Starting phenix.real_space_refine on Fri Jan 17 12:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt8_19482/01_2025/8rt8_19482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt8_19482/01_2025/8rt8_19482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rt8_19482/01_2025/8rt8_19482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt8_19482/01_2025/8rt8_19482.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt8_19482/01_2025/8rt8_19482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt8_19482/01_2025/8rt8_19482.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 34862 2.51 5 N 10180 2.21 5 O 10556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 454 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 55802 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "a" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "d" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "g" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "j" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "m" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "p" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 26.26, per 1000 atoms: 0.47 Number of scatterers: 55802 At special positions: 0 Unit cell: (192.06, 195.261, 156.849, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 10556 8.00 N 10180 7.00 C 34862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS M 215 " - pdb=" SG CYS M 231 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 231 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 231 " distance=2.04 Simple disulfide: pdb=" SG CYS V 215 " - pdb=" SG CYS V 231 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 215 " - pdb=" SG CYS Y 231 " distance=2.03 Simple disulfide: pdb=" SG CYS b 215 " - pdb=" SG CYS b 231 " distance=2.03 Simple disulfide: pdb=" SG CYS e 215 " - pdb=" SG CYS e 231 " distance=2.04 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.05 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 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: 11.09 Conformation dependent library (CDL) restraints added in 5.5 seconds 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13052 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 144 sheets defined 17.7% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.85 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 305 through 329 removed outlier: 6.043A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.685A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.675A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 306 through 329 removed outlier: 5.873A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.593A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 151 removed outlier: 3.980A pdb=" N ALA E 138 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN E 139 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.540A pdb=" N ILE F 42 " --> pdb=" O PRO F 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 148 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 305 through 329 removed outlier: 5.829A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.814A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 150 Processing helix chain 'H' and resid 166 through 169 Processing helix chain 'I' and resid 39 through 43 Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'J' and resid 306 through 329 removed outlier: 6.298A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 358 Processing helix chain 'K' and resid 127 through 151 removed outlier: 4.380A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'L' and resid 39 through 43 removed outlier: 3.633A pdb=" N ILE L 42 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'M' and resid 182 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 6.165A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ALA M 313 " --> pdb=" O ARG M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 359 Processing helix chain 'N' and resid 127 through 151 removed outlier: 3.830A pdb=" N ARG N 151 " --> pdb=" O ALA N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 169 Processing helix chain 'O' and resid 39 through 43 Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 330 removed outlier: 5.425A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY P 330 " --> pdb=" O ALA P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 358 Processing helix chain 'Q' and resid 127 through 151 removed outlier: 3.790A pdb=" N ARG Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 169 Processing helix chain 'R' and resid 39 through 43 Processing helix chain 'S' and resid 136 through 148 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 186 Processing helix chain 'S' and resid 305 through 329 removed outlier: 6.266A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 removed outlier: 3.554A pdb=" N ASN S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 151 removed outlier: 3.508A pdb=" N GLU T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 169 Processing helix chain 'U' and resid 39 through 43 Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'V' and resid 180 through 186 removed outlier: 3.688A pdb=" N ALA V 184 " --> pdb=" O GLY V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.692A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA V 313 " --> pdb=" O ARG V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 359 Processing helix chain 'W' and resid 71 through 75 removed outlier: 3.811A pdb=" N TYR W 75 " --> pdb=" O SER W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 150 removed outlier: 3.502A pdb=" N ARG W 136 " --> pdb=" O ALA W 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 169 Processing helix chain 'Y' and resid 136 through 148 Processing helix chain 'Y' and resid 180 through 187 Processing helix chain 'Y' and resid 202 through 204 No H-bonds generated for 'chain 'Y' and resid 202 through 204' Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.750A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA Y 313 " --> pdb=" O ARG Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 359 Processing helix chain 'Z' and resid 127 through 150 removed outlier: 4.198A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 306 through 329 removed outlier: 6.045A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 removed outlier: 3.771A pdb=" N ASN b 357 " --> pdb=" O GLU b 353 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 151 removed outlier: 3.744A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU c 137 " --> pdb=" O ARG c 133 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 169 Processing helix chain 'd' and resid 39 through 43 Processing helix chain 'e' and resid 136 through 148 Processing helix chain 'e' and resid 180 through 186 Processing helix chain 'e' and resid 202 through 204 No H-bonds generated for 'chain 'e' and resid 202 through 204' Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.756A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.646A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 135 Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.772A pdb=" N ARG f 151 " --> pdb=" O ALA f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 169 Processing helix chain 'g' and resid 39 through 43 removed outlier: 3.547A pdb=" N ILE g 42 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 removed outlier: 3.653A pdb=" N LEU h 140 " --> pdb=" O THR h 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 182 through 187 Processing helix chain 'h' and resid 305 through 330 removed outlier: 5.609A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY h 330 " --> pdb=" O ALA h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.575A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 169 Processing helix chain 'j' and resid 39 through 43 Processing helix chain 'k' and resid 136 through 148 Processing helix chain 'k' and resid 180 through 187 Processing helix chain 'k' and resid 202 through 204 No H-bonds generated for 'chain 'k' and resid 202 through 204' Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.941A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.888A pdb=" N ARG l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'm' and resid 39 through 43 Processing helix chain 'n' and resid 136 through 148 Processing helix chain 'n' and resid 180 through 186 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.201A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 removed outlier: 3.694A pdb=" N ASN n 357 " --> pdb=" O GLU n 353 " (cutoff:3.500A) Processing helix chain 'o' and resid 127 through 150 removed outlier: 3.588A pdb=" N ASN o 139 " --> pdb=" O THR o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'v' and resid 71 through 75 removed outlier: 3.589A pdb=" N TYR v 75 " --> pdb=" O SER v 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 148 Processing helix chain 'z' and resid 71 through 73 No H-bonds generated for 'chain 'z' and resid 71 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.866A pdb=" N SER A 195 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.520A pdb=" N ILE D 283 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.707A pdb=" N ASP A 382 " --> pdb=" O ALA n 197 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ARG n 199 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 282 " --> pdb=" O GLY n 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 217 removed outlier: 3.584A pdb=" N GLY A 255 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 256 " --> pdb=" O TRP A 272 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP A 272 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 287 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.629A pdb=" N LEU A 247 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 391 removed outlier: 3.520A pdb=" N SER A 388 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 390 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.685A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 87 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.668A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 5.014A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB4, first strand: chain 'B' and resid 258 through 261 removed outlier: 3.759A pdb=" N GLU n 390 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 195 through 196 removed outlier: 7.012A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.610A pdb=" N VAL G 282 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 283 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE G 256 " --> pdb=" O TRP G 272 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP G 272 " --> pdb=" O PHE G 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB8, first strand: chain 'D' and resid 237 through 238 removed outlier: 6.933A pdb=" N VAL D 237 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 388 through 391 Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.936A pdb=" N ALA E 124 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL E 36 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 49 Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 3.559A pdb=" N VAL E 196 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.515A pdb=" N ASN E 172 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.408A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 198 through 199 removed outlier: 3.817A pdb=" N VAL J 282 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER J 273 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER J 287 " --> pdb=" O GLN J 271 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN J 271 " --> pdb=" O SER J 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 257 " --> pdb=" O GLY J 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 227 " --> pdb=" O TYR J 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 198 through 199 removed outlier: 3.817A pdb=" N VAL J 282 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS J 231 " --> pdb=" O VAL J 253 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 257 " --> pdb=" O GLY J 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 227 " --> pdb=" O TYR J 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'G' and resid 237 through 238 removed outlier: 6.868A pdb=" N VAL G 237 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AD2, first strand: chain 'G' and resid 387 through 391 removed outlier: 3.761A pdb=" N GLU G 390 " --> pdb=" O ARG K 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.845A pdb=" N ARG H 34 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.600A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG H 113 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR H 48 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN H 96 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE H 69 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE H 98 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS H 67 " --> pdb=" O ILE H 98 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL H 100 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 202 through 203 removed outlier: 3.580A pdb=" N VAL H 196 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.539A pdb=" N THR H 180 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.691A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 198 through 199 removed outlier: 3.771A pdb=" N LEU M 376 " --> pdb=" O PRO M 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY M 227 " --> pdb=" O TYR M 257 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE M 256 " --> pdb=" O TRP M 272 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP M 272 " --> pdb=" O PHE M 256 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG M 274 " --> pdb=" O LEU M 285 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU M 285 " --> pdb=" O ARG M 274 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU M 276 " --> pdb=" O ILE M 283 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE M 283 " --> pdb=" O GLU M 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AE1, first