MET cc_start: 0.5900 (tpt) cc_final: 0.5661 (tpp) REVERT: C 833 MET cc_start: 0.7187 (mtp) cc_final: 0.6852 (mtp) REVERT: C 936 LEU cc_start: 0.8363 (tp) cc_final: 0.7922 (mp) REVERT: C 989 PHE cc_start: 0.8566 (m-80) cc_final: 0.8117 (m-80) REVERT: C 993 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7899 (mmmt) REVERT: C 1037 LEU cc_start: 0.8155 (tp) cc_final: 0.7653 (tp) REVERT: C 1197 LEU cc_start: 0.9592 (tp) cc_final: 0.9364 (tp) REVERT: C 1354 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7793 (ttm) REVERT: C 1786 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: C 2033 PHE cc_start: 0.8548 (t80) cc_final: 0.8128 (t80) REVERT: C 2045 MET cc_start: 0.7611 (tmm) cc_final: 0.7241 (tmm) REVERT: C 2046 PHE cc_start: 0.7525 (m-80) cc_final: 0.6560 (m-80) REVERT: C 2122 MET cc_start: 0.8817 (mmm) cc_final: 0.8528 (mmm) REVERT: C 2137 MET cc_start: 0.8218 (mtm) cc_final: 0.7799 (mtm) REVERT: C 2170 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8318 (mm) REVERT: C 2469 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 2503 LEU cc_start: 0.9340 (tp) cc_final: 0.8620 (tt) REVERT: C 2504 ILE cc_start: 0.9625 (OUTLIER) cc_final: 0.9404 (tp) outliers start: 280 outliers final: 140 residues processed: 789 average time/residue: 0.1951 time to fit residues: 248.4203 Evaluate side-chains 608 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 453 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1310 VAL Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1541 ASP Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1958 THR Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2069 VAL Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2200 VAL Chi-restraints excluded: chain A residue 2401 LEU Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1113 TRP Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1228 SER Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1357 ILE Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1532 PHE Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1652 ARG Chi-restraints excluded: chain B residue 1669 GLN Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1786 ASP Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2069 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2401 LEU Chi-restraints excluded: chain B residue 2443 LEU Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1228 SER Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1310 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1423 SER Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1532 PHE Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1669 GLN Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1802 CYS Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1958 THR Chi-restraints excluded: chain C residue 2004 PHE Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2401 LEU Chi-restraints excluded: chain C residue 2443 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2504 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 346 optimal weight: 2.9990 chunk 339 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 374 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 973 GLN ** A1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 GLN A2011 GLN A2321 ASN A2375 GLN ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1567 GLN B2011 GLN B2228 GLN ** B2321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2375 GLN C 973 GLN C1012 ASN C1052 GLN ** C1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1567 GLN C2011 GLN C2228 GLN C2321 ASN C2375 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.125465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087153 restraints weight = 122322.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.089550 restraints weight = 53330.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.090970 restraints weight = 33633.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.091759 restraints weight = 26055.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092116 restraints weight = 22794.677| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32181 Z= 0.169 Angle : 0.712 12.724 43607 Z= 0.350 Chirality : 0.042 0.299 4983 Planarity : 0.005 0.053 5303 Dihedral : 11.435 156.507 4459 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 6.59 % Allowed : 25.46 % Favored : 67.94 % 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: 0.60 (0.14), residues: 3747 helix: 1.26 (0.10), residues: 2676 sheet: -1.03 (0.29), residues: 252 loop : -1.95 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1652 TYR 0.051 0.002 TYR C 604 PHE 0.038 0.002 PHE C1194 TRP 0.027 0.002 TRP B 841 HIS 0.008 0.001 HIS B1951 Details of bonding type rmsd covalent geometry : bond 0.00367 (32178) covalent geometry : angle 0.71189 (43601) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.26677 ( 6) hydrogen bonds : bond 0.05658 ( 2056) hydrogen bonds : angle 4.58932 ( 6087) *********************** 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 709 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 489 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ARG cc_start: 0.8379 (tpt170) cc_final: 0.7902 (ttt180) REVERT: A 936 LEU cc_start: 0.8370 (tp) cc_final: 0.8024 (mp) REVERT: A 942 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 993 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7797 (mmmt) REVERT: A 1112 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (tp-100) REVERT: A 1157 MET cc_start: 0.8209 (mtm) cc_final: 0.7620 (tpt) REVERT: A 1196 LEU cc_start: 0.9586 (tp) cc_final: 0.9338 (tp) REVERT: A 1215 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7518 (m-90) REVERT: A 1231 MET cc_start: 0.8387 (mmt) cc_final: 0.8162 (mmp) REVERT: A 1355 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 1546 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8899 (tp30) REVERT: A 1719 MET cc_start: 0.8610 (mtm) cc_final: 0.8348 (mtm) REVERT: A 2033 PHE cc_start: 0.8675 (t80) cc_final: 0.8367 (t80) REVERT: A 2045 MET cc_start: 0.7758 (tmm) cc_final: 0.7392 (tmm) REVERT: A 2115 LEU cc_start: 0.9442 (mt) cc_final: 0.9192 (tt) REVERT: A 2459 PHE cc_start: 0.7959 (m-80) cc_final: 0.7443 (m-10) REVERT: A 2469 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 2496 GLU cc_start: 0.8714 (tt0) cc_final: 0.8495 (tt0) REVERT: A 2503 LEU cc_start: 0.9266 (tp) cc_final: 0.8512 (tt) REVERT: A 2504 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9337 (tp) REVERT: B 597 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6108 (mt) REVERT: B 936 LEU cc_start: 0.8376 (tp) cc_final: 0.8063 (mt) REVERT: B 993 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7671 (mmtt) REVERT: B 1037 LEU cc_start: 0.8234 (tp) cc_final: 0.7762 (tp) REVERT: B 1197 LEU cc_start: 0.9602 (tp) cc_final: 0.9342 (tp) REVERT: B 1215 TRP cc_start: 0.8226 (OUTLIER) cc_final: 0.7366 (m-90) REVERT: B 1341 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8489 (mtt180) REVERT: B 1355 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8761 (tm-30) REVERT: B 1546 