Starting phenix.real_space_refine on Fri Jan 17 05:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt7_19481/01_2025/8rt7_19481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt7_19481/01_2025/8rt7_19481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rt7_19481/01_2025/8rt7_19481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt7_19481/01_2025/8rt7_19481.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt7_19481/01_2025/8rt7_19481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt7_19481/01_2025/8rt7_19481.cif" } resolution = 2.93 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= 0.022 sd= 0.070 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 502 residue(s): 0.14s 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: 24.86, per 1000 atoms: 0.45 Number of scatterers: 55802 At special positions: 0 Unit cell: (192.06, 195.261, 154.715, 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.03 Conformation dependent library (CDL) restraints added in 5.4 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: 98 helices and 141 sheets defined 17.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.39 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 305 through 330 removed outlier: 5.704A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.526A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 149 removed outlier: 4.244A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 187 Processing helix chain 'D' and resid 305 through 329 removed outlier: 5.521A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.580A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 150 removed outlier: 3.981A pdb=" N GLN E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 removed outlier: 3.537A pdb=" N ALA E 169 " --> pdb=" O LYS E 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 166 through 169' 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: 5.429A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.648A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 151 removed outlier: 3.507A pdb=" N GLN H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 139 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) 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 180 through 187 Processing helix chain 'J' and resid 305 through 329 removed outlier: 5.401A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.775A pdb=" N ASN J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 151 removed outlier: 3.660A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 removed outlier: 3.614A pdb=" N ALA K 169 " --> pdb=" O LYS K 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 169' Processing helix chain 'L' and resid 39 through 43 Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'M' and resid 180 through 187 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 305 through 329 removed outlier: 5.451A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.477A 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: 3.528A pdb=" N GLN N 131 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 4.251A 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 removed outlier: 3.508A pdb=" N ILE O 42 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'P' and resid 182 through 187 Processing helix chain 'P' and resid 305 through 329 removed outlier: 5.390A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 359 Processing helix chain 'Q' and resid 127 through 151 removed outlier: 4.013A 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 'S' and resid 136 through 148 Processing helix chain 'S' and resid 180 through 186 Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 305 through 329 removed outlier: 5.616A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 Processing helix chain 'T' and resid 127 through 151 removed outlier: 4.127A 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 'V' and resid 136 through 148 Processing helix chain 'V' and resid 180 through 187 removed outlier: 3.510A pdb=" N GLU V 185 " --> pdb=" O GLY V 181 " (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: 5.388A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.404A 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 127 through 150 removed outlier: 4.133A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN W 139 " --> pdb=" O THR W 135 " (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 305 through 329 removed outlier: 5.462A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.453A 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: 3.878A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU Z 137 " --> pdb=" O ARG Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'a' and resid 39 through 43 Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 305 through 329 removed outlier: 5.374A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 Processing helix chain 'c' and resid 127 through 151 removed outlier: 3.550A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) removed outlier: 4.254A 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 187 Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.619A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 Processing helix chain 'f' and