strand: chain 'J' and resid 237 through 238 removed outlier: 7.108A pdb=" N VAL J 237 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AE3, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AE4, first strand: chain 'K' and resid 25 through 26 removed outlier: 4.367A pdb=" N ARG K 34 " --> pdb=" O GLU K 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA K 124 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE K 125 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS K 83 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS K 80 " --> pdb=" O HIS K 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 44 through 49 removed outlier: 7.215A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 46 " --> pdb=" O GLN K 111 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG K 113 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR K 48 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.817A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AE8, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.561A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 198 through 199 removed outlier: 3.573A pdb=" N VAL P 282 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU P 376 " --> pdb=" O PRO P 288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN P 374 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY P 227 " --> pdb=" O TYR P 257 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG P 274 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU P 285 " --> pdb=" O ARG P 274 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU P 276 " --> pdb=" O ILE P 283 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE P 283 " --> pdb=" O GLU P 276 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'M' and resid 237 through 238 removed outlier: 7.016A pdb=" N VAL M 237 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AF4, first strand: chain 'M' and resid 388 through 391 Processing sheet with id=AF5, first strand: chain 'N' and resid 25 through 26 removed outlier: 6.639A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS N 83 " --> pdb=" O LYS N 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.631A pdb=" N VAL N 44 " --> pdb=" O ARG N 109 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN N 111 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL N 46 " --> pdb=" O GLN N 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 160 through 164 removed outlier: 5.103A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL N 196 " --> pdb=" O LYS N 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 172 through 175 removed outlier: 3.561A pdb=" N ASN N 172 " --> pdb=" O LYS N 183 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 206 through 207 removed outlier: 7.204A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE S 283 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER S 287 " --> pdb=" O TRP S 272 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU S 376 " --> pdb=" O PRO S 288 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY S 255 " --> pdb=" O THR S 229 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AG2, first strand: chain 'P' and resid 237 through 238 removed outlier: 6.898A pdb=" N VAL P 237 " --> pdb=" O LEU P 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 267 through 268 Processing sheet with id=AG4, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AG5, first strand: chain 'Q' and resid 25 through 26 removed outlier: 3.805A pdb=" N ARG Q 34 " --> pdb=" O GLU Q 122 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Q 124 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 44 through 49 removed outlier: 6.504A pdb=" N VAL Q 44 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLN Q 111 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL Q 46 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG Q 113 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR Q 48 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 202 through 203 removed outlier: 3.761A pdb=" N ARG Q 229 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 172 through 175 removed outlier: 3.566A pdb=" N ASN Q 172 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP Q 174 " --> pdb=" O TYR Q 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 195 through 196 removed outlier: 7.069A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AH2, first strand: chain 'S' and resid 237 through 238 removed outlier: 6.910A pdb=" N VAL S 237 " --> pdb=" O LEU S 246 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 387 through 391 removed outlier: 3.803A pdb=" N GLU S 390 " --> pdb=" O ARG W 259 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.658A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.436A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.436A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 202 through 203 removed outlier: 3.577A pdb=" N ARG T 229 " --> pdb=" O SER T 192 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL T 196 " --> pdb=" O LYS T 225 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'T' and resid 172 through 175 removed outlier: 3.595A pdb=" N ILE T 216 " --> pdb=" O VAL T 210 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.657A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 198 through 199 removed outlier: 3.720A pdb=" N VAL Y 282 " --> pdb=" O GLY V 198 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY Y 255 " --> pdb=" O THR Y 229 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Y 257 " --> pdb=" O GLY Y 227 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Y 227 " --> pdb=" O TYR Y 257 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 212 through 213 removed outlier: 3.633A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 376 " --> pdb=" O PRO V 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER V 287 " --> pdb=" O TRP V 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR V 257 " --> pdb=" O GLY V 227 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY V 227 " --> pdb=" O TYR V 257 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 212 through 213 removed outlier: 3.633A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 376 " --> pdb=" O PRO V 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER V 287 " --> pdb=" O TRP V 272 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI5, first strand: chain 'V' and resid 237 through 238 removed outlier: 6.820A pdb=" N VAL V 237 " --> pdb=" O LEU V 246 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 388 through 391 Processing sheet with id=AI7, first strand: chain 'W' and resid 25 through 26 removed outlier: 3.749A pdb=" N ARG W 34 " --> pdb=" O GLU W 122 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'W' and resid 44 through 49 removed outlier: 6.825A pdb=" N VAL W 44 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN W 111 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL W 46 " --> pdb=" O GLN W 111 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG W 113 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR W 48 " --> pdb=" O ARG W 113 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL W 99 " --> pdb=" O TYR W 106 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.657A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ2, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.725A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Y' and resid 198 through 199 removed outlier: 3.531A pdb=" N ILE b 283 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE b 275 " --> pdb=" O ILE b 283 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU b 376 " --> pdb=" O PRO b 288 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE b 256 " --> pdb=" O TRP b 272 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TRP b 272 " --> pdb=" O PHE b 256 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Y' and resid 231 through 233 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 221 through 222 removed outlier: 3.521A pdb=" N THR Y 364 " --> pdb=" O ASP Y 303 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP Y 303 " --> pdb=" O THR Y 364 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 237 through 238 removed outlier: 7.040A pdb=" N VAL Y 237 " --> pdb=" O LEU Y 246 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 25 through 26 removed outlier: 3.627A pdb=" N ARG Z 34 " --> pdb=" O GLU Z 122 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Z 124 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR Z 54 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Z 86 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Z 87 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 44 through 49 removed outlier: 6.620A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG Z 113 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR Z 48 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 202 through 203 removed outlier: 4.480A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AK3, first strand: chain 'b' and resid 197 through 199 removed outlier: 7.765A pdb=" N ILE e 283 " --> pdb=" O GLU e 276 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU e 276 " --> pdb=" O ILE e 283 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU e 285 " --> pdb=" O ARG e 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG e 274 " --> pdb=" O LEU e 285 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP e 272 " --> pdb=" O PHE e 256 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE e 256 " --> pdb=" O TRP e 272 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY e 227 " --> pdb=" O TYR e 257 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 197 through 199 removed outlier: 3.698A pdb=" N LEU e 376 " --> pdb=" O PRO e 288 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AK6, first strand: chain 'b' and resid 237 through 238 removed outlier: 6.990A pdb=" N VAL b 237 " --> pdb=" O LEU b 246 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AK8, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.999A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'c' and resid 44 through 49 removed outlier: 6.787A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG c 113 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR c 48 " --> pdb=" O ARG c 113 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'c' and resid 202 through 203 removed outlier: 3.664A pdb=" N VAL c 196 " --> pdb=" O LYS c 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 172 through 175 removed outlier: 3.671A pdb=" N THR c 180 " --> pdb=" O VAL c 219 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.417A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'e' and resid 198 through 199 removed outlier: 3.646A pdb=" N LEU h 376 " --> pdb=" O PRO h 288 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY h 227 " --> pdb=" O TYR h 257 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE h 256 " --> pdb=" O TRP h 272 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP h 272 " --> pdb=" O PHE h 256 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'e' and resid 206 through 207 Processing sheet with id=AL6, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AL7, first strand: chain 'e' and resid 237 through 238 removed outlier: 6.991A pdb=" N VAL e 237 " --> pdb=" O LEU e 246 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'e' and resid 267 through 268 Processing sheet with id=AL9, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AM1, first strand: chain 'f' and resid 25 through 26 removed outlier: 3.511A pdb=" N ALA f 124 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'f' and resid 44 through 48 removed outlier: 6.728A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 202 through 203 removed outlier: 3.825A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AM5, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.474A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'h' and resid 198 through 199 removed outlier: 3.656A pdb=" N VAL k 282 " --> pdb=" O GLY h 198 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER k 287 " --> pdb=" O TRP k 272 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'h' and resid 198 through 199 removed outlier: 3.656A pdb=" N VAL k 282 " --> pdb=" O GLY h 198 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY k 227 " --> pdb=" O TYR k 257 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM9, first strand: chain 'h' and resid 237 through 238 removed outlier: 6.726A pdb=" N VAL h 237 " --> pdb=" O LEU h 246 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AN2, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN3, first strand: chain 'i' and resid 25 through 26 removed outlier: 7.048A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA i 78 " --> pdb=" O PHE i 85 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 44 through 48 removed outlier: 3.583A pdb=" N GLN i 111 " --> pdb=" O VAL i 46 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR i 48 " --> pdb=" O GLN i 111 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE i 98 " --> pdb=" O HIS i 67 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS i 67 " --> pdb=" O ILE i 98 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL i 100 " --> pdb=" O LEU i 65 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'i' and resid 202 through 203 removed outlier: 4.332A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN7, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.779A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'k' and resid 198 through 199 removed outlier: 3.707A pdb=" N LEU n 376 " --> pdb=" O PRO n 288 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'k' and resid 198 through 199 removed outlier: 8.011A pdb=" N ILE n 283 " --> pdb=" O GLU n 276 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU n 276 " --> pdb=" O ILE n 283 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU n 285 " --> pdb=" O ARG n 274 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG n 274 " --> pdb=" O LEU n 285 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER n 287 " --> pdb=" O TRP n 272 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY n 255 " --> pdb=" O THR n 229 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AO2, first strand: chain 'k' and resid 237 through 238 removed outlier: 6.759A pdb=" N VAL k 237 " --> pdb=" O LEU k 246 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AO4, first strand: chain 'k' and resid 387 through 391 removed outlier: 4.239A pdb=" N GLU k 390 " --> pdb=" O ARG o 259 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 25 through 27 removed outlier: 6.221A pdb=" N ILE l 33 " --> pdb=" O SER l 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA l 78 " --> pdb=" O PHE l 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS l 87 " --> pdb=" O ALA l 76 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'l' and resid 44 through 49 removed outlier: 6.537A pdb=" N VAL l 44 " --> pdb=" O ARG l 109 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN l 111 " --> pdb=" O VAL l 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL l 46 " --> pdb=" O GLN l 111 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG l 113 " --> pdb=" O VAL l 46 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR l 48 " --> pdb=" O ARG l 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR l 95 " --> pdb=" O LEU l 110 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'l' and resid 202 through 203 removed outlier: 3.643A pdb=" N ARG l 229 " --> pdb=" O SER l 192 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL l 196 " --> pdb=" O LYS l 225 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AO9, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AP1, first strand: chain 'n' and resid 237 through 238 removed outlier: 6.720A pdb=" N VAL n 237 " --> pdb=" O LEU n 246 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 25 through 26 removed outlier: 3.991A pdb=" N ARG o 34 " --> pdb=" O GLU o 122 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE o 125 " --> pdb=" O MET o 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS o 83 " --> pdb=" O LYS o 80 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA o 78 " --> pdb=" O PHE o 85 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'o' and resid 44 through 49 removed outlier: 3.556A pdb=" N VAL o 99 " --> pdb=" O TYR o 106 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'o' and resid 202 through 204 removed outlier: 3.759A pdb=" N VAL o 196 " --> pdb=" O LYS o 225 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'o' and resid 172 through 175 removed outlier: 3.529A pdb=" N ASN o 172 " --> pdb=" O LYS o 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP o 174 " --> pdb=" O TYR o 181 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'v' and resid 25 through 26 removed outlier: 7.005A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'v' and resid 44 through 49 removed outlier: 6.195A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN v 111 " --> pdb=" O VAL v 44 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL v 46 " --> pdb=" O GLN v 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG v 113 " --> pdb=" O VAL v 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR v 48 " --> pdb=" O ARG v 113 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'z' and resid 25 through 26 removed outlier: 3.503A pdb=" N ARG z 34 " --> pdb=" O GLU z 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA z 124 " --> pdb=" O ARG z 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS z 83 " --> pdb=" O LYS z 80 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS z 87 " --> pdb=" O ALA z 76 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'z' and resid 44 through 48 removed outlier: 3.564A pdb=" N VAL z 46 " --> pdb=" O ARG z 109 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL z 99 " --> pdb=" O TYR z 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR z 66 " --> pdb=" O VAL z 100 " (cutoff:3.500A) 2000 hydrogen bonds defined for protein. 5220 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: 30.13 Time building geometry restraints manager: 13.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 19002 1.33 - 1.45: 9177 1.45 - 1.57: 28349 1.57 - 1.69: 0 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" CA ASP n 286 " pdb=" CB ASP n 286 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.51e-02 4.39e+03 6.97e+00 bond pdb=" C GLU Y 276 " pdb=" N THR Y 277 " ideal model delta sigma weight residual 1.330 1.295 0.036 1.37e-02 5.33e+03 6.83e+00 bond pdb=" CA GLN M 329 " pdb=" C GLN M 329 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.38e-02 5.25e+03 5.80e+00 bond pdb=" CA ASP S 286 " pdb=" CB ASP S 286 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.51e-02 4.39e+03 5.42e+00 bond pdb=" CA ASP k 286 " pdb=" CB ASP k 286 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.70e-02 3.46e+03 5.17e+00 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 76920 4.75 - 9.51: 101 9.51 - 14.26: 6 14.26 - 19.02: 8 19.02 - 23.77: 1 Bond angle restraints: 77036 Sorted by residual: angle pdb=" O GLN F 43 " pdb=" C GLN F 43 " pdb=" N ARG F 44 " ideal model delta sigma weight residual 122.41 98.64 23.77 1.34e+00 5.57e-01 3.15e+02 angle pdb=" O GLN O 43 " pdb=" C GLN O 43 " pdb=" N ARG O 44 " ideal model delta sigma weight residual 122.41 104.63 17.78 1.34e+00 5.57e-01 1.76e+02 angle pdb=" O GLN a 43 " pdb=" C GLN a 43 " pdb=" N ARG a 44 " ideal model delta sigma weight residual 122.41 106.18 16.23 1.34e+00 5.57e-01 1.47e+02 angle pdb=" O GLN m 43 " pdb=" C GLN m 43 " pdb=" N ARG m 44 " ideal model delta sigma weight residual 122.41 106.51 15.90 1.34e+00 5.57e-01 1.41e+02 angle pdb=" O GLN g 43 " pdb=" C GLN g 43 " pdb=" N ARG g 44 " ideal model delta sigma weight residual 122.41 107.16 15.25 1.34e+00 5.57e-01 1.30e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 31071 18.10 - 36.20: 2627 36.20 - 54.30: 349 54.30 - 72.40: 90 72.40 - 90.50: 53 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA MET f 57 " pdb=" C MET f 57 " pdb=" N LEU f 58 " pdb=" CA LEU f 58 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU f 137 " pdb=" C GLU f 137 " pdb=" N ALA f 138 " pdb=" CA ALA f 138 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY V 180 " pdb=" C GLY V 180 " pdb=" N GLY V 181 " pdb=" CA GLY V 181 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 6258 0.049 - 0.097: 1653 0.097 - 0.146: 441 0.146 - 0.195: 16 0.195 - 0.243: 2 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB VAL J 253 " pdb=" CA VAL J 253 " pdb=" CG1 VAL J 253 " pdb=" CG2 VAL J 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE W 33 " pdb=" CA ILE W 33 " pdb=" CG1 ILE W 33 " pdb=" CG2 ILE W 33 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CG LEU N 50 " pdb=" CB LEU N 50 " pdb=" CD1 LEU N 50 " pdb=" CD2 LEU N 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 43 " -0.098 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" C GLN F 43 " 0.296 2.00e-02 2.50e+03 pdb=" O GLN F 43 " -0.108 2.00e-02 2.50e+03 pdb=" N ARG F 44 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN p 43 " -0.086 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C GLN p 43 " 0.269 2.00e-02 2.50e+03 pdb=" O GLN p 43 " -0.099 2.00e-02 2.50e+03 pdb=" N ARG p 44 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN O 43 " 0.084 2.00e-02 2.50e+03 1.53e-01 2.34e+02 pdb=" C GLN O 43 " -0.265 2.00e-02 2.50e+03 pdb=" O GLN O 43 " 0.098 2.00e-02 2.50e+03 pdb=" N ARG O 44 " 0.082 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 742 2.56 - 3.14: 46585 3.14 - 3.73: 87124 3.73 - 4.31: 119120 4.31 - 4.90: 199609 Nonbonded interactions: 453180 Sorted by model distance: nonbonded pdb=" OE1 GLU N 137 " pdb=" NH1 ARG N 141 " model vdw 1.973 3.120 nonbonded pdb=" O GLU D 218 " pdb=" OH TYR E 194 " model vdw 1.998 3.040 nonbonded pdb=" O GLU A 218 " pdb=" OH TYR B 194 " model vdw 2.021 3.040 nonbonded pdb=" O GLU Y 218 " pdb=" OH TYR Z 194 " model vdw 2.044 3.040 nonbonded pdb=" O ARG h 243 " pdb=" OG1 THR l 253 " model vdw 2.059 3.040 ... (remaining 453175 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' } ncs_group { reference = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'v' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.060 Extract box with map and model: 1.740 Check model and map are aligned: 0.350 Set scattering table: 0.410 Process input model: 112.880 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.720 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: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.006 0.076 56894 Z= 0.424 Angle : 0.809 23.773 77036 Z= 0.476 Chirality : 0.046 0.243 8370 Planarity : 0.007 0.171 10228 Dihedral : 13.745 90.502 21096 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.10), residues: 7036 helix: 0.72 (0.16), residues: 1102 sheet: -0.65 (0.11), residues: 2048 loop : -0.89 (0.09), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 307 HIS 0.012 0.002 HIS T 67 PHE 0.025 0.002 PHE o 195 TYR 0.031 0.002 TYR z 127 ARG 0.013 0.001 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 936 time to evaluate : 5.109 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: B 112 MET cc_start: 0.8561 (ttp) cc_final: 0.8298 (tpp) REVERT: D 186 LYS cc_start: 0.9157 (mttm) cc_final: 0.8828 (mttm) REVERT: D 353 GLU cc_start: 0.8792 (tp30) cc_final: 0.8398 (tp30) REVERT: E 120 MET cc_start: 0.7727 (mtm) cc_final: 0.6828 (mmt) REVERT: E 131 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9010 (pt0) REVERT: E 227 MET cc_start: 0.8323 (tpp) cc_final: 0.8042 (tpt) REVERT: H 133 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9209 (tpm170) REVERT: H 134 GLN cc_start: 0.8718 (pp30) cc_final: 0.8462 (pp30) REVERT: J 353 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8000 (tp30) REVERT: K 84 ILE cc_start: 0.8984 (mt) cc_final: 0.8783 (mm) REVERT: K 107 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8146 (mttm) REVERT: M 138 TYR cc_start: 0.8954 (t80) cc_final: 0.8739 (t80) REVERT: M 353 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8077 (tp30) REVERT: N 63 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8672 (mm-40) REVERT: N 98 ILE cc_start: 0.8246 (mm) cc_final: 0.8021 (tp) REVERT: P 353 GLU cc_start: 0.8440 (tp30) cc_final: 0.7926 (tp30) REVERT: Q 120 MET cc_start: 0.6316 (mtt) cc_final: 0.5815 (mtt) REVERT: Q 129 ASP cc_start: 0.8754 (p0) cc_final: 0.8514 (p0) REVERT: V 145 MET cc_start: 0.9010 (ttt) cc_final: 0.8484 (ttt) REVERT: W 67 HIS cc_start: 0.8874 (p-80) cc_final: 0.8580 (p-80) REVERT: W 183 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8914 (ttmm) REVERT: Y 357 ASN cc_start: 0.8855 (m-40) cc_final: 0.8640 (m110) REVERT: Z 108 PHE cc_start: 0.8789 (m-10) cc_final: 0.8584 (m-10) REVERT: e 353 GLU cc_start: 0.8253 (tp30) cc_final: 0.7732 (tp30) REVERT: k 145 MET cc_start: 0.8694 (ttt) cc_final: 0.8223 (tpp) REVERT: k 186 LYS cc_start: 0.9222 (mttm) cc_final: 0.8990 (mtpt) REVERT: l 111 GLN cc_start: 0.8145 (mm110) cc_final: 0.7914 (mp10) REVERT: l 120 MET cc_start: 0.8182 (ptm) cc_final: 0.7726 (tmm) REVERT: l 129 ASP cc_start: 0.8889 (p0) cc_final: 0.8482 (p0) REVERT: n 308 GLU cc_start: 0.8035 (tp30) cc_final: 0.7802 (mm-30) REVERT: u 142 ARG cc_start: 0.9172 (mpt180) cc_final: 0.8888 (mpt180) REVERT: u 145 MET cc_start: 0.9086 (mtt) cc_final: 0.8780 (mmt) REVERT: v 50 LEU cc_start: 0.8479 (tp) cc_final: 0.7556 (tp) REVERT: v 108 PHE cc_start: 0.8775 (m-10) cc_final: 0.8442 (m-80) REVERT: v 115 ASP cc_start: 0.9207 (p0) cc_final: 0.8947 (p0) REVERT: v 117 ASN cc_start: 0.8996 (m110) cc_final: 0.8674 (m-40) REVERT: z 25 SER cc_start: 0.9466 (m) cc_final: 0.9174 (p) REVERT: z 35 TYR cc_start: 0.8895 (m-80) cc_final: 0.8458 (m-80) REVERT: z 89 GLN cc_start: 0.9397 (mp10) cc_final: 0.8870 (mp10) REVERT: z 94 ASN cc_start: 0.8815 (m-40) cc_final: 0.8248 (m-40) REVERT: z 120 MET cc_start: 0.6709 (mtm) cc_final: 0.5909 (mtm) outliers start: 4 outliers final: 0 residues processed: 939 average time/residue: 0.6075 time to fit residues: 911.8764 Evaluate side-chains 530 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 7.