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8894 (tp30) REVERT: B 1731 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8260 (mpp) REVERT: B 1974 ILE cc_start: 0.8956 (mm) cc_final: 0.8572 (tt) REVERT: B 2033 PHE cc_start: 0.8686 (t80) cc_final: 0.8421 (t80) REVERT: B 2044 TRP cc_start: 0.8163 (t-100) cc_final: 0.7916 (t-100) REVERT: B 2123 ASP cc_start: 0.9271 (m-30) cc_final: 0.9068 (m-30) REVERT: B 2288 MET cc_start: 0.6695 (ptm) cc_final: 0.6421 (ptm) REVERT: B 2469 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7035 (tm-30) REVERT: B 2486 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 2503 LEU cc_start: 0.9295 (tp) cc_final: 0.9033 (tp) REVERT: B 2504 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9463 (tp) REVERT: C 808 ARG cc_start: 0.8450 (tpt170) cc_final: 0.7963 (ttt180) REVERT: C 833 MET cc_start: 0.7399 (mtp) cc_final: 0.7104 (mtp) REVERT: C 839 VAL cc_start: 0.8651 (t) cc_final: 0.8450 (t) REVERT: C 936 LEU cc_start: 0.8475 (tp) cc_final: 0.8160 (mp) REVERT: C 993 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7762 (mmtt) REVERT: C 1197 LEU cc_start: 0.9606 (tp) cc_final: 0.9377 (tp) REVERT: C 1215 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.7213 (m-90) REVERT: C 1546 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8999 (tp30) REVERT: C 1547 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8499 (mtm110) REVERT: C 1954 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6740 (p90) REVERT: C 1974 ILE cc_start: 0.9010 (mm) cc_final: 0.8650 (tt) REVERT: C 2033 PHE cc_start: 0.8680 (t80) cc_final: 0.8395 (t80) REVERT: C 2045 MET cc_start: 0.7767 (tmm) cc_final: 0.7505 (tmm) REVERT: C 2046 PHE cc_start: 0.7914 (m-80) cc_final: 0.7607 (m-80) REVERT: C 2122 MET cc_start: 0.8937 (mmm) cc_final: 0.8602 (mmm) REVERT: C 2137 MET cc_start: 0.8487 (mtm) cc_final: 0.8031 (mtm) REVERT: C 2288 MET cc_start: 0.6487 (ptm) cc_final: 0.5760 (tmm) REVERT: C 2290 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7818 (tpt90) REVERT: C 2361 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8277 (ttp80) REVERT: C 2469 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 2503 LEU cc_start: 0.9313 (tp) cc_final: 0.8607 (tt) REVERT: C 2504 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9447 (tp) outliers start: 220 outliers final: 127 residues processed: 647 average time/residue: 0.1623 time to fit residues: 173.9673 Evaluate side-chains 563 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 420 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1310 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2184 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2219 TYR Chi-restraints excluded: chain A residue 2443 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1649 LEU Chi-restraints excluded: chain B residue 1652 ARG Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1731 MET Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1802 CYS Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2184 ILE Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2504 ILE Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 584 CYS Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1310 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1547 ARG Chi-restraints excluded: chain C residue 1649 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1724 ARG Chi-restraints excluded: chain C residue 1746 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1955 ARG Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE 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 144 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 221 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A1012 ASN B 925 ASN B1012 ASN B1414 HIS B2321 ASN C1112 GLN C1230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.124882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086504 restraints weight = 120615.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088892 restraints weight = 52643.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.090268 restraints weight = 33227.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091081 restraints weight = 25859.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.091446 restraints weight = 22547.191| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32181 Z= 0.146 Angle : 0.669 13.144 43607 Z= 0.324 Chirality : 0.041 0.280 4983 Planarity : 0.004 0.046 5303 Dihedral : 10.340 146.209 4403 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 5.66 % Allowed : 26.00 % Favored : 68.33 % 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: 1.03 (0.14), residues: 3747 helix: 1.57 (0.10), residues: 2688 sheet: -1.10 (0.29), residues: 255 loop : -1.72 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 953 TYR 0.027 0.001 TYR C 604 PHE 0.027 0.001 PHE C1194 TRP 0.019 0.001 TRP A2188 HIS 0.008 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00318 (32178) covalent geometry : angle 0.66893 (43601) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.17855 ( 6) hydrogen bonds : bond 0.04951 ( 2056) hydrogen bonds : angle 4.35103 ( 6087) *********************** 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 642 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 453 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ARG cc_start: 0.8406 (tpt170) cc_final: 0.7794 (ttt180) REVERT: A 936 LEU cc_start: 0.8439 (tp) cc_final: 0.8089 (mp) REVERT: A 993 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7623 (mmtt) REVERT: A 1112 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8068 (tp-100) REVERT: A 1231 MET cc_start: 0.8407 (mmt) cc_final: 0.8200 (mmp) REVERT: A 1355 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8731 (tm-30) REVERT: A 2033 PHE cc_start: 0.8719 (t80) cc_final: 0.8400 (t80) REVERT: A 2045 MET cc_start: 0.7805 (tmm) cc_final: 0.7363 (tmm) REVERT: A 2097 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8632 (mtmm) REVERT: A 2115 LEU cc_start: 0.9422 (mt) cc_final: 0.9147 (tt) REVERT: A 2288 MET cc_start: 0.6777 (ptm) cc_final: 0.6521 (ptm) REVERT: A 2469 GLU cc_start: 0.7950 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 2486 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 2503 LEU cc_start: 0.9215 (tp) cc_final: 0.8485 (tt) REVERT: A 2504 ILE cc_start: 0.9639 (OUTLIER) cc_final: 0.9310 (tp) REVERT: B 597 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6135 (mt) REVERT: B 993 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7665 (mmtt) REVERT: B 1037 LEU cc_start: 0.8259 (tp) cc_final: 0.7844 (tp) REVERT: B 1196 LEU cc_start: 0.9588 (tp) cc_final: 0.9240 (tp) REVERT: B 1197 LEU cc_start: 0.9584 (tp) cc_final: 0.9268 (tp) REVERT: B 1215 TRP cc_start: 0.8156 (OUTLIER) cc_final: 0.7270 (m-90) REVERT: B 1355 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8708 (tm-30) REVERT: B 1974 ILE cc_start: 0.8942 (mm) cc_final: 0.8623 (tt) REVERT: B 2033 PHE cc_start: 0.8722 (t80) cc_final: 0.8446 (t80) REVERT: B 2044 TRP cc_start: 0.8186 (t-100) cc_final: 0.7870 (t-100) REVERT: B 2288 MET cc_start: 0.6696 (ptm) cc_final: 0.6391 (ptm) REVERT: B 2469 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7257 (tm-30) REVERT: B 2486 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8747 (tt) REVERT: B 2503 LEU cc_start: 0.9259 (tp) cc_final: 0.8567 (tt) REVERT: C 808 ARG cc_start: 0.8380 (tpt170) cc_final: 0.7861 (ttt180) REVERT: C 833 MET cc_start: 0.7569 (mtp) cc_final: 0.7332 (mtp) REVERT: C 866 ILE cc_start: 0.6551 (mm) cc_final: 0.6099 (mt) REVERT: C 993 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7759 (mmtt) REVERT: C 1197 LEU cc_start: 0.9609 (tp) cc_final: 0.9325 (tp) REVERT: C 1215 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7301 (m-90) REVERT: C 1546 GLU cc_start: 0.9245 (mm-30) cc_final: 0.9039 (tp30) REVERT: C 1954 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6852 (p90) REVERT: C 1974 ILE cc_start: 0.8959 (mm) cc_final: 0.8632 (tt) REVERT: C 2033 PHE cc_start: 0.8692 (t80) cc_final: 0.8164 (t80) REVERT: C 2290 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7823 (tpt90) REVERT: C 2469 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 2503 LEU cc_start: 0.9283 (tp) cc_final: 0.8968 (tp) REVERT: C 2504 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9432 (tp) outliers start: 189 outliers final: 128 residues processed: 585 average time/residue: 0.1692 time to fit residues: 165.4120 Evaluate side-chains 543 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 403 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1310 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1791 MET Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1975 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2401 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2504 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1568 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1791 MET Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2401 LEU Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 838 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 942 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1310 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1649 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1746 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1969 VAL Chi-restraints excluded: chain C residue 1975 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2401 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2504 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 364 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN B1789 GLN ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1230 ASN C1414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.121617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.085712 restraints weight = 121982.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086772 restraints weight = 62076.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086586 restraints weight = 40251.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.086859 restraints weight = 42785.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087090 restraints weight = 35793.393| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32181 Z= 0.280 Angle : 0.799 11.062 43607 Z= 0.400 Chirality : 0.047 0.365 4983 Planarity : 0.005 0.052 5303 Dihedral : 9.849 130.541 4385 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 7.22 % Allowed : 25.94 % Favored : 66.84 % 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: 0.89 (0.14), residues: 3747 helix: 1.43 (0.10), residues: 2667 sheet: -1.21 (0.29), residues: 249 loop : -1.49 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1527 TYR 0.026 0.002 TYR B1418 PHE 0.031 0.002 PHE B1194 TRP 0.022 0.002 TRP C2124 HIS 0.009 0.002 HIS B1309 Details of bonding type rmsd covalent geometry : bond 0.00613 (32178) covalent geometry : angle 0.79934 (43601) SS BOND : bond 0.00046 ( 3) SS BOND : angle 0.06617 ( 6) hydrogen bonds : bond 0.05852 ( 2056) hydrogen bonds : angle 4.86944 ( 6087) *********************** 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 658 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 417 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4848 (tmm) REVERT: A 699 HIS cc_start: 0.5256 (OUTLIER) cc_final: 0.4715 (m-70) REVERT: A 839 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8227 (t) REVERT: A 936 LEU cc_start: 0.8664 (tp) cc_final: 0.8174 (mp) REVERT: A 947 ARG cc_start: 0.8106 (mmt90) cc_final: 0.7795 (mmm-85) REVERT: A 993 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7735 (mmtt) REVERT: A 1112 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8257 (tp-100) REVERT: A 1215 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.7792 (m-90) REVERT: A 1731 MET cc_start: 0.8806 (tpp) cc_final: 0.8367 (mmp) REVERT: A 2033 PHE cc_start: 0.8694 (t80) cc_final: 0.8463 (t80) REVERT: A 2045 MET cc_start: 0.8020 (tmm) cc_final: 0.7708 (tmm) REVERT: A 2115 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9165 (tt) REVERT: A 2288 MET cc_start: 0.6554 (ptm) cc_final: 0.6291 (ptm) REVERT: A 2469 GLU cc_start: 0.7913 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 2496 GLU cc_start: 0.8872 (tt0) cc_final: 0.8660 (tt0) REVERT: B 597 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5787 (tt) REVERT: B 993 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7848 (mmtt) REVERT: B 1197 LEU cc_start: 0.9563 (tp) cc_final: 0.9358 (tp) REVERT: B 1215 TRP cc_start: 0.8597 (OUTLIER) cc_final: 0.7333 (m-90) REVERT: B 1731 MET cc_start: 0.8647 (mpp) cc_final: 0.8312 (mmp) REVERT: B 1954 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6912 (p90) REVERT: B 2288 MET cc_start: 0.6763 (ptm) cc_final: 0.6472 (ptm) REVERT: B 2290 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7771 (tpt90) REVERT: B 2469 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7016 (tm-30) REVERT: B 2486 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 833 MET cc_start: 0.7883 (mtp) cc_final: 0.7641 (mtp) REVERT: C 843 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: C 853 MET cc_start: 0.5020 (pmm) cc_final: 0.4704 (pmm) REVERT: C 866 ILE cc_start: 0.6559 (mm) cc_final: 0.6187 (mt) REVERT: C 993 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7872 (mmtt) REVERT: C 1007 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7749 (tp) REVERT: C 1197 LEU cc_start: 0.9556 (tp) cc_final: 0.9348 (tp) REVERT: C 1215 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.7594 (m-90) REVERT: C 1355 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8669 (tm-30) REVERT: C 1954 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7126 (p90) REVERT: C 2045 MET cc_start: 0.7810 (tmm) cc_final: 0.7563 (tmm) REVERT: C 2178 LEU cc_start: 0.9308 (mm) cc_final: 0.8847 (tt) REVERT: C 2290 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7780 (tpt90) REVERT: C 2469 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7247 (tm-30) outliers start: 241 outliers final: 165 residues processed: 584 average time/residue: 0.1809 time to fit residues: 176.5559 Evaluate side-chains 564 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 