resid 127 through 151 removed outlier: 3.992A 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 'h' and resid 136 through 148 Processing helix chain 'h' and resid 180 through 187 Processing helix chain 'h' and resid 305 through 329 removed outlier: 5.405A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 removed outlier: 3.548A pdb=" N ASN h 357 " --> pdb=" O GLU h 353 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 73 No H-bonds generated for 'chain 'i' and resid 71 through 73' Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.910A 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 305 through 329 removed outlier: 5.399A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 removed outlier: 3.598A pdb=" N ASN k 357 " --> pdb=" O GLU k 353 " (cutoff:3.500A) Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.758A 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 'n' and resid 136 through 148 Processing helix chain 'n' and resid 180 through 187 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.462A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 Processing helix chain 'o' and resid 71 through 73 No H-bonds generated for 'chain 'o' and resid 71 through 73' Processing helix chain 'o' and resid 127 through 151 removed outlier: 3.954A pdb=" N ALA o 138 " --> pdb=" O GLN o 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN o 139 " --> pdb=" O THR o 135 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG o 151 " --> pdb=" O ALA o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'y' and resid 136 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.703A 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: 4.640A pdb=" N VAL D 270 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS D 252 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 275 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 254 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA4, first strand: chain 'n' and resid 198 through 199 removed outlier: 4.616A pdb=" N VAL A 270 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 252 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 275 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 254 " --> pdb=" O SER A 273 " (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 Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 391 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.514A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 86 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.669A 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: 6.537A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 97 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 202 through 204 removed outlier: 4.641A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB3, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AB4, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.653A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 198 through 199 removed outlier: 4.605A pdb=" N VAL G 270 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS G 252 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE G 275 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL G 254 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB7, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AB8, first strand: chain 'D' and resid 387 through 391 Processing sheet with id=AB9, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.353A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS E 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS E 80 " --> pdb=" O HIS E 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 48 removed outlier: 6.571A pdb=" N VAL E 44 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 111 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL E 46 " --> pdb=" O GLN E 111 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 203 removed outlier: 4.565A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.536A pdb=" N ASN E 172 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.670A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 198 through 199 removed outlier: 4.772A pdb=" N VAL J 270 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC7, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AC8, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AC9, first strand: chain 'G' and resid 388 through 391 Processing sheet with id=AD1, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.960A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 44 through 48 removed outlier: 6.296A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 64 through 66 removed outlier: 6.849A pdb=" N VAL H 100 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 202 through 204 removed outlier: 4.686A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AD6, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.651A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 198 through 199 removed outlier: 4.516A pdb=" N VAL M 270 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN M 374 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS M 252 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE M 275 " --> pdb=" O LYS M 252 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL M 254 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AD9, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=AE1, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AE2, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AE3, first strand: chain 'K' and resid 25 through 26 removed outlier: 6.714A pdb=" N HIS K 55 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE K 125 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N MET K 57 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.655A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL K 46 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.552A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AE7, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.764A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 198 through 199 removed outlier: 4.667A pdb=" N VAL P 270 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AF1, first strand: chain 'M' and resid 237 through 238 Processing sheet with id=AF2, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AF3, first strand: chain 'M' and resid 388 through 391 Processing sheet with id=AF4, first strand: chain 'N' and resid 25 through 26 removed outlier: 3.570A pdb=" N ALA N 124 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 64 through 69 removed outlier: 7.108A pdb=" N VAL N 100 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HIS N 67 " --> pdb=" O ILE N 98 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE N 98 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 202 through 204 removed outlier: 3.504A pdb=" N VAL N 196 " --> pdb=" O LYS N 225 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 172 through 175 Processing sheet with id=AF8, first strand: chain 'P' and resid 195 through 196 removed outlier: 6.714A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 198 through 199 removed outlier: 6.402A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG S 274 " --> pdb=" O LEU S 285 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU S 285 " --> pdb=" O ARG S 274 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU S 276 " --> pdb=" O ILE S 283 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE S 283 " --> pdb=" O GLU S 276 " (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 Processing sheet with id=AG3, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AG4, first strand: chain 'Q' and resid 25 through 26 removed outlier: 6.253A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 44 through 48 removed outlier: 7.029A pdb=" N VAL Q 44 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN Q 111 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL Q 46 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 202 through 203 removed outlier: 3.685A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 172 through 175 Processing sheet with id=AG8, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.548A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 198 through 199 removed outlier: 4.685A pdb=" N VAL V 270 " --> pdb=" O GLY V 289 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (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 Processing sheet with id=AH3, first strand: chain 'S' and resid 267 through 268 Processing sheet with id=AH4, first strand: chain 'S' and resid 387 through 391 Processing sheet with id=AH5, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.573A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 44 through 48 Processing sheet with id=AH7, first strand: chain 'T' and resid 44 through 48 Processing sheet with id=AH8, first strand: chain 'T' and resid 202 through 203 removed outlier: 4.563A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'T' and resid 172 through 175 Processing sheet with id=AI1, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.747A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 198 through 199 removed outlier: 4.624A pdb=" N VAL Y 270 " --> pdb=" O GLY Y 289 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI4, first strand: chain 'V' and resid 237 through 238 Processing sheet with id=AI5, first strand: chain 'V' and resid 267 through 268 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: 6.648A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.385A 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 48 removed outlier: 3.762A pdb=" N LEU W 97 " --> pdb=" O PHE W 108 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 44 through 48 Processing sheet with id=AJ1, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.547A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ3, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.886A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Y' and resid 198 through 199 removed outlier: 4.683A pdb=" N VAL b 270 " --> pdb=" O GLY b 289 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS b 252 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE b 275 " --> pdb=" O LYS b 252 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL b 254 " --> pdb=" O SER b 273 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Y' and resid 221 through 222 Processing sheet with id=AJ6, first strand: chain 'Y' and resid 237 through 