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 354 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 543 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 404 optimal weight: 3.9990 chunk 630 optimal weight: 3.9990 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 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN E 214 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN N 139 ASN ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 GLN P 305 HIS P 357 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 201 ASN ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 ASN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 172 ASN Z 220 HIS c 89 GLN c 249 ASN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN n 360 ASN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.036377 restraints weight = 242934.327| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.75 r_work: 0.2559 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56894 Z= 0.289 Angle : 0.643 10.758 77036 Z= 0.336 Chirality : 0.046 0.178 8370 Planarity : 0.005 0.056 10228 Dihedral : 4.611 22.280 7996 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.09 % Allowed : 8.28 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.10), residues: 7036 helix: 1.53 (0.16), residues: 1111 sheet: -0.35 (0.11), residues: 2125 loop : -0.49 (0.10), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 272 HIS 0.009 0.001 HIS z 55 PHE 0.029 0.002 PHE o 195 TYR 0.024 0.002 TYR n 238 ARG 0.014 0.001 ARG S 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 611 time to evaluate : 5.341 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: A 371 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8708 (mt-10) REVERT: B 161 MET cc_start: 0.9442 (mmm) cc_final: 0.8674 (mmm) REVERT: D 145 MET cc_start: 0.9118 (ttt) cc_final: 0.8713 (mtp) REVERT: D 188 GLN cc_start: 0.9222 (tt0) cc_final: 0.8500 (tm-30) REVERT: E 120 MET cc_start: 0.8025 (mtm) cc_final: 0.6488 (mmt) REVERT: E 131 GLN cc_start: 0.9477 (tm-30) cc_final: 0.8997 (pt0) REVERT: G 218 GLU cc_start: 0.9174 (tt0) cc_final: 0.8598 (pt0) REVERT: H 161 MET cc_start: 0.9418 (mmm) cc_final: 0.9176 (mmm) REVERT: H 221 LYS cc_start: 0.9286 (tptp) cc_final: 0.9048 (tppt) REVERT: J 147 ARG cc_start: 0.9429 (mtm110) cc_final: 0.9140 (ptp90) REVERT: J 182 GLU cc_start: 0.9032 (tt0) cc_final: 0.8723 (tt0) REVERT: J 185 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9192 (pp20) REVERT: J 205 MET cc_start: 0.9427 (tpp) cc_final: 0.8895 (mmm) REVERT: J 353 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8722 (tp30) REVERT: J 357 ASN cc_start: 0.9015 (m110) cc_final: 0.8783 (m110) REVERT: K 86 ILE cc_start: 0.9472 (pt) cc_final: 0.9078 (mm) REVERT: K 161 MET cc_start: 0.9350 (mmm) cc_final: 0.8907 (mmm) REVERT: K 162 MET cc_start: 0.9149 (ptp) cc_final: 0.8198 (ptp) REVERT: M 143 GLU cc_start: 0.9656 (pp20) cc_final: 0.9347 (pp20) REVERT: M 182 GLU cc_start: 0.9126 (tp30) cc_final: 0.8905 (tt0) REVERT: M 188 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8440 (tm-30) REVERT: M 371 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8234 (mp0) REVERT: N 54 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8710 (p) REVERT: N 98 ILE cc_start: 0.8480 (mm) cc_final: 0.8136 (tp) REVERT: N 120 MET cc_start: 0.8845 (ttp) cc_final: 0.7987 (tpt) REVERT: P 371 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8472 (mt-10) REVERT: Q 54 THR cc_start: 0.9111 (m) cc_final: 0.8756 (t) REVERT: Q 120 MET cc_start: 0.7276 (mtt) cc_final: 0.6740 (mtt) REVERT: Q 227 MET cc_start: 0.9401 (tpp) cc_final: 0.9201 (tpp) REVERT: T 73 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8862 (pp20) REVERT: T 263 LYS cc_start: 0.9420 (ptmm) cc_final: 0.9023 (ptmm) REVERT: V 138 TYR cc_start: 0.9631 (t80) cc_final: 0.8824 (t80) REVERT: V 142 ARG cc_start: 0.9529 (mmm-85) cc_final: 0.8844 (ttm110) REVERT: V 185 GLU cc_start: 0.9052 (pm20) cc_final: 0.8777 (pm20) REVERT: V 371 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8523 (mt-10) REVERT: W 80 LYS cc_start: 0.8912 (tttm) cc_final: 0.8675 (tttt) REVERT: W 150 GLN cc_start: 0.9454 (tm-30) cc_final: 0.9248 (tm-30) REVERT: W 183 LYS cc_start: 0.9548 (ttpt) cc_final: 0.9264 (ttmm) REVERT: X 30 ASN cc_start: 0.8691 (p0) cc_final: 0.8129 (p0) REVERT: Y 136 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9276 (t) REVERT: Y 252 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8828 (ttpp) REVERT: Y 357 ASN cc_start: 0.9239 (m-40) cc_final: 0.8751 (m110) REVERT: Z 112 MET cc_start: 0.8562 (tpp) cc_final: 0.7447 (mmm) REVERT: Z 131 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8908 (tm-30) REVERT: b 143 GLU cc_start: 0.9481 (tp30) cc_final: 0.9255 (tm-30) REVERT: e 188 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: e 390 GLU cc_start: 0.8395 (pp20) cc_final: 0.8010 (pp20) REVERT: f 80 LYS cc_start: 0.9529 (ttpt) cc_final: 0.9280 (pttt) REVERT: f 120 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7526 (tpp) REVERT: f 161 MET cc_start: 0.9317 (mmm) cc_final: 0.8678 (mmm) REVERT: f 263 LYS cc_start: 0.9297 (ptmm) cc_final: 0.8768 (ptmm) REVERT: i 57 MET cc_start: 0.8992 (ttt) cc_final: 0.8779 (ttp) REVERT: i 263 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9132 (ttpp) REVERT: k 145 MET cc_start: 0.8504 (ttt) cc_final: 0.7617 (mmt) REVERT: k 188 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8434 (tp-100) REVERT: l 80 LYS cc_start: 0.9495 (tppt) cc_final: 0.9265 (tppp) REVERT: l 120 MET cc_start: 0.8939 (ptm) cc_final: 0.7905 (tmm) REVERT: l 129 ASP cc_start: 0.9400 (p0) cc_final: 0.9150 (p0) REVERT: l 161 MET cc_start: 0.9131 (mmm) cc_final: 0.8747 (mmm) REVERT: n 188 GLN cc_start: 0.9301 (mm-40) cc_final: 0.9039 (mm-40) REVERT: n 371 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8478 (mt-10) REVERT: o 120 MET cc_start: 0.8778 (mtm) cc_final: 0.8406 (mtm) REVERT: o 162 MET cc_start: 0.9440 (mtm) cc_final: 0.8502 (ptp) REVERT: p 32 GLU cc_start: 0.9328 (pt0) cc_final: 0.8877 (pm20) REVERT: u 145 MET cc_start: 0.9181 (mtt) cc_final: 0.8782 (mmm) REVERT: v 22 ASP cc_start: 0.9094 (m-30) cc_final: 0.8819 (m-30) REVERT: v 73 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8465 (pt0) REVERT: v 89 GLN cc_start: 0.8987 (mp10) cc_final: 0.8735 (mp10) REVERT: v 108 PHE cc_start: 0.9147 (m-10) cc_final: 0.8850 (m-80) REVERT: v 115 ASP cc_start: 0.9486 (p0) cc_final: 0.9123 (p0) REVERT: v 117 ASN cc_start: 0.9367 (m110) cc_final: 0.8921 (m110) REVERT: z 67 HIS cc_start: 0.8749 (p-80) cc_final: 0.8473 (p-80) REVERT: z 89 GLN cc_start: 0.9539 (mp10) cc_final: 0.9251 (mp10) REVERT: z 111 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8856 (tm-30) outliers start: 64 outliers final: 24 residues processed: 645 average time/residue: 0.5938 time to fit residues: 627.8381 Evaluate side-chains 522 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 492 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain b residue 357 ASN Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain z residue 22 ASP Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 86 ILE Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 215 optimal weight: 8.9990 chunk 670 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 615 optimal weight: 0.9980 chunk 516 optimal weight: 2.9990 chunk 637 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 271 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 GLN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 HIS N 89 GLN ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 GLN ** T 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 209 GLN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 258 GLN i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035064 restraints weight = 243475.185| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.74 r_work: 0.2501 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56894 Z= 0.276 Angle : 0.590 12.984 77036 Z= 0.303 Chirality : 0.044 0.175 8370 Planarity : 0.004 0.049 10228 Dihedral : 4.265 21.700 7996 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.43 % Allowed : 10.77 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7036 helix: 1.79 (0.16), residues: 1114 sheet: -0.28 (0.11), residues: 2212 loop : -0.28 (0.10), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 272 HIS 0.005 0.001 HIS z 83 PHE 0.024 0.001 PHE B 195 TYR 0.021 0.001 TYR T 194 ARG 0.010 0.000 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 539 time to evaluate : 7.269 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 371 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 161 MET cc_start: 0.9470 (mmm) cc_final: 0.8857 (mmm) REVERT: B 263 LYS cc_start: 0.9415 (ptmt) cc_final: 0.9191 (ptmm) REVERT: D 145 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8684 (mtp) REVERT: E 120 MET cc_start: 0.8135 (mtm) cc_final: 0.6751 (mmt) REVERT: E 131 GLN cc_start: 0.9548 (tm-30) cc_final: 0.9137 (pt0) REVERT: E 161 MET cc_start: 0.9368 (mmm) cc_final: 0.8797 (mmm) REVERT: F 41 GLU cc_start: 0.8867 (mp0) cc_final: 0.8660 (mp0) REVERT: G 276 GLU cc_start: 0.8823 (tt0) cc_final: 0.8587 (tm-30) REVERT: H 145 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9027 (mp0) REVERT: H 161 MET cc_start: 0.9449 (mmm) cc_final: 0.9189 (mmm) REVERT: H 221 LYS cc_start: 0.9266 (tptp) cc_final: 0.9037 (tppt) REVERT: J 182 GLU cc_start: 0.9075 (tt0) cc_final: 0.8768 (tt0) REVERT: J 185 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9138 (pp20) REVERT: J 205 MET cc_start: 0.9513 (tpp) cc_final: 0.8878 (mmm) REVERT: J 353 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8736 (tp30) REVERT: J 357 ASN cc_start: 0.8965 (m110) cc_final: 0.8512 (m110) REVERT: K 112 MET cc_start: 0.8797 (tpp) cc_final: 0.7751 (mmm) REVERT: K 159 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9225 (mppt) REVERT: K 161 MET cc_start: 0.9292 (mmm) cc_final: 0.8970 (mmm) REVERT: M 147 ARG cc_start: 0.8791 (ppt90) cc_final: 0.8391 (ppt170) REVERT: M 371 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8228 (mp0) REVERT: N 54 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8805 (p) REVERT: N 120 MET cc_start: 0.8926 (ttp) cc_final: 0.8104 (tpt) REVERT: N 134 GLN cc_start: 0.9211 (pp30) cc_final: 0.8949 (pp30) REVERT: P 218 GLU cc_start: 0.8931 (tt0) cc_final: 0.8655 (tt0) REVERT: P 371 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8442 (mt-10) REVERT: Q 54 THR cc_start: 0.9172 (m) cc_final: 0.8715 (t) REVERT: Q 112 MET cc_start: 0.8905 (tpt) cc_final: 0.7549 (mmm) REVERT: S 188 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9174 (mm-40) REVERT: T 57 MET cc_start: 0.7343 (pmm) cc_final: 0.7086 (pmm) REVERT: T 73 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8883 (pp20) REVERT: T 120 MET cc_start: 0.8351 (tpt) cc_final: 0.7960 (tpp) REVERT: T 131 GLN cc_start: 0.9544 (tp40) cc_final: 0.9342 (mt0) REVERT: T 263 LYS cc_start: 0.9553 (ptmm) cc_final: 0.9164 (ptmm) REVERT: V 138 TYR cc_start: 0.9644 (t80) cc_final: 0.9235 (t80) REVERT: V 147 ARG cc_start: 0.9433 (ptt90) cc_final: 0.9211 (ptt90) REVERT: W 120 MET cc_start: 0.6995 (mmt) cc_final: 0.6293 (mmm) REVERT: W 150 GLN cc_start: 0.9473 (tm-30) cc_final: 0.9163 (tm-30) REVERT: W 183 LYS cc_start: 0.9551 (ttpt) cc_final: 0.9249 (ttmm) REVERT: X 32 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: Y 353 GLU cc_start: 0.9202 (tp30) cc_final: 0.8950 (tp30) REVERT: Y 357 ASN cc_start: 0.9145 (m-40) cc_final: 0.8680 (m110) REVERT: Y 390 GLU cc_start: 0.8285 (pm20) cc_final: 0.8081 (pm20) REVERT: Z 161 MET cc_start: 0.9209 (mtm) cc_final: 0.8959 (mtp) REVERT: b 143 GLU cc_start: 0.9529 (tp30) cc_final: 0.9171 (tm-30) REVERT: b 190 MET cc_start: 0.9184 (ttp) cc_final: 0.8623 (ttp) REVERT: e 145 MET cc_start: 0.9170 (ttm) cc_final: 0.8934 (ttt) REVERT: e 188 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: e 218 GLU cc_start: 0.9127 (tt0) cc_final: 0.8686 (tt0) REVERT: e 353 GLU cc_start: 0.9242 (tp30) cc_final: 0.9014 (tp30) REVERT: e 390 GLU cc_start: 0.8520 (pp20) cc_final: 0.8097 (pp20) REVERT: f 80 LYS cc_start: 0.9489 (ttpt) cc_final: 0.9202 (pttt) REVERT: f 227 MET cc_start: 0.9485 (tpp) cc_final: 0.9263 (tpp) REVERT: f 263 LYS cc_start: 0.9403 (ptmm) cc_final: 0.8914 (ptmm) REVERT: h 205 MET cc_start: 0.9645 (tpp) cc_final: 0.9201 (mpp) REVERT: i 161 MET cc_start: 0.9513 (mmm) cc_final: 0.9278 (mmm) REVERT: k 145 MET cc_start: 0.8540 (ttt) cc_final: 0.7710 (mmt) REVERT: k 147 ARG cc_start: 0.9383 (ttp-110) cc_final: 0.9179 (ptt90) REVERT: l 80 LYS cc_start: 0.9559 (tppt) cc_final: 0.9350 (tppp) REVERT: l 120 MET cc_start: 0.8928 (ptm) cc_final: 0.8044 (tmm) REVERT: l 129 ASP cc_start: 0.9388 (p0) cc_final: 0.9161 (p0) REVERT: n 188 GLN cc_start: 0.9357 (mm-40) cc_final: 0.8958 (mm-40) REVERT: n 315 MET cc_start: 0.9241 (tpp) cc_final: 0.9032 (tmm) REVERT: n 371 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8276 (mt-10) REVERT: o 120 MET cc_start: 0.8985 (mtm) cc_final: 0.8633 (mtm) REVERT: o 162 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.7834 (ptp) REVERT: p 32 GLU cc_start: 0.9260 (pt0) cc_final: 0.8597 (pm20) REVERT: u 145 MET cc_start: 0.9166 (mtt) cc_final: 0.8887 (mtp) REVERT: u 147 ARG cc_start: 0.9536 (ptt-90) cc_final: 0.9310 (ptt-90) REVERT: v 22 ASP cc_start: 0.9080 (m-30) cc_final: 0.8738 (m-30) REVERT: v 73 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8585 (pt0) REVERT: v 91 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9135 (tp30) REVERT: v 108 PHE cc_start: 0.9214 (m-10) cc_final: 0.8933 (m-80) REVERT: v 115 ASP cc_start: 0.9466 (p0) cc_final: 0.9221 (p0) REVERT: v 117 ASN cc_start: 0.9365 (m110) cc_final: 0.8993 (m-40) REVERT: z 47 ASP cc_start: 0.8843 (p0) cc_final: 0.8625 (p0) REVERT: z 57 MET cc_start: 0.7977 (mpp) cc_final: 0.7635 (mmt) REVERT: z 63 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8871 (mm-40) REVERT: z 67 HIS cc_start: 0.8917 (p-80) cc_final: 0.8638 (p-80) REVERT: z 89 GLN cc_start: 0.9586 (mt0) cc_final: 0.9296 (mp10) outliers start: 84 outliers final: 44 residues processed: 593 average time/residue: 0.5838 time to fit residues: 575.5083 Evaluate side-chains 518 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 467 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 228 MET Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain z residue 22 ASP Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 619 optimal weight: 5.9990 chunk 416 optimal weight: 2.9990 chunk 263 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 658 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 339 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 458 optimal weight: 4.9990 chunk 191 optimal weight: 0.0570 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS D 188 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.055199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.034569 restraints weight = 242606.440| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.74 r_work: 0.2480 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 56894 Z= 0.257 Angle : 0.562 11.759 77036 Z= 0.288 Chirality : 0.043 0.188 8370 Planarity : 0.004 0.051 10228 Dihedral : 4.108 21.183 7996 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.84 % Allowed : 11.80 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 7036 helix: 1.94 (0.16), residues: 1122 sheet: -0.13 (0.12), residues: 2110 loop : -0.18 (0.10), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 272 HIS 0.005 0.001 HIS W 67 PHE 0.024 0.001 PHE B 195 TYR 0.018 0.001 TYR T 194 ARG 0.012 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 503 time to evaluate : 5.