382 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1296 LEU Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2401 LEU Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1357 ILE Chi-restraints excluded: chain B residue 1412 VAL Chi-restraints excluded: chain B residue 1423 SER Chi-restraints excluded: chain B residue 1649 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1739 ILE Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1786 ASP Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 1970 VAL Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2062 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2184 ILE Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2219 TYR Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2401 LEU Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 843 PHE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1176 VAL Chi-restraints excluded: chain C residue 1184 ILE Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1714 VAL Chi-restraints excluded: chain C residue 1739 ILE Chi-restraints excluded: chain C residue 1746 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1790 LEU Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1969 VAL Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2062 VAL Chi-restraints excluded: chain C residue 2069 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2401 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 376 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 331 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 357 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN ** A2092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 GLN B 932 HIS B1789 GLN C 873 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.124721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087756 restraints weight = 120856.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090130 restraints weight = 52121.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091496 restraints weight = 32508.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.092331 restraints weight = 25044.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.092695 restraints weight = 21695.593| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.7346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32181 Z= 0.133 Angle : 0.667 11.606 43607 Z= 0.320 Chirality : 0.042 0.430 4983 Planarity : 0.004 0.052 5303 Dihedral : 9.296 122.928 4378 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.94 % Allowed : 28.82 % Favored : 66.24 % 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: 1.37 (0.14), residues: 3747 helix: 1.80 (0.10), residues: 2676 sheet: -1.17 (0.29), residues: 249 loop : -1.41 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1323 TYR 0.027 0.001 TYR C 604 PHE 0.021 0.001 PHE C 989 TRP 0.027 0.001 TRP C 841 HIS 0.004 0.001 HIS B1951 Details of bonding type rmsd covalent geometry : bond 0.00282 (32178) covalent geometry : angle 0.66748 (43601) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.15718 ( 6) hydrogen bonds : bond 0.04682 ( 2056) hydrogen bonds : angle 4.25962 ( 6087) *********************** 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 627 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 462 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 TYR cc_start: 0.7843 (m-80) cc_final: 0.7601 (m-80) REVERT: A 638 MET cc_start: 0.5071 (OUTLIER) cc_final: 0.4758 (tmm) REVERT: A 699 HIS cc_start: 0.5315 (OUTLIER) cc_final: 0.4648 (m-70) REVERT: A 936 LEU cc_start: 0.8526 (tp) cc_final: 0.8190 (mp) REVERT: A 947 ARG cc_start: 0.8220 (mmt90) cc_final: 0.8000 (mmm-85) REVERT: A 993 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7372 (mmtt) REVERT: A 1112 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8045 (tp-100) REVERT: A 1215 TRP cc_start: 0.8110 (OUTLIER) cc_final: 0.7800 (m-90) REVERT: A 1731 MET cc_start: 0.8684 (tpp) cc_final: 0.8293 (mmp) REVERT: A 1738 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8076 (tt0) REVERT: A 2043 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 2115 LEU cc_start: 0.9403 (mt) cc_final: 0.9157 (tt) REVERT: A 2178 LEU cc_start: 0.9208 (mm) cc_final: 0.8862 (tt) REVERT: A 2288 MET cc_start: 0.6588 (ptm) cc_final: 0.6308 (ptm) REVERT: A 2469 GLU cc_start: 0.7841 (tm-30) cc_final: 0.6574 (tm-30) REVERT: A 2470 GLU cc_start: 0.8778 (tp30) cc_final: 0.8243 (tp30) REVERT: B 597 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.5839 (tt) REVERT: B 833 MET cc_start: 0.7695 (mtt) cc_final: 0.7248 (mmm) REVERT: B 931 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7600 (p0) REVERT: B 936 LEU cc_start: 0.8545 (tp) cc_final: 0.8238 (mp) REVERT: B 993 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7692 (mmtt) REVERT: B 1196 LEU cc_start: 0.9634 (tp) cc_final: 0.9355 (tp) REVERT: B 1197 LEU cc_start: 0.9568 (tp) cc_final: 0.9345 (tp) REVERT: B 1215 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.7280 (m-90) REVERT: B 1547 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8360 (mtm110) REVERT: B 1731 MET cc_start: 0.8576 (mpp) cc_final: 0.8218 (mmp) REVERT: B 1954 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6549 (p90) REVERT: B 2033 PHE cc_start: 0.8580 (t80) cc_final: 0.8306 (t80) REVERT: B 2043 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8838 (mt) REVERT: B 2178 LEU cc_start: 0.9272 (mm) cc_final: 0.8893 (tp) REVERT: B 2288 MET cc_start: 0.6744 (ptm) cc_final: 0.6421 (ptm) REVERT: B 2469 GLU cc_start: 0.7727 (tm-30) cc_final: 0.6823 (tm-30) REVERT: B 2486 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 2503 LEU cc_start: 0.9246 (tp) cc_final: 0.8545 (tt) REVERT: C 833 MET cc_start: 0.7702 (mtp) cc_final: 0.7351 (mmm) REVERT: C 866 ILE cc_start: 0.6845 (mm) cc_final: 0.6450 (mt) REVERT: C 989 PHE cc_start: 0.8599 (m-80) cc_final: 0.8339 (m-80) REVERT: C 993 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7676 (mmtt) REVERT: C 1007 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7675 (mp) REVERT: C 1197 LEU cc_start: 0.9564 (tp) cc_final: 0.9318 (tp) REVERT: C 1215 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7604 (m-90) REVERT: C 1954 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6646 (p90) REVERT: C 2033 PHE cc_start: 0.8509 (t80) cc_final: 0.8258 (t80) REVERT: C 2043 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 2178 LEU cc_start: 0.9281 (mm) cc_final: 0.8924 (tt) REVERT: C 2290 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7898 (ttp80) REVERT: C 2361 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8201 (ptm-80) REVERT: C 2469 GLU cc_start: 0.7855 (tm-30) cc_final: 0.6901 (tm-30) REVERT: C 2470 GLU cc_start: 0.8780 (tp30) cc_final: 0.8513 (tp30) REVERT: C 2503 LEU cc_start: 0.9271 (tp) cc_final: 0.8590 (tt) outliers start: 165 outliers final: 108 residues processed: 569 average time/residue: 0.1860 time to fit residues: 176.9887 Evaluate side-chains 540 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 413 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 931 ASN Chi-restraints excluded: chain B residue 932 HIS Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1217 CYS Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1286 ILE Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2043 LEU Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1973 ILE Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 82 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 308 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN B 932 HIS ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086318 restraints weight = 122777.