238 Processing sheet with id=AJ7, first strand: chain 'Y' and resid 267 through 268 Processing sheet with id=AJ8, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ9, first strand: chain 'Z' and resid 25 through 26 removed outlier: 6.957A pdb=" N ARG Z 34 " --> pdb=" O ALA Z 124 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ARG Z 126 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL Z 36 " --> pdb=" O ARG Z 126 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N PHE Z 125 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N MET Z 57 " --> pdb=" O PHE Z 125 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS Z 83 " --> pdb=" O LYS Z 80 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 44 through 49 removed outlier: 6.692A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG Z 113 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR Z 48 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 202 through 204 removed outlier: 4.687A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AK4, first strand: chain 'b' and resid 195 through 196 removed outlier: 6.847A pdb=" N SER b 195 " --> pdb=" O ASP e 382 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 198 through 199 removed outlier: 4.643A pdb=" N VAL e 270 " --> pdb=" O GLY e 289 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS e 252 " --> pdb=" O ILE e 275 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE e 275 " --> pdb=" O LYS e 252 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL e 254 " --> pdb=" O SER e 273 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AK7, first strand: chain 'b' and resid 237 through 238 Processing sheet with id=AK8, first strand: chain 'b' and resid 387 through 391 removed outlier: 3.533A pdb=" N GLU b 390 " --> pdb=" O ARG f 259 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.591A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'c' and resid 44 through 49 removed outlier: 6.658A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG c 113 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR c 48 " --> pdb=" O ARG c 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU c 97 " --> pdb=" O PHE c 108 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 202 through 204 removed outlier: 4.623A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'c' and resid 172 through 175 Processing sheet with id=AL4, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.695A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'e' and resid 198 through 199 removed outlier: 4.566A pdb=" N VAL h 270 " --> pdb=" O GLY h 289 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS h 252 " --> pdb=" O ILE h 275 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE h 275 " --> pdb=" O LYS h 252 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL h 254 " --> pdb=" O SER h 273 " (cutoff:3.500A) 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 Processing sheet with id=AL8, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AL9, first strand: chain 'f' and resid 25 through 26 removed outlier: 6.830A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'f' and resid 44 through 47 removed outlier: 6.698A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN f 96 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE f 69 " --> pdb=" O ASN f 96 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE f 98 " --> pdb=" O HIS f 67 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS f 67 " --> pdb=" O ILE f 98 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL f 100 " --> pdb=" O LEU f 65 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'f' and resid 202 through 203 removed outlier: 3.504A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AM4, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.753A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'h' and resid 198 through 199 removed outlier: 4.632A pdb=" N VAL k 270 " --> pdb=" O GLY k 289 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM7, first strand: chain 'h' and resid 237 through 238 Processing sheet with id=AM8, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AM9, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN1, first strand: chain 'i' and resid 25 through 26 removed outlier: 6.504A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'i' and resid 44 through 48 removed outlier: 6.806A pdb=" N VAL i 44 " --> pdb=" O ARG i 109 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN i 111 " --> pdb=" O VAL i 44 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL i 46 " --> pdb=" O GLN i 111 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'i' and resid 202 through 203 removed outlier: 3.537A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN5, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.769A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'k' and resid 198 through 199 removed outlier: 4.718A pdb=" N VAL n 270 " --> pdb=" O GLY n 289 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AN8, first strand: chain 'k' and resid 237 through 238 Processing sheet with id=AN9, first strand: chain 'k' and resid 387 through 391 Processing sheet with id=AO1, first strand: chain 'l' and resid 25 through 26 