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8569 (mt-10) REVERT: B 161 MET cc_start: 0.9467 (mmm) cc_final: 0.8823 (mmm) REVERT: C 28 ASP cc_start: 0.9186 (p0) cc_final: 0.8952 (t0) REVERT: D 145 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8762 (mtp) REVERT: E 120 MET cc_start: 0.8243 (mtm) cc_final: 0.6871 (mmt) REVERT: E 131 GLN cc_start: 0.9450 (tm-30) cc_final: 0.9247 (mt0) REVERT: G 139 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8816 (pp20) REVERT: G 276 GLU cc_start: 0.8858 (tt0) cc_final: 0.8601 (tm-30) REVERT: H 145 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9032 (mp0) REVERT: H 161 MET cc_start: 0.9472 (mmm) cc_final: 0.9104 (mmm) REVERT: H 221 LYS cc_start: 0.9256 (tptp) cc_final: 0.9006 (tppt) REVERT: J 371 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8550 (mt-10) REVERT: K 63 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8736 (mm-40) REVERT: K 112 MET cc_start: 0.8910 (tpp) cc_final: 0.7632 (mmm) REVERT: K 159 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9205 (mppt) REVERT: K 161 MET cc_start: 0.9298 (mmm) cc_final: 0.8898 (mmm) REVERT: M 185 GLU cc_start: 0.9377 (pp20) cc_final: 0.9163 (pp20) REVERT: M 371 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8273 (mp0) REVERT: N 54 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8873 (p) REVERT: N 112 MET cc_start: 0.8621 (mmm) cc_final: 0.8374 (tpt) REVERT: N 120 MET cc_start: 0.8942 (ttp) cc_final: 0.8188 (tpt) REVERT: N 134 GLN cc_start: 0.9204 (pp30) cc_final: 0.8933 (pp30) REVERT: O 28 ASP cc_start: 0.9438 (p0) cc_final: 0.8698 (t0) REVERT: P 218 GLU cc_start: 0.8861 (tt0) cc_final: 0.8565 (tt0) REVERT: P 371 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8392 (mt-10) REVERT: Q 112 MET cc_start: 0.8868 (tpt) cc_final: 0.7481 (mmm) REVERT: Q 120 MET cc_start: 0.7796 (mtt) cc_final: 0.7405 (mtt) REVERT: Q 161 MET cc_start: 0.9118 (mpp) cc_final: 0.8523 (mmm) REVERT: S 371 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8351 (mt-10) REVERT: T 57 MET cc_start: 0.7459 (pmm) cc_final: 0.7179 (pmm) REVERT: T 73 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8906 (pp20) REVERT: T 112 MET cc_start: 0.7066 (mmm) cc_final: 0.6763 (mmm) REVERT: T 120 MET cc_start: 0.8418 (tpt) cc_final: 0.8053 (tpp) REVERT: T 263 LYS cc_start: 0.9591 (ptmm) cc_final: 0.9188 (ptmm) REVERT: V 138 TYR cc_start: 0.9653 (t80) cc_final: 0.9233 (t80) REVERT: V 144 ARG cc_start: 0.9524 (mtp-110) cc_final: 0.9245 (mtm110) REVERT: V 147 ARG cc_start: 0.9328 (ptt90) cc_final: 0.8988 (ptt90) REVERT: V 188 GLN cc_start: 0.9411 (mm-40) cc_final: 0.9176 (mm-40) REVERT: W 120 MET cc_start: 0.7348 (mmp) cc_final: 0.6847 (mmm) REVERT: W 150 GLN cc_start: 0.9467 (tm-30) cc_final: 0.9074 (tm-30) REVERT: W 183 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9329 (ttmm) REVERT: Y 357 ASN cc_start: 0.9126 (m-40) cc_final: 0.8696 (m110) REVERT: b 182 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8368 (tm-30) REVERT: b 190 MET cc_start: 0.9159 (ttp) cc_final: 0.8685 (ttp) REVERT: c 161 MET cc_start: 0.9275 (mmm) cc_final: 0.9054 (mmm) REVERT: e 185 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8833 (tm-30) REVERT: e 188 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: e 390 GLU cc_start: 0.8521 (pp20) cc_final: 0.8101 (pp20) REVERT: f 80 LYS cc_start: 0.9482 (ttpt) cc_final: 0.9180 (pttt) REVERT: f 161 MET cc_start: 0.9437 (mmm) cc_final: 0.9220 (mmm) REVERT: f 263 LYS cc_start: 0.9441 (ptmm) cc_final: 0.9016 (ttpp) REVERT: h 205 MET cc_start: 0.9617 (tpp) cc_final: 0.9160 (mpp) REVERT: i 120 MET cc_start: 0.8811 (ttp) cc_final: 0.8374 (ttp) REVERT: i 159 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9262 (mmtm) REVERT: i 161 MET cc_start: 0.9513 (mmm) cc_final: 0.9305 (mmm) REVERT: i 263 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9185 (ttpp) REVERT: j 32 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8808 (pm20) REVERT: k 145 MET cc_start: 0.8565 (ttt) cc_final: 0.7812 (mmt) REVERT: k 147 ARG cc_start: 0.9354 (ttp-110) cc_final: 0.8910 (ptt90) REVERT: k 188 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8699 (tp-100) REVERT: l 120 MET cc_start: 0.8995 (ptm) cc_final: 0.8149 (tmm) REVERT: l 162 MET cc_start: 0.9336 (ptp) cc_final: 0.8930 (ptp) REVERT: n 188 GLN cc_start: 0.9400 (mm-40) cc_final: 0.9078 (mm-40) REVERT: n 315 MET cc_start: 0.9222 (tpp) cc_final: 0.9010 (tmm) REVERT: n 371 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8313 (mt-10) REVERT: o 120 MET cc_start: 0.9055 (mtm) cc_final: 0.8818 (mtm) REVERT: o 162 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8848 (ptp) REVERT: p 32 GLU cc_start: 0.9295 (pt0) cc_final: 0.8835 (pm20) REVERT: u 144 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8640 (ttp-110) REVERT: u 145 MET cc_start: 0.9101 (mtt) cc_final: 0.8736 (mtt) REVERT: v 22 ASP cc_start: 0.9108 (m-30) cc_final: 0.8788 (m-30) REVERT: v 73 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8419 (pt0) REVERT: v 91 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9064 (tp30) REVERT: v 108 PHE cc_start: 0.9278 (m-10) cc_final: 0.9012 (m-80) REVERT: v 115 ASP cc_start: 0.9461 (p0) cc_final: 0.8927 (p0) REVERT: v 117 ASN cc_start: 0.9354 (m110) cc_final: 0.8769 (m-40) REVERT: z 29 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7591 (t80) REVERT: z 47 ASP cc_start: 0.8746 (p0) cc_final: 0.8511 (p0) REVERT: z 57 MET cc_start: 0.8118 (mpp) cc_final: 0.7760 (mmt) REVERT: z 63 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8788 (mm-40) REVERT: z 67 HIS cc_start: 0.8930 (p-80) cc_final: 0.8367 (p-80) REVERT: z 89 GLN cc_start: 0.9618 (mt0) cc_final: 0.9264 (mp10) outliers start: 108 outliers final: 59 residues processed: 581 average time/residue: 0.5532 time to fit residues: 538.8828 Evaluate side-chains 526 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 457 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 147 ARG Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 228 MET Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 22 ASP Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 584 optimal weight: 0.8980 chunk 659 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 417 optimal weight: 8.9990 chunk 687 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 602 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 512 optimal weight: 20.0000 chunk 353 optimal weight: 0.8980 chunk 445 optimal weight: 0.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS J 357 ASN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 284 ASN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN i 150 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.034561 restraints weight = 242026.456| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 3.73 r_work: 0.2479 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 56894 Z= 0.220 Angle : 0.549 11.320 77036 Z= 0.280 Chirality : 0.043 0.180 8370 Planarity : 0.004 0.053 10228 Dihedral : 3.993 25.940 7996 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.95 % Allowed : 12.77 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.10), residues: 7036 helix: 1.93 (0.16), residues: 1132 sheet: 0.02 (0.12), residues: 2067 loop : -0.15 (0.10), residues: 3837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 272 HIS 0.003 0.001 HIS T 83 PHE 0.024 0.001 PHE B 195 TYR 0.026 0.001 TYR c 64 ARG 0.006 0.000 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 489 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 161 MET cc_start: 0.9512 (mmm) cc_final: 0.8866 (mmm) REVERT: C 28 ASP cc_start: 0.9169 (p0) cc_final: 0.8948 (t0) REVERT: D 145 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8799 (mtp) REVERT: E 120 MET cc_start: 0.8425 (mtm) cc_final: 0.7086 (mmt) REVERT: G 139 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8854 (pp20) REVERT: G 276 GLU cc_start: 0.8868 (tt0) cc_final: 0.8615 (tm-30) REVERT: G 390 GLU cc_start: 0.8968 (pt0) cc_final: 0.8450 (pm20) REVERT: H 145 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9036 (mp0) REVERT: H 161 MET cc_start: 0.9487 (mmm) cc_final: 0.9208 (mmm) REVERT: H 221 LYS cc_start: 0.9239 (tptp) cc_final: 0.8978 (tppt) REVERT: J 145 MET cc_start: 0.9060 (ttt) cc_final: 0.8613 (ppp) REVERT: J 205 MET cc_start: 0.9516 (tpp) cc_final: 0.8995 (mmm) REVERT: J 371 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8577 (mt-10) REVERT: K 63 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8771 (mm-40) REVERT: K 112 MET cc_start: 0.8857 (tpp) cc_final: 0.7540 (mmm) REVERT: K 159 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9172 (mppt) REVERT: K 161 MET cc_start: 0.9292 (mmm) cc_final: 0.8927 (mmm) REVERT: M 185 GLU cc_start: 0.9375 (pp20) cc_final: 0.9171 (pp20) REVERT: M 371 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8324 (mp0) REVERT: N 54 THR cc_start: 0.9159 (m) cc_final: 0.8900 (p) REVERT: N 112 MET cc_start: 0.8663 (mmm) cc_final: 0.8410 (tpt) REVERT: N 120 MET cc_start: 0.8947 (ttp) cc_final: 0.8217 (tpt) REVERT: N 134 GLN cc_start: 0.9246 (pp30) cc_final: 0.8992 (pp30) REVERT: N 227 MET cc_start: 0.9309 (tpp) cc_final: 0.9006 (tpp) REVERT: O 28 ASP cc_start: 0.9457 (p0) cc_final: 0.8809 (t0) REVERT: P 218 GLU cc_start: 0.8864 (tt0) cc_final: 0.8601 (tt0) REVERT: P 371 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8384 (mt-10) REVERT: P 390 GLU cc_start: 0.8810 (pp20) cc_final: 0.8607 (tm-30) REVERT: Q 54 THR cc_start: 0.8987 (p) cc_final: 0.8764 (t) REVERT: Q 112 MET cc_start: 0.8811 (tpt) cc_final: 0.7396 (mmm) REVERT: Q 120 MET cc_start: 0.8076 (mtt) cc_final: 0.7731 (mtt) REVERT: Q 161 MET cc_start: 0.9170 (mpp) cc_final: 0.8581 (mmm) REVERT: S 371 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8323 (mt-10) REVERT: T 57 MET cc_start: 0.7721 (pmm) cc_final: 0.7415 (pmm) REVERT: T 73 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8980 (pp20) REVERT: T 112 MET cc_start: 0.7127 (mmm) cc_final: 0.6879 (mmm) REVERT: T 120 MET cc_start: 0.8458 (tpt) cc_final: 0.8129 (tpp) REVERT: T 263 LYS cc_start: 0.9598 (ptmm) cc_final: 0.9210 (ptmm) REVERT: V 138 TYR cc_start: 0.9662 (t80) cc_final: 0.9243 (t80) REVERT: W 150 GLN cc_start: 0.9461 (tm-30) cc_final: 0.9033 (tm-30) REVERT: X 30 ASN cc_start: 0.8596 (p0) cc_final: 0.8116 (p0) REVERT: X 32 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8644 (pm20) REVERT: X 41 GLU cc_start: 0.9068 (mp0) cc_final: 0.8811 (mp0) REVERT: Y 357 ASN cc_start: 0.9108 (m-40) cc_final: 0.8695 (m110) REVERT: Z 161 MET cc_start: 0.9213 (mtm) cc_final: 0.8899 (mtm) REVERT: b 190 MET cc_start: 0.9149 (ttp) cc_final: 0.8719 (ttp) REVERT: b 205 MET cc_start: 0.9593 (mmm) cc_final: 0.8517 (mmm) REVERT: c 63 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8660 (tm-30) REVERT: e 185 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8810 (tm-30) REVERT: e 188 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8321 (mp10) REVERT: e 218 GLU cc_start: 0.9146 (tt0) cc_final: 0.8737 (tt0) REVERT: e 276 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8594 (tm-30) REVERT: e 390 GLU cc_start: 0.8548 (pp20) cc_final: 0.8142 (pp20) REVERT: f 63 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9047 (tm-30) REVERT: f 162 MET cc_start: 0.8998 (ptp) cc_final: 0.8668 (ptp) REVERT: f 263 LYS cc_start: 0.9491 (ptmm) cc_final: 0.9077 (ttpp) REVERT: h 205 MET cc_start: 0.9611 (tpp) cc_final: 0.9151 (mpp) REVERT: i 120 MET cc_start: 0.8819 (ttp) cc_final: 0.8383 (ttp) REVERT: i 159 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9252 (mmtm) REVERT: i 263 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9203 (ttpp) REVERT: j 32 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: k 145 MET cc_start: 0.8496 (ttt) cc_final: 0.7651 (mmt) REVERT: k 147 ARG cc_start: 0.9388 (ttp-110) cc_final: 0.8949 (ptt90) REVERT: k 212 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8981 (mm-40) REVERT: l 120 MET cc_start: 0.9051 (ptm) cc_final: 0.8268 (tmm) REVERT: n 182 GLU cc_start: 0.9020 (tt0) cc_final: 0.8819 (tt0) REVERT: n 186 LYS cc_start: 0.9658 (ttmm) cc_final: 0.9403 (ttmm) REVERT: n 188 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9032 (mm-40) REVERT: n 371 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8348 (mt-10) REVERT: o 120 MET cc_start: 0.9064 (mtm) cc_final: 0.8826 (mtm) REVERT: o 162 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.7750 (ptp) REVERT: p 32 GLU cc_start: 0.9292 (pt0) cc_final: 0.8647 (pm20) REVERT: u 144 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8675 (ttp-110) REVERT: u 145 MET cc_start: 0.9081 (mtt) cc_final: 0.8711 (mtt) REVERT: u 151 THR cc_start: 0.9225 (p) cc_final: 0.8904 (m) REVERT: v 22 ASP cc_start: 0.9179 (m-30) cc_final: 0.8878 (m-30) REVERT: v 73 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8551 (pt0) REVERT: v 91 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9074 (tp30) REVERT: v 108 PHE cc_start: 0.9269 (m-10) cc_final: 0.9059 (m-80) REVERT: v 115 ASP cc_start: 0.9453 (p0) cc_final: 0.8920 (p0) REVERT: v 117 ASN cc_start: 0.9393 (m110) cc_final: 0.8861 (m-40) REVERT: z 29 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7724 (t80) REVERT: z 57 MET cc_start: 0.8110 (mpp) cc_final: 0.6986 (mmm) REVERT: z 58 LEU cc_start: 0.9287 (mm) cc_final: 0.8993 (tp) REVERT: z 60 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9392 (mm-30) REVERT: z 63 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8870 (mm-40) REVERT: z 67 HIS cc_start: 0.8821 (p-80) cc_final: 0.8376 (p90) REVERT: z 89 GLN cc_start: 0.9621 (mt0) cc_final: 0.9265 (mp10) outliers start: 114 outliers final: 64 residues processed: 578 average time/residue: 0.5621 time to fit residues: 542.3880 Evaluate side-chains 533 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 459 time to evaluate : 5.