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.088643 restraints weight = 53923.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.090031 restraints weight = 33843.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090840 restraints weight = 26171.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091207 restraints weight = 22711.921| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32181 Z= 0.134 Angle : 0.675 11.732 43607 Z= 0.323 Chirality : 0.041 0.292 4983 Planarity : 0.004 0.052 5303 Dihedral : 8.869 115.034 4370 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.85 % Allowed : 28.85 % Favored : 66.30 % 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: 1.43 (0.14), residues: 3747 helix: 1.82 (0.10), residues: 2682 sheet: -1.20 (0.29), residues: 249 loop : -1.25 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1652 TYR 0.027 0.001 TYR B2067 PHE 0.041 0.001 PHE A1194 TRP 0.036 0.001 TRP B 841 HIS 0.018 0.001 HIS B 932 Details of bonding type rmsd covalent geometry : bond 0.00297 (32178) covalent geometry : angle 0.67530 (43601) SS BOND : bond 0.00058 ( 3) SS BOND : angle 0.15044 ( 6) hydrogen bonds : bond 0.04530 ( 2056) hydrogen bonds : angle 4.24609 ( 6087) *********************** 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 595 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 433 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4732 (tmm) REVERT: A 699 HIS cc_start: 0.5404 (OUTLIER) cc_final: 0.4829 (m-70) REVERT: A 936 LEU cc_start: 0.8659 (tp) cc_final: 0.8371 (mp) REVERT: A 993 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7339 (mmtt) REVERT: A 1215 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7866 (m-90) REVERT: A 1731 MET cc_start: 0.8710 (tpp) cc_final: 0.8328 (mmp) REVERT: A 2043 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 2115 LEU cc_start: 0.9406 (mt) cc_final: 0.9129 (tt) REVERT: A 2137 MET cc_start: 0.8389 (mmm) cc_final: 0.8098 (mmm) REVERT: A 2178 LEU cc_start: 0.9242 (mm) cc_final: 0.8895 (tt) REVERT: A 2288 MET cc_start: 0.6600 (ptm) cc_final: 0.6362 (ptm) REVERT: A 2469 GLU cc_start: 0.7904 (tm-30) cc_final: 0.6824 (tm-30) REVERT: A 2503 LEU cc_start: 0.9251 (tp) cc_final: 0.8889 (tp) REVERT: B 597 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5871 (tt) REVERT: B 993 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7622 (mmtt) REVERT: B 1196 LEU cc_start: 0.9621 (tp) cc_final: 0.9335 (tp) REVERT: B 1197 LEU cc_start: 0.9580 (tp) cc_final: 0.9373 (tp) REVERT: B 1215 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7282 (m-90) REVERT: B 1543 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8787 (mm) REVERT: B 1547 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8236 (mtm110) REVERT: B 1731 MET cc_start: 0.8573 (mpp) cc_final: 0.8203 (mmp) REVERT: B 1954 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6592 (p90) REVERT: B 2033 PHE cc_start: 0.8625 (t80) cc_final: 0.8316 (t80) REVERT: B 2043 LEU cc_start: 0.9061 (pp) cc_final: 0.8857 (mt) REVERT: B 2178 LEU cc_start: 0.9295 (mm) cc_final: 0.8945 (tp) REVERT: B 2288 MET cc_start: 0.6730 (ptm) cc_final: 0.6433 (ptm) REVERT: B 2469 GLU cc_start: 0.7761 (tm-30) cc_final: 0.6891 (tm-30) REVERT: B 2486 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8822 (tt) REVERT: B 2503 LEU cc_start: 0.9256 (tp) cc_final: 0.8559 (tt) REVERT: C 833 MET cc_start: 0.7714 (mtp) cc_final: 0.7373 (mmm) REVERT: C 866 ILE cc_start: 0.6811 (mm) cc_final: 0.6398 (mt) REVERT: C 989 PHE cc_start: 0.8616 (m-80) cc_final: 0.8410 (m-80) REVERT: C 993 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7633 (mmtt) REVERT: C 1007 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7787 (pt) REVERT: C 1197 LEU cc_start: 0.9550 (tp) cc_final: 0.9300 (tp) REVERT: C 1215 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7679 (m-90) REVERT: C 1334 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9084 (mmtm) REVERT: C 1954 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6647 (p90) REVERT: C 2033 PHE cc_start: 0.8635 (t80) cc_final: 0.8374 (t80) REVERT: C 2043 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8735 (mt) REVERT: C 2044 TRP cc_start: 0.7959 (t-100) cc_final: 0.7682 (t-100) REVERT: C 2178 LEU cc_start: 0.9307 (mm) cc_final: 0.8952 (tt) REVERT: C 2290 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7864 (ttp80) REVERT: C 2469 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 2503 LEU cc_start: 0.9308 (tp) cc_final: 0.8618 (tt) REVERT: C 2504 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9292 (tp) outliers start: 162 outliers final: 117 residues processed: 539 average time/residue: 0.1904 time to fit residues: 170.6684 Evaluate side-chains 545 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 409 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1543 LEU Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2008 LEU Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1334 LYS Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1790 LEU Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2043 LEU Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2420 MET Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 335 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 358 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 878 ASN A1112 GLN B 878 ASN ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 878 ASN ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.121372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083087 restraints weight = 122122.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.085315 restraints weight = 54765.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.086643 restraints weight = 34867.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087414 restraints weight = 27037.