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 147 ARG Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 150 GLN Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 389 optimal weight: 6.9990 chunk 459 optimal weight: 40.0000 chunk 357 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 543 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 95 optimal weight: 0.0970 chunk 360 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 GLN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.034515 restraints weight = 241682.989| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.73 r_work: 0.2479 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 56894 Z= 0.210 Angle : 0.546 12.735 77036 Z= 0.279 Chirality : 0.043 0.164 8370 Planarity : 0.004 0.060 10228 Dihedral : 3.921 23.735 7996 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.72 % Allowed : 13.74 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7036 helix: 1.91 (0.16), residues: 1131 sheet: 0.09 (0.12), residues: 2059 loop : -0.11 (0.10), residues: 3846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 272 HIS 0.003 0.001 HIS T 83 PHE 0.023 0.001 PHE B 195 TYR 0.019 0.001 TYR c 64 ARG 0.010 0.000 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 493 time to evaluate : 5.222 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 371 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8467 (mt-10) REVERT: B 152 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8690 (t) REVERT: B 161 MET cc_start: 0.9501 (mmm) cc_final: 0.8814 (mmm) REVERT: C 28 ASP cc_start: 0.9163 (p0) cc_final: 0.8950 (t0) REVERT: D 145 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8823 (mtp) REVERT: D 188 GLN cc_start: 0.9334 (tt0) cc_final: 0.8888 (tm-30) REVERT: E 57 MET cc_start: 0.7193 (mmm) cc_final: 0.6691 (mmm) REVERT: E 120 MET cc_start: 0.8427 (mtm) cc_final: 0.7105 (mmt) REVERT: E 161 MET cc_start: 0.9339 (mmm) cc_final: 0.9112 (mmm) REVERT: F 41 GLU cc_start: 0.8892 (mp0) cc_final: 0.8686 (mp0) REVERT: G 139 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8838 (pp20) REVERT: G 276 GLU cc_start: 0.8857 (tt0) cc_final: 0.8621 (tm-30) REVERT: G 390 GLU cc_start: 0.8962 (pt0) cc_final: 0.8431 (pm20) REVERT: H 145 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9058 (mp0) REVERT: H 161 MET cc_start: 0.9477 (mmm) cc_final: 0.9178 (mmm) REVERT: H 221 LYS cc_start: 0.9241 (tptp) cc_final: 0.8974 (tppt) REVERT: J 145 MET cc_start: 0.9032 (ttt) cc_final: 0.8692 (ppp) REVERT: J 205 MET cc_start: 0.9501 (tpp) cc_final: 0.8980 (mmm) REVERT: J 371 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8593 (mt-10) REVERT: K 63 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8780 (mm-40) REVERT: K 112 MET cc_start: 0.8832 (tpp) cc_final: 0.8470 (tpp) REVERT: K 161 MET cc_start: 0.9284 (mmm) cc_final: 0.8890 (mmm) REVERT: K 221 LYS cc_start: 0.9319 (tptt) cc_final: 0.9037 (tptp) REVERT: M 185 GLU cc_start: 0.9368 (pp20) cc_final: 0.9146 (pp20) REVERT: M 357 ASN cc_start: 0.8759 (m110) cc_final: 0.8462 (m110) REVERT: M 371 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8358 (mp0) REVERT: N 54 THR cc_start: 0.9133 (m) cc_final: 0.8880 (p) REVERT: N 112 MET cc_start: 0.8660 (mmm) cc_final: 0.8363 (tpt) REVERT: N 120 MET cc_start: 0.8990 (ttp) cc_final: 0.8294 (tpt) REVERT: N 134 GLN cc_start: 0.9242 (pp30) cc_final: 0.8976 (pp30) REVERT: O 28 ASP cc_start: 0.9431 (p0) cc_final: 0.8787 (t0) REVERT: P 147 ARG cc_start: 0.9351 (ttp-110) cc_final: 0.9001 (ttp-110) REVERT: P 190 MET cc_start: 0.8927 (ttm) cc_final: 0.8678 (ttm) REVERT: P 218 GLU cc_start: 0.8885 (tt0) cc_final: 0.8635 (tt0) REVERT: P 371 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8375 (mt-10) REVERT: P 390 GLU cc_start: 0.8826 (pp20) cc_final: 0.8620 (tm-30) REVERT: Q 112 MET cc_start: 0.8738 (tpt) cc_final: 0.7656 (mmm) REVERT: Q 120 MET cc_start: 0.8154 (mtt) cc_final: 0.7703 (mtt) REVERT: Q 161 MET cc_start: 0.9223 (mpp) cc_final: 0.8656 (mmm) REVERT: S 371 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8338 (mt-10) REVERT: S 374 ASN cc_start: 0.8962 (t0) cc_final: 0.8724 (t0) REVERT: T 57 MET cc_start: 0.7688 (pmm) cc_final: 0.7336 (pmm) REVERT: T 73 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8933 (pt0) REVERT: T 112 MET cc_start: 0.7091 (mmm) cc_final: 0.6817 (mmm) REVERT: T 120 MET cc_start: 0.8428 (tpt) cc_final: 0.8137 (tpp) REVERT: T 161 MET cc_start: 0.9196 (tpp) cc_final: 0.8987 (mmm) REVERT: T 263 LYS cc_start: 0.9601 (ptmm) cc_final: 0.9379 (ttpp) REVERT: V 138 TYR cc_start: 0.9665 (t80) cc_final: 0.9268 (t80) REVERT: V 145 MET cc_start: 0.8247 (ttt) cc_final: 0.7986 (tmm) REVERT: V 147 ARG cc_start: 0.9210 (ptt90) cc_final: 0.8940 (ptt90) REVERT: V 218 GLU cc_start: 0.9167 (tt0) cc_final: 0.8959 (tt0) REVERT: W 150 GLN cc_start: 0.9452 (tm-30) cc_final: 0.8995 (tm-30) REVERT: X 30 ASN cc_start: 0.8601 (p0) cc_final: 0.8121 (p0) REVERT: X 32 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8721 (pm20) REVERT: Y 357 ASN cc_start: 0.9114 (m-40) cc_final: 0.8707 (m110) REVERT: Z 161 MET cc_start: 0.9178 (mtm) cc_final: 0.8839 (mmm) REVERT: b 182 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8459 (tm-30) REVERT: b 190 MET cc_start: 0.9163 (ttp) cc_final: 0.8736 (ttp) REVERT: c 80 LYS cc_start: 0.9527 (ttpt) cc_final: 0.9254 (ttpt) REVERT: c 111 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8725 (tm-30) REVERT: e 185 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8792 (tm-30) REVERT: e 188 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8321 (mp10) REVERT: e 218 GLU cc_start: 0.9162 (tt0) cc_final: 0.8721 (tt0) REVERT: e 390 GLU cc_start: 0.8526 (pp20) cc_final: 0.8132 (pp20) REVERT: f 63 GLN cc_start: 0.9271 (tm-30) cc_final: 0.9051 (tm-30) REVERT: f 162 MET cc_start: 0.8981 (ptp) cc_final: 0.8658 (ptp) REVERT: f 263 LYS cc_start: 0.9499 (ptmm) cc_final: 0.9227 (ptmm) REVERT: h 205 MET cc_start: 0.9582 (tpp) cc_final: 0.9133 (mpp) REVERT: i 120 MET cc_start: 0.8874 (ttp) cc_final: 0.8459 (ttp) REVERT: i 150 GLN cc_start: 0.9556 (OUTLIER) cc_final: 0.9333 (pp30) REVERT: i 159 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9291 (mmtm) REVERT: i 263 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9195 (ttpp) REVERT: j 32 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8646 (pm20) REVERT: k 145 MET cc_start: 0.8440 (ttt) cc_final: 0.7650 (mmt) REVERT: k 147 ARG cc_start: 0.9387 (ttp-110) cc_final: 0.8945 (ptt90) REVERT: l 120 MET cc_start: 0.9075 (ptm) cc_final: 0.8292 (tmm) REVERT: l 161 MET cc_start: 0.9229 (mmm) cc_final: 0.8440 (mmm) REVERT: n 188 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9055 (mm-40) REVERT: n 371 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8384 (mt-10) REVERT: o 120 MET cc_start: 0.9108 (mtm) cc_final: 0.8865 (mtm) REVERT: o 162 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.7704 (ptp) REVERT: p 32 GLU cc_start: 0.9294 (pt0) cc_final: 0.8455 (pm20) REVERT: u 144 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8816 (ttp-110) REVERT: u 145 MET cc_start: 0.9099 (mtt) cc_final: 0.8722 (mtt) REVERT: u 147 ARG cc_start: 0.9585 (ptt-90) cc_final: 0.9180 (ptt90) REVERT: v 22 ASP cc_start: 0.9189 (m-30) cc_final: 0.8879 (m-30) REVERT: v 73 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8597 (pt0) REVERT: v 91 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9119 (tp30) REVERT: v 108 PHE cc_start: 0.9262 (m-10) cc_final: 0.9044 (m-80) REVERT: v 115 ASP cc_start: 0.9433 (p0) cc_final: 0.8888 (p0) REVERT: v 117 ASN cc_start: 0.9417 (m110) cc_final: 0.8883 (m-40) REVERT: z 29 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7743 (t80) REVERT: z 60 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9387 (mm-30) REVERT: z 63 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8593 (mm-40) REVERT: z 77 PHE cc_start: 0.9115 (t80) cc_final: 0.8828 (t80) REVERT: z 89 GLN cc_start: 0.9622 (mt0) cc_final: 0.9259 (mp10) outliers start: 101 outliers final: 69 residues processed: 573 average time/residue: 0.5608 time to fit residues: 536.7548 Evaluate side-chains 540 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 459 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 67 HIS Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 190 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain i residue 150 GLN Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 208 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 556 optimal weight: 30.0000 chunk 580 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 221 optimal weight: 0.0670 chunk 142 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 271 GLN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN i 150 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033765 restraints weight = 243934.665| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 3.71 r_work: 0.2451 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 56894 Z= 0.286 Angle : 0.570 11.991 77036 Z= 0.291 Chirality : 0.043 0.182 8370 Planarity : 0.004 0.052 10228 Dihedral : 3.947 20.880 7996 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.00 % Allowed : 14.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7036 helix: 1.96 (0.16), residues: 1131 sheet: 0.11 (0.12), residues: 2041 loop : -0.07 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 272 HIS 0.004 0.001 HIS N 67 PHE 0.021 0.001 PHE B 195 TYR 0.023 0.001 TYR W 64 ARG 0.016 0.000 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 477 time to evaluate : 5.105 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 138 TYR cc_start: 0.9432 (OUTLIER) cc_final: 0.9175 (t80) REVERT: A 371 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 134 GLN cc_start: 0.9149 (mp10) cc_final: 0.8828 (mm110) REVERT: B 161 MET cc_start: 0.9492 (mmm) cc_final: 0.8863 (mmm) REVERT: C 28 ASP cc_start: 0.9175 (p0) cc_final: 0.8970 (t0) REVERT: D 145 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8815 (mtp) REVERT: E 120 MET cc_start: 0.8505 (mtm) cc_final: 0.7236 (mmt) REVERT: E 161 MET cc_start: 0.9339 (mmm) cc_final: 0.9065 (mmm) REVERT: G 139 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8847 (pp20) REVERT: G 276 GLU cc_start: 0.8885 (tt0) cc_final: 0.8567 (tm-30) REVERT: G 390 GLU cc_start: 0.8973 (pt0) cc_final: 0.8426 (pm20) REVERT: H 145 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9054 (mp0) REVERT: H 161 MET cc_start: 0.9475 (mmm) cc_final: 0.9089 (mmm) REVERT: J 145 MET cc_start: 0.9064 (ttt) cc_final: 0.8619 (ppp) REVERT: J 205 MET cc_start: 0.9553 (tpp) cc_final: 0.8990 (mmm) REVERT: J 371 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8603 (mt-10) REVERT: J 390 GLU cc_start: 0.8979 (pt0) cc_final: 0.8689 (pp20) REVERT: K 63 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8748 (mm-40) REVERT: K 161 MET cc_start: 0.9310 (mmm) cc_final: 0.8898 (mmm) REVERT: M 182 GLU cc_start: 0.9104 (tt0) cc_final: 0.8894 (tt0) REVERT: M 185 GLU cc_start: 0.9373 (pp20) cc_final: 0.9145 (pp20) REVERT: M 357 ASN cc_start: 0.8743 (m110) cc_final: 0.8447 (m110) REVERT: M 371 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8329 (mp0) REVERT: N 54 THR cc_start: 0.9268 (m) cc_final: 0.9044 (p) REVERT: N 98 ILE cc_start: 0.8907 (mt) cc_final: 0.8370 (tt) REVERT: N 112 MET cc_start: 0.8691 (mmm) cc_final: 0.8422 (tpt) REVERT: N 134 GLN cc_start: 0.9243 (pp30) cc_final: 0.8974 (pp30) REVERT: O 28 ASP cc_start: 0.9434 (p0) cc_final: 0.8786 (t0) REVERT: P 147 ARG cc_start: 0.9276 (ttp-110) cc_final: 0.8909 (ttp-110) REVERT: P 190 MET cc_start: 0.9050 (ttm) cc_final: 0.8742 (ttm) REVERT: P 218 GLU cc_start: 0.8912 (tt0) cc_final: 0.8653 (tt0) REVERT: P 371 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8406 (mt-10) REVERT: Q 112 MET cc_start: 0.9045 (tpt) cc_final: 0.7617 (mmm) REVERT: Q 161 MET cc_start: 0.9261 (mpp) cc_final: 0.8734 (mmm) REVERT: R 30 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7581 (p0) REVERT: T 57 MET cc_start: 0.7827 (pmm) cc_final: 0.7411 (pmm) REVERT: T 73 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8960 (pt0) REVERT: T 120 MET cc_start: 0.8511 (tpt) cc_final: 0.8243 (tpp) REVERT: T 161 MET cc_start: 0.9185 (tpp) cc_final: 0.8528 (mpp) REVERT: T 263 LYS cc_start: 0.9588 (ptmm) cc_final: 0.9383 (ttpp) REVERT: V 138 TYR cc_start: 0.9687 (t80) cc_final: 0.9305 (t80) REVERT: V 147 ARG cc_start: 0.9202 (ptt90) cc_final: 0.8948 (ptt90) REVERT: V 218 GLU cc_start: 0.9184 (tt0) cc_final: 0.8984 (tt0) REVERT: W 150 GLN cc_start: 0.9462 (tm-30) cc_final: 0.8993 (tm-30) REVERT: X 30 ASN cc_start: 0.8574 (p0) cc_final: 0.8070 (p0) REVERT: X 32 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: Y 357 ASN cc_start: 0.9110 (m-40) cc_final: 0.8709 (m110) REVERT: Z 161 MET cc_start: 0.9186 (mtm) cc_final: 0.8865 (mmm) REVERT: b 182 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8494 (tm-30) REVERT: b 190 MET cc_start: 0.9225 (ttp) cc_final: 0.8826 (ttp) REVERT: b 205 MET cc_start: 0.9587 (mmm) cc_final: 0.8533 (mmm) REVERT: c 111 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8720 (tm-30) REVERT: e 185 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8805 (tm-30) REVERT: e 188 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: e 218 GLU cc_start: 0.9185 (tt0) cc_final: 0.8739 (tt0) REVERT: e 390 GLU cc_start: 0.8535 (pp20) cc_final: 0.8277 (pp20) REVERT: f 80 LYS cc_start: 0.9433 (ttpt) cc_final: 0.9201 (ttpt) REVERT: f 161 MET cc_start: 0.9320 (mmm) cc_final: 0.9116 (mmm) REVERT: f 263 LYS cc_start: 0.9510 (ptmm) cc_final: 0.9225 (ptmm) REVERT: h 147 ARG cc_start: 0.9336 (ttp-110) cc_final: 0.8837 (ptt90) REVERT: h 205 MET cc_start: 0.9619 (tpp) cc_final: 0.9136 (mpp) REVERT: i 120 MET cc_start: 0.8892 (ttp) cc_final: 0.8495 (ttp) REVERT: i 159 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9280 (mmtm) REVERT: i 263 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9162 (ttpp) REVERT: j 32 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: k 145 MET cc_start: 0.8418 (ttt) cc_final: 0.7574 (mmt) REVERT: k 186 LYS cc_start: 0.9549 (mttm) cc_final: 0.9096 (mtpp) REVERT: l 120 MET cc_start: 0.9194 (ptm) cc_final: 0.8403 (tmm) REVERT: l 161 MET cc_start: 0.9288 (mmm) cc_final: 0.8900 (mmm) REVERT: n 188 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9124 (mm-40) REVERT: n 371 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8425 (mt-10) REVERT: o 120 MET cc_start: 0.9106 (mtm) cc_final: 0.8805 (mtm) REVERT: o 162 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.7864 (ptp) REVERT: p 32 GLU cc_start: 