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.087775 restraints weight = 23548.331| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32181 Z= 0.204 Angle : 0.741 13.803 43607 Z= 0.357 Chirality : 0.043 0.243 4983 Planarity : 0.004 0.054 5303 Dihedral : 8.627 101.278 4365 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.33 % Allowed : 29.24 % Favored : 65.43 % 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: 1.41 (0.14), residues: 3747 helix: 1.81 (0.10), residues: 2670 sheet: -1.28 (0.28), residues: 249 loop : -1.22 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1653 TYR 0.024 0.002 TYR A2067 PHE 0.030 0.002 PHE C2033 TRP 0.027 0.002 TRP B 841 HIS 0.007 0.001 HIS B 932 Details of bonding type rmsd covalent geometry : bond 0.00454 (32178) covalent geometry : angle 0.74078 (43601) SS BOND : bond 0.00021 ( 3) SS BOND : angle 0.12320 ( 6) hydrogen bonds : bond 0.04913 ( 2056) hydrogen bonds : angle 4.48779 ( 6087) *********************** 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 596 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 418 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4975 (tmm) REVERT: A 699 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.5022 (m-70) REVERT: A 936 LEU cc_start: 0.8714 (tp) cc_final: 0.8455 (mp) REVERT: A 993 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7408 (mmtt) REVERT: A 1215 TRP cc_start: 0.8342 (OUTLIER) cc_final: 0.7912 (m-90) REVERT: A 1708 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 1731 MET cc_start: 0.8784 (tpp) cc_final: 0.8366 (mmp) REVERT: A 1739 ILE cc_start: 0.9407 (mm) cc_final: 0.8967 (mm) REVERT: A 2043 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8757 (mt) REVERT: A 2045 MET cc_start: 0.8112 (tmm) cc_final: 0.7831 (tmm) REVERT: A 2115 LEU cc_start: 0.9427 (mt) cc_final: 0.9083 (tt) REVERT: A 2178 LEU cc_start: 0.9286 (mm) cc_final: 0.8851 (tp) REVERT: A 2288 MET cc_start: 0.6592 (ptm) cc_final: 0.6318 (ptm) REVERT: A 2469 GLU cc_start: 0.7950 (tm-30) cc_final: 0.6891 (tm-30) REVERT: B 597 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.5863 (tt) REVERT: B 993 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7664 (mmtt) REVERT: B 1197 LEU cc_start: 0.9587 (tp) cc_final: 0.9367 (tp) REVERT: B 1215 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.7345 (m-90) REVERT: B 1543 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8758 (mm) REVERT: B 1547 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8228 (mtm110) REVERT: B 1731 MET cc_start: 0.8618 (mpp) cc_final: 0.8224 (mmp) REVERT: B 1954 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.7105 (p90) REVERT: B 2043 LEU cc_start: 0.9080 (pp) cc_final: 0.8807 (mt) REVERT: B 2178 LEU cc_start: 0.9319 (mm) cc_final: 0.8931 (tp) REVERT: B 2288 MET cc_start: 0.6793 (ptm) cc_final: 0.6493 (ptm) REVERT: B 2469 GLU cc_start: 0.7887 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 2486 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8866 (tt) REVERT: C 833 MET cc_start: 0.7935 (mtp) cc_final: 0.7443 (mmm) REVERT: C 866 ILE cc_start: 0.6762 (mm) cc_final: 0.6309 (mt) REVERT: C 989 PHE cc_start: 0.8663 (m-80) cc_final: 0.8431 (m-80) REVERT: C 993 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7657 (mmtt) REVERT: C 1007 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7794 (tp) REVERT: C 1197 LEU cc_start: 0.9595 (tp) cc_final: 0.9347 (tp) REVERT: C 1215 TRP cc_start: 0.8469 (OUTLIER) cc_final: 0.7825 (m-90) REVERT: C 1334 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9077 (mmtm) REVERT: C 1653 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6808 (tpm170) REVERT: C 1731 MET cc_start: 0.8558 (mpp) cc_final: 0.8303 (mmp) REVERT: C 1954 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6699 (p90) REVERT: C 2043 LEU cc_start: 0.9085 (pp) cc_final: 0.8783 (mt) REVERT: C 2044 TRP cc_start: 0.8143 (t-100) cc_final: 0.7882 (t-100) REVERT: C 2178 LEU cc_start: 0.9353 (mm) cc_final: 0.8996 (tt) REVERT: C 2290 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7803 (tpt90) REVERT: C 2469 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: C 2504 ILE cc_start: 0.9635 (OUTLIER) cc_final: 0.9385 (tp) outliers start: 178 outliers final: 131 residues processed: 537 average time/residue: 0.1894 time to fit residues: 169.1642 Evaluate side-chains 550 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 398 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1952 THR Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1184 ILE Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1289 SER Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1543 LEU Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1696 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1184 ILE Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1334 LYS Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1653 ARG Chi-restraints excluded: chain C residue 1669 GLN Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1790 LEU Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1970 VAL Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2008 LEU Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2420 MET Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 103 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 ASN ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.121263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.083077 restraints weight = 122718.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.085288 restraints weight = 54940.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086633 restraints weight = 35016.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.087371 restraints weight = 27200.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 75)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.087828 restraints weight = 23671.404| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.8060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32181 Z= 0.191 Angle : 0.745 13.241 43607 Z= 0.354 Chirality : 0.043 0.257 4983 Planarity : 0.004 0.055 5303 Dihedral : 8.459 92.905 4365 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.27 % Allowed : 29.09 % Favored : 65.64 % 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: 1.40 (0.14), residues: 3747 helix: 1.80 (0.10), residues: 2682 sheet: -1.29 (0.29), residues: 264 loop : -1.22 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1652 TYR 0.020 0.002 TYR B2067 PHE 0.025 0.002 PHE A2012 TRP 0.026 0.002 TRP B2188 HIS 0.005 0.001 HIS C1309 Details of bonding type rmsd covalent geometry : bond 0.00428 (32178) covalent geometry : angle 0.74465 (43601) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.15768 ( 6) hydrogen bonds : bond 0.04812 ( 2056) hydrogen bonds : angle 4.46021 ( 6087) *********************** 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 584 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 408 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.4888 (tmm) REVERT: A 699 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.5049 (m-70) REVERT: A 833 MET cc_start: 0.7891 (mtp) cc_final: 0.7417 (mmp) REVERT: A 1215 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.7944 (m-90) REVERT: A 1708 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8568 (tp) REVERT: A 1731 MET cc_start: 0.8743 (tpp) cc_final: 0.8331 (mmp) REVERT: A 2043 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8780 (mt) REVERT: A 2045 MET cc_start: 0.8137 (tmm) cc_final: 0.7858 (tmm) REVERT: A 2115 LEU cc_start: 0.9404 (mt) cc_final: 0.9070 (tt) REVERT: A 2178 LEU cc_start: 0.9303 (mm) cc_final: 0.8917 (tp) REVERT: A 2288 MET cc_start: 0.6610 (ptm) cc_final: 0.6335 (ptm) REVERT: A 2469 GLU cc_start: 0.7935 (tm-30) cc_final: 0.6855 (tm-30) REVERT: B 597 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5769 (tt) REVERT: B 827 LEU cc_start: 0.8459 (mt) cc_final: 0.8013 (mt) REVERT: B 936 LEU cc_start: 0.8748 (tp) cc_final: 0.8485 (mp) REVERT: B 993 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7682 (mmtt) REVERT: B 1103 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 1215 TRP cc_start: 0.8390 (OUTLIER) cc_final: 0.7368 (m-90) REVERT: B 1547 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8246 (mtm110) REVERT: B 1731 MET cc_start: 0.8556 (mpp) cc_final: 0.8189 (mmp) REVERT: B 1954 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.7008 (p90) REVERT: B 2043 LEU cc_start: 0.9067 (pp) cc_final: 0.8833 (mt) REVERT: B 2178 LEU cc_start: 0.9324 (mm) cc_final: 0.9065 (tp) REVERT: B 2288 MET cc_start: 0.6782 (ptm) cc_final: 0.6487 (ptm) REVERT: B 2469 GLU cc_start: 0.7847 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 2483 ASP cc_start: 0.8522 (m-30) cc_final: 0.8312 (m-30) REVERT: B 2486 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 833 MET cc_start: 0.7996 (mtp) cc_final: 0.7510 (mmm) REVERT: C 866 ILE cc_start: 0.6701 (mm) cc_final: 0.6211 (mt) REVERT: C 921 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5992 (tptt) REVERT: C 989 PHE cc_start: 0.8676 (m-80) cc_final: 0.8457 (m-80) REVERT: C 993 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7678 (mmtt) REVERT: C 1011 MET cc_start: 0.8799 (tpp) cc_final: 0.8217 (tpp) REVERT: C 1197 LEU cc_start: 0.9605 (tp) cc_final: 0.9388 (tp) REVERT: C 1215 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7832 (m-90) REVERT: C 1334 LYS cc_start: 0.9561 (OUTLIER) cc_final: 0.9089 (mmtm) REVERT: C 1731 MET cc_start: 0.8508 (mpp) cc_final: 0.8270 (mmp) REVERT: C 1954 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6715 (p90) REVERT: C 2043 LEU cc_start: 0.9031 (pp) cc_final: 0.8760 (mt) REVERT: C 2044 TRP cc_start: 0.8112 (t-100) cc_final: 0.7901 (t-100) REVERT: C 2178 LEU cc_start: 0.9344 (mm) cc_final: 0.9013 (tt) REVERT: C 2194 MET cc_start: 0.8733 (ttm) cc_final: 0.8114 (tmm) REVERT: C 2290 ARG cc_start: 0.8445 (mtt180) cc_final: 0.7802 (tpt90) REVERT: C 2469 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: C 2504 ILE cc_start: 0.9619 (OUTLIER) cc_final: 0.9390 (tp) outliers start: 176 outliers final: 139 residues processed: 529 average time/residue: 0.1886 time to fit residues: 166.5842 Evaluate side-chains 547 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 389 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1211 ARG Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1289 SER Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1301 VAL Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ILE Chi-restraints excluded: chain C residue 1286 ILE Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1334 LYS Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1669 GLN Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1790 LEU Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1970 VAL Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2008 LEU Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2219 TYR Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2420 MET Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 253 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 361 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A1205 GLN ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.121397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.084118 restraints weight = 122319.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.086698 restraints weight = 58460.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.087205 restraints weight = 34945.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.087485 restraints weight = 27349.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.087640 restraints weight = 28131.070| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32181 Z= 0.172 Angle : 0.746 12.722 43607 Z= 0.350 Chirality : 0.043 0.321 4983 Planarity : 0.004 0.056 5303 Dihedral : 8.266 92.713 4363 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.97 % Allowed : 29.21 % Favored : 65.82 % 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: 1.47 (0.14), residues: 3747 helix: 1.82 (0.10), residues: 2691 sheet: -1.34 (0.28), residues: 264 loop : -1.11 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1652 TYR 0.014 0.001 TYR A1961 PHE 0.034 0.002 PHE C 588 TRP 0.028 0.002 TRP C2188 HIS 0.004 0.001 HIS B1309 Details of bonding type rmsd covalent geometry : bond 0.00386 (32178) covalent geometry : angle 0.74619 (43601) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.16956 ( 6) hydrogen bonds : bond 0.04697 ( 2056) hydrogen bonds : angle 4.40092 ( 6087) ********************** 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 575 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 409 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4972 (tmm) REVERT: A 699 HIS cc_start: 0.5467 (OUTLIER) cc_final: 0.5032 (m-70) REVERT: A 833 MET cc_start: 0.7966 (mtp) cc_final: 0.7458 (mmp) REVERT: A 1215 TRP cc_start: 0.8275 (OUTLIER) cc_final: 0.7913 (m-90) REVERT: A 1708 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 1731 MET cc_start: 0.8685 (tpp) cc_final: 0.8283 (mmp) REVERT: A 2043 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8768 (mt) REVERT: A 2044 TRP cc_start: 0.8017 (t-100) cc_final: 0.7355 (t-100) REVERT: A 2115 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9044 (tt) REVERT: A 2178 LEU cc_start: 0.9324 (mm) cc_final: 0.8975 (tt) REVERT: A 2186 ILE cc_start: 0.9546 (mm) cc_final: 0.9340 (mt) REVERT: A 2288 MET cc_start: 0.6620 (ptm) cc_final: 0.6346 (ptm) REVERT: A 2469 GLU cc_start: 0.7884 (tm-30) cc_final: 0.6810 (tm-30) REVERT: B 597 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5606 (tt) REVERT: B 827 LEU cc_start: 0.8364 (mt) cc_final: 0.7917 (mt) REVERT: B 936 LEU cc_start: 0.8848 (tp) cc_final: 0.8584 (mp) REVERT: B 993 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7723 (mmtt) REVERT: B 1103 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: B 1215 TRP cc_start: 0.8411 (OUTLIER) cc_final: 0.7474 (m-90) REVERT: B 1547 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8171 (mtm110) REVERT: B 1731 MET cc_start: 0.8529 (mpp) cc_final: 0.8147 (mmp) REVERT: B 1954 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6981 (p90) REVERT: B 2043 LEU cc_start: 0.9034 (pp) cc_final: 0.8827 (mt) REVERT: B 2288 MET cc_start: 0.6818 (ptm) cc_final: 0.6523 (ptm) REVERT: B 2469 GLU cc_start: 0.7813 (tm-30) cc_final: 0.6875 (tm-30) REVERT: B 2483 ASP cc_start: 0.8514 (m-30) cc_final: 0.8275 (m-30) REVERT: B 2486 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8860 (tt) REVERT: C 833 MET cc_start: 0.8025 (mtp) cc_final: 0.7593 (mmm) REVERT: C 866 ILE cc_start: 0.6739 (mm) cc_final: 0.6303 (mt) REVERT: C 872 TYR cc_start: 0.5189 (t80) cc_final: 0.4980 (t80) REVERT: C 947 ARG cc_start: 0.7877 (mmt90) cc_final: 0.7581 (mmm-85) REVERT: C 993 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7677 (mmtt) REVERT: C 1011 MET cc_start: 0.8819 (tpp) cc_final: 0.8351 (tpp) REVERT: C 1197 LEU cc_start: 0.9585 (tp) cc_final: 0.9373 (tp) REVERT: C 1215 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.7837 (m-90) REVERT: C 1334 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9120 (mmtm) REVERT: C 1731 MET cc_start: 0.8445 (mpp) cc_final: 0.8207 (mmp) REVERT: C 1954 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6782 (p90) REVERT: C 2043 LEU cc_start: 0.9005 (pp) cc_final: 0.8750 (mt) REVERT: C 2178 LEU cc_start: 0.9369 (mm) cc_final: 0.9135 (tt) REVERT: C 2194 MET cc_start: 0.8662 (ttm) cc_final: 0.8113 (tmm) REVERT: C 2290 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7765 (ttp80) REVERT: C 2469 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: C 2504 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9377 (tp) outliers start: 166 outliers final: 135 residues processed: 520 average time/residue: 0.1814 time to fit residues: 158.7780 Evaluate side-chains 543 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 389 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 993 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1193 CYS Chi-restraints excluded: chain A residue 1215 TRP Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1301 VAL Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1532 PHE Chi-restraints excluded: chain A residue 1543 LEU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1722 ILE Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1954 TYR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1970 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2008 LEU Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2100 HIS Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2129 THR Chi-restraints excluded: chain A residue 2155 THR Chi-restraints excluded: chain A residue 2187 ILE Chi-restraints excluded: chain A residue 2192 LEU Chi-restraints excluded: chain A residue 2222 LEU Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2486 LEU Chi-restraints excluded: chain A residue 2519 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1170 VAL Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1215 TRP Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1289 SER Chi-restraints excluded: chain B residue 1295 LEU Chi-restraints excluded: chain B residue 1328 TYR Chi-restraints excluded: chain B residue 1354 MET Chi-restraints excluded: chain B residue 1547 ARG Chi-restraints excluded: chain B residue 1550 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1694 ILE Chi-restraints excluded: chain B residue 1708 LEU Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1787 LEU Chi-restraints excluded: chain B residue 1954 TYR Chi-restraints excluded: chain B residue 1973 ILE Chi-restraints excluded: chain B residue 1974 ILE Chi-restraints excluded: chain B residue 1976 ILE Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2027 VAL Chi-restraints excluded: chain B residue 2072 ILE Chi-restraints excluded: chain B residue 2100 HIS Chi-restraints excluded: chain B residue 2155 THR Chi-restraints excluded: chain B residue 2170 ILE Chi-restraints excluded: chain B residue 2187 ILE Chi-restraints excluded: chain B residue 2192 LEU Chi-restraints excluded: chain B residue 2222 LEU Chi-restraints excluded: chain B residue 2231 SER Chi-restraints excluded: chain B residue 2471 LEU Chi-restraints excluded: chain B residue 2484 ILE Chi-restraints excluded: chain B residue 2486 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2518 ARG Chi-restraints excluded: chain B residue 2519 GLU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 593 PHE Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 805 PHE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 993 LYS Chi-restraints excluded: chain C residue 1044 PHE Chi-restraints excluded: chain C residue 1105 LEU Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1169 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1215 TRP Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1301 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1334 LYS Chi-restraints excluded: chain C residue 1354 MET Chi-restraints excluded: chain C residue 1529 LEU Chi-restraints excluded: chain C residue 1550 LEU Chi-restraints excluded: chain C residue 1568 LEU Chi-restraints excluded: chain C residue 1669 GLN Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1694 ILE Chi-restraints excluded: chain C residue 1696 ILE Chi-restraints excluded: chain C residue 1708 LEU Chi-restraints excluded: chain C residue 1716 LEU Chi-restraints excluded: chain C residue 1786 ASP Chi-restraints excluded: chain C residue 1954 TYR Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1976 ILE Chi-restraints excluded: chain C residue 2008 LEU Chi-restraints excluded: chain C residue 2027 VAL Chi-restraints excluded: chain C residue 2072 ILE Chi-restraints excluded: chain C residue 2100 HIS Chi-restraints excluded: chain C residue 2170 ILE Chi-restraints excluded: chain C residue 2187 ILE Chi-restraints excluded: chain C residue 2192 LEU Chi-restraints excluded: chain C residue 2222 LEU Chi-restraints excluded: chain C residue 2420 MET Chi-restraints excluded: chain C residue 2469 GLU Chi-restraints excluded: chain C residue 2471 LEU Chi-restraints excluded: chain C residue 2484 ILE Chi-restraints excluded: chain C residue 2504 ILE Chi-restraints excluded: chain C residue 2519 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 219 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 237 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A1205 GLN ** B1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.121552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083550 restraints weight = 123320.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085784 restraints weight = 55184.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087119 restraints weight = 35143.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.087847 restraints weight = 27255.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088194 restraints weight = 23782.186| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.8359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32181 Z= 0.163 Angle : 0.749 12.838 43607 Z= 0.350 Chirality : 0.043 0.303 4983 Planarity : 0.004 0.058 5303 Dihedral : 8.150 92.369 4363 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.94 % Allowed : 29.42 % Favored : 65.64 % 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: 1.53 (0.14), residues: 3747 helix: 1.86 (0.10), residues: 2685 sheet: -1.30 (0.29), residues: 249 loop : -1.07 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1652 TYR 0.024 0.001 TYR B2067 PHE 0.024 0.001 PHE A2012 TRP 0.038 0.002 TRP B2188 HIS 0.006 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00368 (32178) covalent geometry : angle 0.74855 (43601) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.18289 ( 6) hydrogen bonds : bond 0.04613 ( 2056) hydrogen bonds : angle 4.38507 ( 6087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9504.54 seconds wall clock time: 163 minutes 23.52 seconds (9803.52 seconds total)