0.9351 (pt0) cc_final: 0.8814 (pm20) REVERT: u 144 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8878 (ttp-110) REVERT: u 147 ARG cc_start: 0.9576 (ptt-90) cc_final: 0.9120 (ptt90) REVERT: v 22 ASP cc_start: 0.9168 (m-30) cc_final: 0.8846 (m-30) REVERT: v 73 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8455 (pt0) REVERT: v 91 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9140 (tp30) REVERT: v 115 ASP cc_start: 0.9449 (p0) cc_final: 0.9048 (p0) REVERT: v 117 ASN cc_start: 0.9385 (m110) cc_final: 0.8932 (m-40) REVERT: z 29 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7794 (t80) REVERT: z 63 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8687 (mm-40) REVERT: z 77 PHE cc_start: 0.9132 (t80) cc_final: 0.8747 (t80) REVERT: z 89 GLN cc_start: 0.9574 (mt0) cc_final: 0.9212 (mp10) outliers start: 117 outliers final: 81 residues processed: 566 average time/residue: 0.5397 time to fit residues: 514.5919 Evaluate side-chains 543 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 450 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 67 HIS Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain c residue 253 THR Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 190 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain i residue 150 GLN Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 231 CYS Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 66 THR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 236 optimal weight: 0.0070 chunk 448 optimal weight: 5.9990 chunk 447 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 551 optimal weight: 30.0000 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 519 optimal weight: 10.0000 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN N 111 GLN ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 188 GLN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN i 150 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.033820 restraints weight = 242971.828| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.69 r_work: 0.2454 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 56894 Z= 0.247 Angle : 0.573 13.301 77036 Z= 0.292 Chirality : 0.043 0.179 8370 Planarity : 0.004 0.052 10228 Dihedral : 3.930 26.650 7996 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 14.44 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.10), residues: 7036 helix: 1.96 (0.16), residues: 1139 sheet: 0.16 (0.12), residues: 2001 loop : -0.07 (0.10), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 272 HIS 0.004 0.001 HIS T 83 PHE 0.022 0.001 PHE B 195 TYR 0.024 0.001 TYR k 138 ARG 0.007 0.000 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 459 time to evaluate : 5.160 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 138 TYR cc_start: 0.9459 (OUTLIER) cc_final: 0.9052 (t80) REVERT: A 371 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8639 (mt-10) REVERT: B 134 GLN cc_start: 0.9189 (mp10) cc_final: 0.8892 (mm110) REVERT: B 161 MET cc_start: 0.9491 (mmm) cc_final: 0.8901 (mmm) REVERT: C 28 ASP cc_start: 0.9172 (p0) cc_final: 0.8889 (t0) REVERT: D 145 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8796 (mtp) REVERT: D 188 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8691 (tm-30) REVERT: D 218 GLU cc_start: 0.9105 (tt0) cc_final: 0.8482 (pt0) REVERT: E 57 MET cc_start: 0.7981 (mmm) cc_final: 0.7558 (mmm) REVERT: E 120 MET cc_start: 0.8506 (mtm) cc_final: 0.7254 (mmt) REVERT: E 161 MET cc_start: 0.9293 (mmm) cc_final: 0.9003 (mmm) REVERT: G 139 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8858 (pp20) REVERT: G 276 GLU cc_start: 0.8900 (tt0) cc_final: 0.8645 (tm-30) REVERT: G 371 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8702 (mm-30) REVERT: G 390 GLU cc_start: 0.8977 (pt0) cc_final: 0.8390 (pm20) REVERT: H 63 GLN cc_start: 0.9703 (mm110) cc_final: 0.8960 (tm-30) REVERT: H 145 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9048 (mp0) REVERT: H 161 MET cc_start: 0.9481 (mmm) cc_final: 0.9089 (mmm) REVERT: J 145 MET cc_start: 0.9044 (ttt) cc_final: 0.8650 (ppp) REVERT: J 205 MET cc_start: 0.9556 (tpp) cc_final: 0.9018 (mmm) REVERT: J 353 GLU cc_start: 0.9235 (tp30) cc_final: 0.9025 (tp30) REVERT: J 371 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8613 (mt-10) REVERT: J 390 GLU cc_start: 0.8966 (pt0) cc_final: 0.8688 (pp20) REVERT: K 63 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8790 (mm-40) REVERT: K 161 MET cc_start: 0.9299 (mmm) cc_final: 0.8878 (mmm) REVERT: K 221 LYS cc_start: 0.9328 (tptt) cc_final: 0.8860 (tppp) REVERT: K 259 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8535 (ttm-80) REVERT: M 182 GLU cc_start: 0.9119 (tt0) cc_final: 0.8723 (tt0) REVERT: M 185 GLU cc_start: 0.9367 (pp20) cc_final: 0.9136 (pp20) REVERT: M 357 ASN cc_start: 0.8708 (m110) cc_final: 0.8422 (m110) REVERT: M 371 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8356 (mp0) REVERT: N 98 ILE cc_start: 0.8906 (mt) cc_final: 0.8330 (tt) REVERT: N 112 MET cc_start: 0.8697 (mmm) cc_final: 0.8431 (tpt) REVERT: N 134 GLN cc_start: 0.9243 (pp30) cc_final: 0.8952 (pp30) REVERT: O 28 ASP cc_start: 0.9418 (p0) cc_final: 0.8762 (t0) REVERT: P 147 ARG cc_start: 0.9276 (ttp-110) cc_final: 0.8940 (ttp-110) REVERT: P 190 MET cc_start: 0.8987 (ttm) cc_final: 0.8693 (ttm) REVERT: P 218 GLU cc_start: 0.8938 (tt0) cc_final: 0.8693 (tt0) REVERT: P 371 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8416 (mt-10) REVERT: Q 112 MET cc_start: 0.9064 (tpt) cc_final: 0.7678 (mmm) REVERT: Q 120 MET cc_start: 0.8433 (mtt) cc_final: 0.8149 (mtt) REVERT: Q 161 MET cc_start: 0.9278 (mpp) cc_final: 0.8769 (mmm) REVERT: T 57 MET cc_start: 0.7957 (pmm) cc_final: 0.7550 (pmm) REVERT: T 73 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8998 (pt0) REVERT: T 120 MET cc_start: 0.8470 (tpt) cc_final: 0.8230 (tpp) REVERT: T 161 MET cc_start: 0.9177 (tpp) cc_final: 0.8552 (mpp) REVERT: V 138 TYR cc_start: 0.9702 (t80) cc_final: 0.9300 (t80) REVERT: V 147 ARG cc_start: 0.9251 (ptt90) cc_final: 0.9042 (ptt90) REVERT: W 150 GLN cc_start: 0.9445 (tm-30) cc_final: 0.8980 (tm-30) REVERT: X 30 ASN cc_start: 0.8589 (p0) cc_final: 0.8064 (p0) REVERT: X 32 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: Y 357 ASN cc_start: 0.9093 (m-40) cc_final: 0.8698 (m110) REVERT: Z 161 MET cc_start: 0.9177 (mtm) cc_final: 0.8852 (mmm) REVERT: b 182 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8455 (tm-30) REVERT: b 190 MET cc_start: 0.9206 (ttp) cc_final: 0.8826 (ttp) REVERT: b 205 MET cc_start: 0.9572 (mmm) cc_final: 0.8510 (mmm) REVERT: c 111 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8727 (tm-30) REVERT: e 147 ARG cc_start: 0.9032 (ttp80) cc_final: 0.8495 (ptt90) REVERT: e 185 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8791 (tm-30) REVERT: e 188 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: e 218 GLU cc_start: 0.9195 (tt0) cc_final: 0.8764 (tt0) REVERT: e 390 GLU cc_start: 0.8523 (pp20) cc_final: 0.8282 (pp20) REVERT: f 80 LYS cc_start: 0.9414 (ttpt) cc_final: 0.9119 (ttpt) REVERT: f 161 MET cc_start: 0.9353 (mmm) cc_final: 0.9108 (mmm) REVERT: f 263 LYS cc_start: 0.9516 (ptmm) cc_final: 0.9215 (ptmm) REVERT: h 147 ARG cc_start: 0.9307 (ttp-110) cc_final: 0.8779 (ptt90) REVERT: h 205 MET cc_start: 0.9593 (tpp) cc_final: 0.9116 (mpp) REVERT: i 120 MET cc_start: 0.8901 (ttp) cc_final: 0.8523 (ttp) REVERT: i 159 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9225 (mmtm) REVERT: i 263 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9138 (ttpp) REVERT: j 32 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8629 (pm20) REVERT: k 145 MET cc_start: 0.8375 (ttt) cc_final: 0.7524 (mmt) REVERT: k 147 ARG cc_start: 0.9313 (ttp80) cc_final: 0.8822 (ptt-90) REVERT: k 186 LYS cc_start: 0.9560 (mttm) cc_final: 0.9101 (mtpp) REVERT: l 120 MET cc_start: 0.9210 (ptm) cc_final: 0.8464 (tmm) REVERT: l 161 MET cc_start: 0.9244 (mmm) cc_final: 0.8876 (mmm) REVERT: n 145 MET cc_start: 0.8388 (ttp) cc_final: 0.8182 (tmm) REVERT: n 188 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9107 (mm-40) REVERT: n 371 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8430 (mt-10) REVERT: o 120 MET cc_start: 0.9116 (mtm) cc_final: 0.8894 (mtm) REVERT: o 162 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.7587 (ptp) REVERT: p 32 GLU cc_start: 0.9320 (pt0) cc_final: 0.8557 (pm20) REVERT: u 144 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8785 (ttp-110) REVERT: v 22 ASP cc_start: 0.9150 (m-30) cc_final: 0.8829 (m-30) REVERT: v 73 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8348 (pt0) REVERT: v 91 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9126 (tp30) REVERT: v 115 ASP cc_start: 0.9451 (p0) cc_final: 0.9054 (p0) REVERT: v 117 ASN cc_start: 0.9375 (m110) cc_final: 0.8919 (m-40) REVERT: z 21 LEU cc_start: 0.9087 (mm) cc_final: 0.8818 (mm) REVERT: z 29 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7763 (t80) REVERT: z 63 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8673 (mm-40) REVERT: z 77 PHE cc_start: 0.9120 (t80) cc_final: 0.8841 (t80) REVERT: z 89 GLN cc_start: 0.9576 (mt0) cc_final: 0.9165 (mp10) outliers start: 119 outliers final: 80 residues processed: 547 average time/residue: 0.5569 time to fit residues: 510.5101 Evaluate side-chains 542 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 449 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 259 ARG Chi-restraints excluded: chain K residue 263 LYS Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 283 ILE Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 253 THR Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 231 CYS Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain o residue 253 THR Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 58 LEU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 152 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 415 optimal weight: 40.0000 chunk 136 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 588 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 614 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN i 150 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.033594 restraints weight = 243724.085| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 3.68 r_work: 0.2445 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 56894 Z= 0.274 Angle : 0.585 12.798 77036 Z= 0.296 Chirality : 0.043 0.170 8370 Planarity : 0.004 0.053 10228 Dihedral : 3.946 27.451 7996 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.89 % Allowed : 14.63 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 7036 helix: 1.94 (0.16), residues: 1137 sheet: 0.17 (0.12), residues: 1991 loop : -0.04 (0.10), residues: 3908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 272 HIS 0.005 0.001 HIS T 83 PHE 0.021 0.001 PHE B 195 TYR 0.020 0.001 TYR M 138 ARG 0.010 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 462 time to evaluate : 5.751 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 188 GLN cc_start: 0.9508 (mm-40) cc_final: 0.9270 (mm-40) REVERT: A 371 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8637 (mt-10) REVERT: B 57 MET cc_start: 0.7720 (mmm) cc_final: 0.7433 (mmm) REVERT: B 134 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8929 (mm110) REVERT: B 161 MET cc_start: 0.9472 (mmm) cc_final: 0.8877 (mmm) REVERT: C 28 ASP cc_start: 0.9168 (p0) cc_final: 0.8868 (t0) REVERT: D 145 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8783 (mtp) REVERT: D 188 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: D 218 GLU cc_start: 0.9180 (tt0) cc_final: 0.8418 (pt0) REVERT: E 120 MET cc_start: 0.8529 (mtm) cc_final: 0.7312 (mmt) REVERT: E 161 MET cc_start: 0.9315 (mmm) cc_final: 0.9020 (mmm) REVERT: G 139 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8868 (pp20) REVERT: G 188 GLN cc_start: 0.9390 (mm-40) cc_final: 0.9043 (mm-40) REVERT: G 276 GLU cc_start: 0.8917 (tt0) cc_final: 0.8647 (tm-30) REVERT: G 371 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8685 (mm-30) REVERT: H 63 GLN cc_start: 0.9711 (mm110) cc_final: 0.9020 (tm-30) REVERT: H 161 MET cc_start: 0.9472 (mmm) cc_final: 0.9081 (mmm) REVERT: J 142 ARG cc_start: 0.9552 (mmm-85) cc_final: 0.9291 (mtp-110) REVERT: J 145 MET cc_start: 0.9045 (ttt) cc_final: 0.8645 (ppp) REVERT: J 205 MET cc_start: 0.9553 (tpp) cc_final: 0.8987 (mmm) REVERT: J 353 GLU cc_start: 0.9249 (tp30) cc_final: 0.9038 (tp30) REVERT: J 371 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8606 (mt-10) REVERT: J 390 GLU cc_start: 0.8968 (pt0) cc_final: 0.8708 (pp20) REVERT: K 63 GLN cc_start: 0.9349 (mm-40) cc_final: 0.8828 (mm-40) REVERT: K 161 MET cc_start: 0.9292 (mmm) cc_final: 0.8877 (mmm) REVERT: K 221 LYS cc_start: 0.9338 (tptt) cc_final: 0.8863 (tppp) REVERT: M 138 TYR cc_start: 0.9311 (t80) cc_final: 0.8998 (t80) REVERT: M 147 ARG cc_start: 0.9193 (ptt90) cc_final: 0.8700 (ppt90) REVERT: M 182 GLU cc_start: 0.9139 (tt0) cc_final: 0.8740 (tt0) REVERT: M 185 GLU cc_start: 0.9367 (pp20) cc_final: 0.9133 (pp20) REVERT: M 357 ASN cc_start: 0.8703 (m110) cc_final: 0.8429 (m110) REVERT: M 371 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8336 (mp0) REVERT: N 112 MET cc_start: 0.8702 (mmm) cc_final: 0.8415 (tpt) REVERT: N 120 MET cc_start: 0.9102 (ttp) cc_final: 0.8530 (mtm) REVERT: N 134 GLN cc_start: 0.9279 (pp30) cc_final: 0.9029 (pp30) REVERT: O 28 ASP cc_start: 0.9395 (p0) cc_final: 0.8762 (t0) REVERT: P 147 ARG cc_start: 0.9312 (ttp-110) cc_final: 0.8956 (ttp-110) REVERT: P 190 MET cc_start: 0.9025 (ttm) cc_final: 0.8733 (ttm) REVERT: P 218 GLU cc_start: 0.9020 (tt0) cc_final: 0.8775 (tt0) REVERT: P 371 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8423 (mt-10) REVERT: Q 120 MET cc_start: 0.8434 (mtt) cc_final: 0.8150 (mtt) REVERT: Q 161 MET cc_start: 0.9285 (mpp) cc_final: 0.8796 (mmm) REVERT: S 205 MET cc_start: 0.9540 (mmm) cc_final: 0.8282 (mmm) REVERT: T 57 MET cc_start: 0.7853 (pmm) cc_final: 0.7517 (pmm) REVERT: T 73 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8964 (pt0) REVERT: T 161 MET cc_start: 0.9191 (tpp) cc_final: 0.8567 (mpp) REVERT: V 138 TYR cc_start: 0.9711 (t80) cc_final: 0.9301 (t80) REVERT: V 144 ARG cc_start: 0.9432 (mtm110) cc_final: 0.9061 (ptt-90) REVERT: W 150 GLN cc_start: 0.9448 (tm-30) cc_final: 0.8980 (tm-30) REVERT: X 30 ASN cc_start: 0.8609 (p0) cc_final: 0.8102 (p0) REVERT: X 32 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8724 (pm20) REVERT: Y 214 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7877 (p0) REVERT: Y 357 ASN cc_start: 0.9091 (m-40) cc_final: 0.8698 (m110) REVERT: Z 161 MET cc_start: 0.9196 (mtm) cc_final: 0.8877 (mmm) REVERT: b 190 MET cc_start: 0.9201 (ttp) cc_final: 0.8832 (ttp) REVERT: b 205 MET cc_start: 0.9567 (mmm) cc_final: 0.8516 (mmm) REVERT: c 57 MET cc_start: 0.9199 (mmm) cc_final: 0.8884 (mmm) REVERT: c 111 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8722 (tm-30) REVERT: e 147 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8533 (ptt90) REVERT: e 185 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8768 (tm-30) REVERT: e 188 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: e 205 MET cc_start: 0.9621 (mmp) cc_final: 0.9017 (mmp) REVERT: e 218 GLU cc_start: 0.9204 (tt0) cc_final: 0.8766 (tt0) REVERT: e 276 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8627 (tm-30) REVERT: e 390 GLU cc_start: 0.8532 (pp20) cc_final: 0.8299 (pp20) REVERT: f 80 LYS cc_start: 0.9416 (ttpt) cc_final: 0.9189 (ttpt) REVERT: f 161 MET cc_start: 0.9392 (mmm) cc_final: 0.9113 (mmm) REVERT: f 263 LYS cc_start: 0.9523 (ptmm) cc_final: 0.9276 (ptmm) REVERT: h 147 ARG cc_start: 0.9317 (ttp-110) cc_final: 0.8620 (ptt-90) REVERT: h 205 MET cc_start: 0.9591 (tpp) cc_final: 0.9104 (mpp) REVERT: i 120 MET cc_start: 0.8909 (ttp) cc_final: 0.8533 (ttp) REVERT: i 263 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9139 (ttpp) REVERT: j 32 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8630 (pm20) REVERT: k 145 MET cc_start: 0.8390 (ttt) cc_final: 0.7696 (mmm) REVERT: k 147 ARG cc_start: 0.9360 (ttp80) cc_final: 0.8814 (ptt90) REVERT: k 186 LYS cc_start: 0.9567 (mttm) cc_final: 0.9110 (mtpp) REVERT: l 120 MET cc_start: 0.9264 (ptm) cc_final: 0.8506 (tmm) REVERT: l 161 MET cc_start: 0.9256 (mmm) cc_final: 0.8892 (mmm) REVERT: l 204 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9260 (mp) REVERT: n 188 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9112 (mm-40) REVERT: n 371 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8456 (mt-10) REVERT: o 57 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5881 (mmp) REVERT: o 120 MET cc_start: 0.9062 (mtm) cc_final: 0.8827 (mtm) REVERT: u 144 ARG cc_start: 0.9259 (ttp80) cc_final: 0.8881 (ttp-110) REVERT: u 147 ARG cc_start: 0.9531 (ptt-90) cc_final: 0.9086 (ptt90) REVERT: v 22 ASP cc_start: 0.9135 (m-30) cc_final: 0.8823 (m-30) REVERT: v 73 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8499 (pt0) REVERT: v 91 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9106 (tp30) REVERT: v 115 ASP cc_start: 0.9445 (p0) cc_final: 0.9044 (p0) REVERT: v 117 ASN cc_start: 0.9371 (m110) cc_final: 0.8905 (m-40) REVERT: z 21 LEU cc_start: 0.9036 (mm) cc_final: 0.8742 (mm) REVERT: z 29 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7840 (t80) REVERT: z 63 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8666 (mm-40) REVERT: z 77 PHE cc_start: 0.9118 (t80) cc_final: 0.8833 (t80) REVERT: z 89 GLN cc_start: 0.9565 (mt0) cc_final: 0.9182 (mp10) outliers start: 111 outliers final: 82 residues processed: 546 average time/residue: 0.5559 time to fit residues: 507.4398 Evaluate side-chains 532 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 437 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 263 LYS Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 253 THR Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 150 GLN Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 204 LEU Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 231 CYS Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain o residue 253 THR Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 58 LEU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 242 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 338 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 502 optimal weight: 0.0060 chunk 143 optimal weight: 0.9990 chunk 426 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 220 HIS ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.054981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.034537 restraints weight = 240582.739| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.69 r_work: 0.2483 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56894 Z= 0.165 Angle : 0.585 13.378 77036 Z= 0.295 Chirality : 0.043 0.183 8370 Planarity : 0.004 0.054 10228 Dihedral : 3.845 27.802 7996 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.57 % Allowed : 15.14 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7036 helix: 1.87 (0.16), residues: 1136 sheet: 0.16 (0.12), residues: 2009 loop : -0.05 (0.10), residues: 3891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 272 HIS 0.004 0.000 HIS T 83 PHE 0.022 0.001 PHE B 195 TYR 0.022 0.001 TYR M 138 ARG 0.019 0.000 ARG D 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 464 time to evaluate : 5.189 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 188 GLN cc_start: 0.9478 (mm-40) cc_final: 0.9258 (mm-40) REVERT: A 371 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8472 (mt-10) REVERT: A 390 GLU cc_start: 0.8569 (pm20) cc_final: 0.8301 (pm20) REVERT: B 57 MET cc_start: 0.7647 (mmm) cc_final: 0.7336 (mmm) REVERT: B 134 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8938 (mm110) REVERT: B 161 MET cc_start: 0.9469 (mmm) cc_final: 0.8991 (mmm) REVERT: C 28 ASP cc_start: 0.9145 (p0) cc_final: 0.8862 (t0) REVERT: D 145 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8796 (mtp) REVERT: D 188 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9050 (tm-30) REVERT: D 218 GLU cc_start: 0.9057 (tt0) cc_final: 0.8362 (pt0) REVERT: E 57 MET cc_start: 0.8052 (mmm) cc_final: 0.7660 (mmm) REVERT: E 120 MET cc_start: 0.8523 (mtm) cc_final: 0.7324 (mmt) REVERT: E 161 MET cc_start: 0.9402 (mmm) cc_final: 0.9021 (mmm) REVERT: G 139 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8945 (pp20) REVERT: G 188 GLN cc_start: 0.9365 (mm-40) cc_final: 0.8981 (mm-40) REVERT: G 218 GLU cc_start: 0.9149 (tt0) cc_final: 0.8719 (pt0) REVERT: G 276 GLU cc_start: 0.8839 (tt0) cc_final: 0.8559 (tm-30) REVERT: H 63 GLN cc_start: 0.9718 (mm110) cc_final: 0.8975 (tm-30) REVERT: H 161 MET cc_start: 0.9454 (mmm) cc_final: 0.9160 (mmm) REVERT: J 142 ARG cc_start: 0.9562 (mmm-85) cc_final: 0.9307 (mtp-110) REVERT: J 145 MET cc_start: 0.9106 (ttt) cc_final: 0.8707 (ppp) REVERT: J 205 MET cc_start: 0.9486 (tpp) cc_final: 0.8893 (mmm) REVERT: J 353 GLU cc_start: 0.9216 (tp30) cc_final: 0.8995 (tp30) REVERT: J 371 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8584 (mt-10) REVERT: K 63 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8821 (mm-40) REVERT: K 112 MET cc_start: 0.9166 (tpp) cc_final: 0.8958 (tpp) REVERT: K 161 MET cc_start: 0.9317 (mmm) cc_final: 0.8884 (mmm) REVERT: K 221 LYS cc_start: 0.9302 (tptt) cc_final: 0.8993 (tptp) REVERT: M 147 ARG cc_start: 0.9181 (ptt90) cc_final: 0.8683 (ppt90) REVERT: M 357 ASN cc_start: 0.8647 (m110) cc_final: 0.8380 (m110) REVERT: N 98 ILE cc_start: 0.9009 (mt) cc_final: 0.8453 (tt) REVERT: N 112 MET cc_start: 0.8688 (mmm) cc_final: 0.8413 (tpt) REVERT: N 120 MET cc_start: 0.9152 (ttp) cc_final: 0.8476 (tpp) REVERT: N 134 GLN cc_start: 0.9277 (pp30) cc_final: 0.9011 (pp30) REVERT: O 28 ASP cc_start: 0.9387 (p0) cc_final: 0.8749 (t0) REVERT: P 147 ARG cc_start: 0.9322 (ttp-110) cc_final: 0.9000 (ttp-110) REVERT: P 218 GLU cc_start: 0.8971 (tt0) cc_final: 0.8760 (tt0) REVERT: P 371 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8431 (mt-10) REVERT: Q 120 MET cc_start: 0.8443 (mtt) cc_final: 0.8191 (mtt) REVERT: Q 161 MET cc_start: 0.9289 (mpp) cc_final: 0.8806 (mmm) REVERT: S 205 MET cc_start: 0.9530 (mmm) cc_final: 0.8350 (mmm) REVERT: T 57 MET cc_start: 0.7811 (pmm) cc_final: 0.7473 (pmm) REVERT: T 73 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.9023 (pt0) REVERT: T 112 MET cc_start: 0.6913 (mmm) cc_final: 0.6611 (mmm) REVERT: V 138 TYR cc_start: 0.9687 (t80) cc_final: 0.9018 (t80) REVERT: V 142 ARG cc_start: 0.9659 (mmm-85) cc_final: 0.9008 (ttm110) REVERT: V 145 MET cc_start: 0.8108 (ttt) cc_final: 0.7582 (tmm) REVERT: W 150 GLN cc_start: 0.9441 (tm-30) cc_final: 0.8960 (tm-30) REVERT: X 30 ASN cc_start: 0.8602 (p0) cc_final: 0.8100 (p0) REVERT: X 32 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: Y 214 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.7884 (p0) REVERT: Y 357 ASN cc_start: 0.9052 (m-40) cc_final: 0.8669 (m110) REVERT: Z 161 MET cc_start: 0.9137 (mtm) cc_final: 0.8781 (mmm) REVERT: b 182 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8415 (tm-30) REVERT: b 190 MET cc_start: 0.9165 (ttp) cc_final: 0.8774 (ttp) REVERT: b 205 MET cc_start: 0.9536 (mmm) cc_final: 0.8489 (mmm) REVERT: c 111 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8706 (tm-30) REVERT: e 143 GLU cc_start: 0.9476 (tm-30) cc_final: 0.9240 (pp20) REVERT: e 145 MET cc_start: 0.8551 (tmm) cc_final: 0.8244 (tmm) REVERT: e 185 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8759 (tm-30) REVERT: e 188 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: e 218 GLU cc_start: 0.9158 (tt0) cc_final: 0.8768 (tt0) REVERT: e 276 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8602 (tm-30) REVERT: e 390 GLU cc_start: 0.8537 (pp20) cc_final: 0.8294 (pp20) REVERT: f 80 LYS cc_start: 0.9439 (ttpt) cc_final: 0.9186 (ttpt) REVERT: f 161 MET cc_start: 0.9392 (mmm) cc_final: 0.9155 (mmm) REVERT: f 263 LYS cc_start: 0.9542 (ptmm) cc_final: 0.9235 (ptmm) REVERT: h 147 ARG cc_start: 0.9337 (ttp-110) cc_final: 0.8792 (ptt90) REVERT: h 205 MET cc_start: 0.9546 (tpp) cc_final: 0.9113 (mpp) REVERT: i 120 MET cc_start: 0.8907 (ttp) cc_final: 0.8615 (ttp) REVERT: i 150 GLN cc_start: 0.9521 (tt0) cc_final: 0.9300 (pp30) REVERT: i 263 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9180 (ttpp) REVERT: j 32 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8582 (pm20) REVERT: k 145 MET cc_start: 0.8414 (ttt) cc_final: 0.7620 (mmt) REVERT: k 147 ARG cc_start: 0.9392 (ttp80) cc_final: 0.8852 (ptt90) REVERT: l 120 MET cc_start: 0.9237 (ptm) cc_final: 0.8490 (tmm) REVERT: l 161 MET cc_start: 0.9208 (mmm) cc_final: 0.8844 (mmm) REVERT: n 188 GLN cc_start: 0.9344 (mm-40) cc_final: 0.9081 (mm-40) REVERT: n 371 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8420 (mt-10) REVERT: o 57 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5601 (mmp) REVERT: o 162 MET cc_start: 0.9238 (ptp) cc_final: 0.7884 (ptp) REVERT: p 32 GLU cc_start: 0.9278 (pt0) cc_final: 0.8658 (pm20) REVERT: u 142 ARG cc_start: 0.9308 (mpt180) cc_final: 0.9041 (mpt180) REVERT: u 144 ARG cc_start: 0.9249 (ttp80) cc_final: 0.8893 (ttp-110) REVERT: u 147 ARG cc_start: 0.9530 (ptt-90) cc_final: 0.9106 (ptt90) REVERT: v 22 ASP cc_start: 0.9161 (m-30) cc_final: 0.8845 (m-30) REVERT: v 73 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8576 (pt0) REVERT: v 91 GLU cc_start: 0.9521 (mm-30) cc_final: 0.9144 (tp30) REVERT: v 115 ASP cc_start: 0.9448 (p0) cc_final: 0.9030 (p0) REVERT: v 117 ASN cc_start: 0.9382 (m110) cc_final: 0.8917 (m-40) REVERT: z 21 LEU cc_start: 0.9015 (mm) cc_final: 0.8701 (mm) REVERT: z 29 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7812 (t80) REVERT: z 47 ASP cc_start: 0.8944 (p0) cc_final: 0.8264 (p0) REVERT: z 54 THR cc_start: 0.9349 (p) cc_final: 0.9115 (t) REVERT: z 63 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8686 (mm-40) REVERT: z 77 PHE cc_start: 0.9079 (t80) cc_final: 0.8729 (t80) REVERT: z 89 GLN cc_start: 0.9575 (mt0) cc_final: 0.9200 (mp10) REVERT: z 120 MET cc_start: 0.8023 (ptt) cc_final: 0.7553 (mpp) outliers start: 92 outliers final: 66 residues processed: 534 average time/residue: 0.5661 time to fit residues: 503.8897 Evaluate side-chains 527 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 449 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 263 LYS Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 73 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 253 THR Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain l residue 253 THR Chi-restraints excluded: chain n residue 231 CYS Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain o residue 253 THR Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 60 GLU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 58 LEU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 177 optimal weight: 6.9990 chunk 633 optimal weight: 9.9990 chunk 563 optimal weight: 20.0000 chunk 577 optimal weight: 50.0000 chunk 171 optimal weight: 2.9990 chunk 596 optimal weight: 0.9980 chunk 460 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 600 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN i 150 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.054370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.033954 restraints weight = 242494.361| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.67 r_work: 0.2457 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 56894 Z= 0.242 Angle : 0.597 13.913 77036 Z= 0.301 Chirality : 0.043 0.175 8370 Planarity : 0.004 0.053 10228 Dihedral : 3.850 28.615 7996 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.59 % Allowed : 15.26 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 7036 helix: 1.89 (0.16), residues: 1136 sheet: 0.16 (0.12), residues: 2041 loop : 0.01 (0.10), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 272 HIS 0.005 0.001 HIS W 83 PHE 0.020 0.001 PHE B 195 TYR 0.014 0.001 TYR T 194 ARG 0.026 0.000 ARG D 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25709.86 seconds wall clock time: 442 minutes 37.72 seconds (26557.72 seconds total)