removed outlier: 6.967A pdb=" N ARG l 34 " --> pdb=" O ALA l 124 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ARG l 126 " --> pdb=" O ARG l 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL l 36 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'l' and resid 44 through 48 removed outlier: 3.563A pdb=" N VAL l 44 " --> pdb=" O LYS l 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR l 66 " --> pdb=" O VAL l 100 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'l' and resid 202 through 204 removed outlier: 3.584A pdb=" N VAL l 196 " --> pdb=" O LYS l 225 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'l' and resid 172 through 175 removed outlier: 3.541A pdb=" N ASN l 172 " --> pdb=" O LYS l 183 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AO6, first strand: chain 'n' and resid 237 through 238 Processing sheet with id=AO7, first strand: chain 'n' and resid 267 through 268 Processing sheet with id=AO8, first strand: chain 'o' and resid 25 through 26 removed outlier: 6.861A pdb=" N HIS o 55 " --> pdb=" O LEU o 123 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE o 125 " --> pdb=" O HIS o 55 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET o 57 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'o' and resid 44 through 48 removed outlier: 3.622A pdb=" N VAL o 46 " --> pdb=" O ARG o 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN o 111 " --> pdb=" O VAL o 46 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR o 66 " --> pdb=" O VAL o 100 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'o' and resid 202 through 203 removed outlier: 3.536A pdb=" N VAL o 196 " --> pdb=" O LYS o 225 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 172 through 175 Processing sheet with id=AP3, first strand: chain 'v' and resid 25 through 26 removed outlier: 6.580A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE v 125 " --> pdb=" O MET v 57 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE v 84 " --> pdb=" O ILE v 56 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'v' and resid 44 through 46 removed outlier: 6.894A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'z' and resid 25 through 26 removed outlier: 6.403A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'z' and resid 44 through 48 removed outlier: 6.914A pdb=" N VAL z 44 " --> pdb=" O ARG z 109 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN z 111 " --> pdb=" O VAL z 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL z 46 " --> pdb=" O GLN z 111 " (cutoff:3.500A) 2167 hydrogen bonds defined for protein. 5634 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: 27.09 Time building geometry restraints manager: 12.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18627 1.33 - 1.45: 8488 1.45 - 1.57: 29412 1.57 - 1.69: 1 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" C GLU J 276 " pdb=" N THR J 277 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 9.14e+00 bond pdb=" C GLU n 276 " pdb=" N THR n 277 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.47e-02 4.63e+03 7.25e+00 bond pdb=" N GLU e 276 " pdb=" CA GLU e 276 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.09e+00 bond pdb=" CB LYS E 221 " pdb=" CG LYS E 221 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.73e+00 bond pdb=" CA THR e 277 " pdb=" C THR e 277 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.18e-02 7.18e+03 4.51e+00 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.32: 77003 6.32 - 12.65: 27 12.65 - 18.97: 1 18.97 - 25.29: 3 25.29 - 31.62: 2 Bond angle restraints: 77036 Sorted by residual: angle pdb=" O GLN a 43 " pdb=" C GLN a 43 " pdb=" N ARG a 44 " ideal model delta sigma weight residual 122.67 91.93 30.74 1.13e+00 7.83e-01 7.40e+02 angle pdb=" O GLN L 43 " pdb=" C GLN L 43 " pdb=" N ARG L 44 " ideal model delta sigma weight residual 122.41 90.79 31.62 1.34e+00 5.57e-01 5.57e+02 angle pdb=" O GLN U 43 " pdb=" C GLN U 43 " pdb=" N ARG U 44 " ideal model delta sigma weight residual 122.91 100.63 22.28 1.19e+00 7.06e-01 3.51e+02 angle pdb=" O GLN p 43 " pdb=" C GLN p 43 " pdb=" N ARG p 44 " ideal model delta sigma weight residual 122.58 100.83 21.75 1.20e+00 6.94e-01 3.29e+02 angle pdb=" O GLN m 43 " pdb=" C GLN m 43 " pdb=" N ARG m 44 " ideal model delta sigma weight residual 122.41 102.50 19.91 1.34e+00 5.57e-01 2.21e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 31021 17.78 - 35.57: 2576 35.57 - 53.35: 471 53.35 - 71.13: 83 71.13 - 88.92: 39 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA ARG v 113 " pdb=" C ARG v 113 " pdb=" N ASN v 114 " pdb=" CA ASN v 114 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" C THR e 277 " pdb=" N THR e 277 " pdb=" CA THR e 277 " pdb=" CB THR e 277 " ideal model delta harmonic sigma weight residual -122.00 -134.55 12.55 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" CA ARG E 79 " pdb=" C ARG E 79 " pdb=" N LYS E 80 " pdb=" CA LYS E 80 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 7516 0.086 - 0.172: 845 0.172 - 0.258: 7 0.258 - 0.344: 1 0.344 - 0.430: 1 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB ILE l 98 " pdb=" CA ILE l 98 " pdb=" CG1 ILE l 98 " pdb=" CG2 ILE l 98 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA THR e 277 " pdb=" N THR e 277 " pdb=" C THR e 277 " pdb=" CB THR e 277 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE T 217 " pdb=" CA ILE T 217 " pdb=" CG1 ILE T 217 " pdb=" CG2 ILE T 217 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 43 " 0.119 2.00e-02 2.50e+03 1.99e-01 3.96e+02 pdb=" C GLN L 43 " -0.344 2.00e-02 2.50e+03 pdb=" O GLN L 43 " 0.124 2.00e-02 2.50e+03 pdb=" N ARG L 44 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 43 " 0.118 2.00e-02 2.50e+03 1.98e-01 3.92e+02 pdb=" C GLN a 43 " -0.343 2.00e-02 2.50e+03 pdb=" O GLN a 43 " 0.124 2.00e-02 2.50e+03 pdb=" N ARG a 44 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN U 43 " 0.096 2.00e-02 2.50e+03 1.70e-01 2.90e+02 pdb=" C GLN U 43 " -0.295 2.00e-02 2.50e+03 pdb=" O GLN U 43 " 0.109 2.00e-02 2.50e+03 pdb=" N ARG U 44 " 0.090 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 693 2.62 - 3.19: 46942 3.19 - 3.76: 84886 3.76 - 4.33: 127728 4.33 - 4.90: 214652 Nonbonded interactions: 474901 Sorted by model distance: nonbonded pdb=" NZ LYS i 87 " pdb=" O MET k 145 " model vdw 2.051 3.120 nonbonded pdb=" NH2 ARG N 116 " pdb=" O ASN Q 94 " model vdw 2.123 3.120 nonbonded pdb=" O HIS z 31 " pdb=" NH1 ARG z 34 " model vdw 2.141 3.120 nonbonded pdb=" NZ LYS S 367 " pdb=" OE1 GLU S 371 " model vdw 2.151 3.120 nonbonded pdb=" OH TYR W 106 " pdb=" OH TYR W 127 " model vdw 2.154 3.040 ... (remaining 474896 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: 1.220 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: 0.080 Extract box with map and model: 1.620 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 105.040 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.009 0.095 56894 Z= 0.605 Angle : 0.749 31.619 77036 Z= 0.435 Chirality : 0.051 0.430 8370 Planarity : 0.007 0.199 10228 Dihedral : 13.722 88.917 21096 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.07 % Allowed : 0.82 % Favored : 99.11 % Cbeta Deviations : 0.02 % 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: -0.67 (0.09), residues: 7036 helix: 1.13 (0.15), residues: 1130 sheet: -0.55 (0.12), residues: 1911 loop : -0.82 (0.09), residues: 3995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP h 325 HIS 0.008 0.001 HIS l 55 PHE 0.053 0.002 PHE o 148 TYR 0.034 0.002 TYR Z 127 ARG 0.014 0.001 ARG N 113 *********************** 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 846 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 842 time to evaluate : 4.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 28 ASP cc_start: 0.6756 (t0) cc_final: 0.6541 (t0) REVERT: e 140 LEU cc_start: 0.9027 (mt) cc_final: 0.8759 (mm) REVERT: i 131 GLN cc_start: 0.8216 (pp30) cc_final: 0.7614 (pp30) REVERT: l 129 ASP cc_start: 0.7669 (p0) cc_final: 0.7434 (p0) REVERT: y 144 ARG cc_start: 0.8399 (tmm-80) cc_final: 0.8136 (tmm-80) REVERT: z 48 THR cc_start: 0.8663 (p) cc_final: 0.8273 (t) REVERT: z 50 LEU cc_start: 0.8609 (tp) cc_final: 0.8247 (tp) REVERT: z 115 ASP cc_start: 0.8208 (p0) cc_final: 0.7480 (p0) outliers start: 4 outliers final: 4 residues processed: 845 average time/residue: 1.8908 time to fit residues: 1904.9596 Evaluate side-chains 507 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 503 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 111 GLN Chi-restraints excluded: chain c residue 111 GLN Chi-restraints excluded: chain o residue 84 ILE Chi-restraints excluded: chain v residue 114 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 4.9990 chunk 526 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 354 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 543 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 330 optimal weight: 0.8980 chunk 404 optimal weight: 5.9990 chunk 630 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 360 ASN B 89 GLN D 271 GLN E 201 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 GLN P 271 GLN S 374 ASN T 31 HIS V 271 GLN V 284 ASN V 357 ASN Y 263 GLN Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 ASN b 360 ASN c 45 GLN ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 271 GLN e 357 ASN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 232 HIS h 271 GLN h 374 ASN ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN k 374 ASN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 188 GLN n 357 ASN o 89 GLN z 83 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.033850 restraints weight = 225856.113| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 3.57 r_work: 0.2409 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1829 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= 0.246 Angle : 0.659 11.452 77036 Z= 0.342 Chirality : 0.046 0.260 8370 Planarity : 0.005 0.072 10228 Dihedral : 4.787 41.456 8006 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.01 % Allowed : 10.84 % Favored : 88.15 % 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: -0.21 (0.10), residues: 7036 helix: 1.76 (0.16), residues: 1134 sheet: -0.41 (0.12), residues: 1845 loop : -0.51 (0.09), residues: 4057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 325 HIS 0.007 0.001 HIS Z 55 PHE 0.031 0.002 PHE c 195 TYR 0.019 0.001 TYR A 138 ARG 0.010 0.001 ARG A 147 *********************** 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 649 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 590 time to evaluate : 4.898 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: A 252 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9279 (ttpt) REVERT: B 263 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8517 (ttpp) REVERT: D 138 TYR cc_start: 0.9615 (t80) cc_final: 0.9316 (t80) REVERT: D 185 GLU cc_start: 0.8776 (pp20) cc_final: 0.8520 (pp20) REVERT: E 89 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: E 120 MET cc_start: 0.9406 (ttp) cc_final: 0.9103 (ttm) REVERT: E 131 GLN cc_start: 0.8979 (mp10) cc_final: 0.8766 (mp10) REVERT: G 139 GLU cc_start: 0.9436 (pt0) cc_final: 0.9207 (pp20) REVERT: G 147 ARG cc_start: 0.9424 (ttp-110) cc_final: 0.8834 (mtm110) REVERT: H 80 LYS cc_start: 0.9439 (tttt) cc_final: 0.9120 (mtmt) REVERT: H 134 GLN cc_start: 0.8679 (mp10) cc_final: 0.8291 (mm110) REVERT: H 137 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8950 (pt0) REVERT: H 161 MET cc_start: 0.9303 (mmm) cc_final: 0.8962 (mmm) REVERT: J 185 GLU cc_start: 0.9287 (tm-30) cc_final: 0.9082 (tm-30) REVERT: K 134 GLN cc_start: 0.8677 (pp30) cc_final: 0.8248 (pp30) REVERT: K 161 MET cc_start: 0.9318 (mmm) cc_final: 0.8714 (mmm) REVERT: K 162 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.7983 (ptp) REVERT: L 32 GLU cc_start: 0.9186 (pt0) cc_final: 0.8737 (pm20) REVERT: M 146 LEU cc_start: 0.9358 (mm) cc_final: 0.9082 (mm) REVERT: N 63 GLN cc_start: 0.9378 (tp-100) cc_final: 0.8913 (tm-30) REVERT: N 80 LYS cc_start: 0.9580 (OUTLIER) cc_final: 0.9369 (ttpt) REVERT: P 139 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8590 (pp20) REVERT: P 353 GLU cc_start: 0.9223 (tp30) cc_final: 0.9011 (tp30) REVERT: P 390 GLU cc_start: 0.8040 (pp20) cc_final: 0.7730 (pp20) REVERT: Q 22 ASP cc_start: 0.8350 (t0) cc_final: 0.7956 (p0) REVERT: Q 63 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8875 (tm-30) REVERT: Q 131 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8896 (tp-100) REVERT: Q 161 MET cc_start: 0.9248 (mmm) cc_final: 0.8906 (mmm) REVERT: S 147 ARG cc_start: 0.9377 (ttp-110) cc_final: 0.9116 (mtm110) REVERT: S 371 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8559 (mt-10) REVERT: T 120 MET cc_start: 0.8252 (tmm) cc_final: 0.7899 (tmm) REVERT: T 263 LYS cc_start: 0.9284 (ttmt) cc_final: 0.9038 (ttpp) REVERT: U 32 GLU cc_start: 0.9236 (pt0) cc_final: 0.8588 (pm20) REVERT: V 182 GLU cc_start: 0.8723 (tt0) cc_final: 0.8332 (tt0) REVERT: V 185 GLU cc_start: 0.8910 (pp20) cc_final: 0.8676 (pp20) REVERT: W 137 GLU cc_start: 0.9323 (mp0) cc_final: 0.9106 (mp0) REVERT: W 227 MET cc_start: 0.9366 (tpp) cc_final: 0.9106 (tpt) REVERT: Y 138 TYR cc_start: 0.9365 (t80) cc_final: 0.9007 (t80) REVERT: Y 139 GLU cc_start: 0.9653 (mt-10) cc_final: 0.9442 (pp20) REVERT: Y 205 MET cc_start: 0.9375 (mpp) cc_final: 0.9047 (mpp) REVERT: Y 276 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8653 (tm-30) REVERT: Y 371 GLU cc_start: 0.7820 (mp0) cc_final: 0.7256 (mp0) REVERT: Y 390 GLU cc_start: 0.7966 (pp20) cc_final: 0.7734 (pp20) REVERT: Z 57 MET cc_start: 0.8914 (mtm) cc_final: 0.8527 (mmm) REVERT: Z 80 LYS cc_start: 0.9090 (tttm) cc_final: 0.8865 (ttpt) REVERT: Z 150 GLN cc_start: 0.9247 (pp30) cc_final: 0.9008 (pp30) REVERT: Z 161 MET cc_start: 0.9269 (mmm) cc_final: 0.9024 (mmm) REVERT: b 143 GLU cc_start: 0.9720 (mm-30) cc_final: 0.9408 (mp0) REVERT: b 205 MET cc_start: 0.9418 (mpp) cc_final: 0.9105 (mpp) REVERT: b 276 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8749 (tm-30) REVERT: b 371 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8397 (mt-10) REVERT: b 390 GLU cc_start: 0.8224 (pp20) cc_final: 0.7991 (pp20) REVERT: c 45 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.8888 (tm-30) REVERT: c 120 MET cc_start: 0.9435 (ttp) cc_final: 0.9231 (ttp) REVERT: c 161 MET cc_start: 0.9408 (mmm) cc_final: 0.8863 (mmm) REVERT: e 147 ARG cc_start: 0.9562 (mtm110) cc_final: 0.9344 (ptp-110) REVERT: e 218 GLU cc_start: 0.9377 (tt0) cc_final: 0.8997 (tt0) REVERT: e 276 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8840 (tm-30) REVERT: e 371 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8446 (mt-10) REVERT: f 89 GLN cc_start: 0.9639 (mt0) cc_final: 0.9219 (mm110) REVERT: f 263 LYS cc_start: 0.9540 (ttmt) cc_final: 0.9189 (ttpp) REVERT: g 32 GLU cc_start: 0.9141 (pt0) cc_final: 0.8881 (pm20) REVERT: h 139 GLU cc_start: 0.9307 (pt0) cc_final: 0.9014 (pp20) REVERT: h 218 GLU cc_start: 0.8994 (tt0) cc_final: 0.8708 (tt0) REVERT: h 276 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8666 (tm-30) REVERT: h 371 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8248 (mt-10) REVERT: i 131 GLN cc_start: 0.9191 (pp30) cc_final: 0.8979 (pp30) REVERT: i 161 MET cc_start: 0.9167 (mmm) cc_final: 0.8699 (mmm) REVERT: i 225 LYS cc_start: 0.9416 (tttt) cc_final: 0.9179 (tttm) REVERT: k 139 GLU cc_start: 0.8767 (pp20) cc_final: 0.8465 (pp20) REVERT: k 185 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8966 (pp20) REVERT: k 205 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.8517 (mmt) REVERT: k 308 GLU cc_start: 0.8653 (mp0) cc_final: 0.8417 (mp0) REVERT: l 63 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8867 (mm-40) REVERT: l 73 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8854 (mp0) REVERT: l 134 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8999 (mm-40) REVERT: l 150 GLN cc_start: 0.9390 (tp-100) cc_final: 0.9102 (tp-100) REVERT: n 146 LEU cc_start: 0.9546 (mm) cc_final: 0.9062 (mm) REVERT: n 147 ARG cc_start: 0.9609 (ttp-110) cc_final: 0.8993 (mtm110) REVERT: n 371 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: o 57 MET cc_start: 0.9169 (tpt) cc_final: 0.8877 (mmm) REVERT: o 120 MET cc_start: 0.9571 (OUTLIER) cc_final: 0.8870 (tpp) REVERT: o 161 MET cc_start: 0.9141 (mmm) cc_final: 0.8934 (mmm) REVERT: o 162 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8724 (ptp) REVERT: u 143 GLU cc_start: 0.9744 (mm-30) cc_final: 0.9524 (pp20) REVERT: u 145 MET cc_start: 0.9189 (mtt) cc_final: 0.8880 (ttm) REVERT: u 147 ARG cc_start: 0.9356 (ttp80) cc_final: 0.8946 (ttp-110) REVERT: v 22 ASP cc_start: 0.8363 (m-30) cc_final: 0.7952 (m-30) REVERT: v 57 MET cc_start: 0.7379 (mmm) cc_final: 0.6522 (mmm) REVERT: v 59 GLU cc_start: 0.8319 (tt0) cc_final: 0.8096 (pt0) REVERT: v 71 ASP cc_start: 0.6962 (t70) cc_final: 0.6497 (t0) REVERT: v 112 MET cc_start: 0.9103 (tpp) cc_final: 0.8849 (tpp) REVERT: v 125 PHE cc_start: 0.8529 (m-80) cc_final: 0.8069 (t80) REVERT: z 22 ASP cc_start: 0.8678 (t0) cc_final: 0.8395 (t0) REVERT: z 47 ASP cc_start: 0.8107 (p0) cc_final: 0.7904 (p0) REVERT: z 50 LEU cc_start: 0.9423 (tp) cc_final: 0.9156 (tp) REVERT: z 57 MET cc_start: 0.8991 (tpt) cc_final: 0.8786 (mmm) REVERT: z 58 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8834 (tp) REVERT: z 59 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.9002 (mt-10) REVERT: z 60 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8919 (mm-30) REVERT: z 91 GLU cc_start: 0.9238 (tp30) cc_final: 0.8954 (tp30) REVERT: z 102 ASP cc_start: 0.9398 (OUTLIER) cc_final: 0.8869 (p0) REVERT: z 115 ASP cc_start: 0.9681 (p0) cc_final: 0.9443 (p0) outliers start: 59 outliers final: 14 residues processed: 619 average time/residue: 1.8663 time to fit residues: 1381.3371 Evaluate side-chains 529 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 502 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 58 LEU Chi-restraints excluded: chain z residue 59 GLU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 215 optimal weight: 0.9990 chunk 670 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 213 optimal weight: 20.0000 chunk 615 optimal weight: 8.9990 chunk 516 optimal weight: 10.0000 chunk 637 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 271 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 89 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN S 374 ASN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 188 GLN V 374 ASN W 89 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 ASN c 45 GLN c 111 GLN f 131 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 188 GLN l 89 GLN n 357 ASN v 67 HIS z 63 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.033214 restraints weight = 228447.080| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 3.59 r_work: 0.2394 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56894 Z= 0.234 Angle : 0.598 12.623 77036 Z= 0.308 Chirality : 0.044 0.178 8370 Planarity : 0.004 0.085 10228 Dihedral : 4.369 22.563 7998 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.38 % Allowed : 12.62 % Favored : 86.00 % 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: -0.01 (0.10), residues: 7036 helix: 1.98 (0.16), residues: 1130 sheet: -0.31 (0.12), residues: 1839 loop : -0.37 (0.09), residues: 4067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 325 HIS 0.009 0.001 HIS c 55 PHE 0.027 0.001 PHE Z 195 TYR 0.023 0.001 TYR M 138 ARG 0.011 0.000 ARG D 147 *********************** 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 644 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 563 time to evaluate : 5.226 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 145 MET cc_start: 0.9214 (mtt) cc_final: 0.9011 (ttm) REVERT: A 252 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9256 (ttpp) REVERT: B 227 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9049 (tpt) REVERT: D 147 ARG cc_start: 0.9492 (ttp-110) cc_final: 0.8971 (mtm110) REVERT: D 185 GLU cc_start: 0.8839 (pp20) cc_final: 0.8543 (pp20) REVERT: E 89 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8189 (mp10) REVERT: E 120 MET cc_start: 0.9447 (ttp) cc_final: 0.9015 (ttm) REVERT: E 131 GLN cc_start: 0.9121 (mp10) cc_final: 0.8792 (mp10) REVERT: G 139 GLU cc_start: 0.9500 (pt0) cc_final: 0.9262 (pp20) REVERT: G 146 LEU cc_start: 0.9383 (mm) cc_final: 0.8874 (mm) REVERT: G 147 ARG cc_start: 0.9216 (ttp-110) cc_final: 0.8918 (mtm110) REVERT: H 134 GLN cc_start: 0.8834 (mp10) cc_final: 0.8351 (mm110) REVERT: H 137 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8935 (pt0) REVERT: H 161 MET cc_start: 0.9340 (mmm) cc_final: 0.8691 (mmm) REVERT: J 139 GLU cc_start: 0.9136 (pp20) cc_final: 0.8835 (pp20) REVERT: J 147 ARG cc_start: 0.9153 (ttp-110) cc_final: 0.8949 (mtm110) REVERT: J 185 GLU cc_start: 0.9291 (tm-30) cc_final: 0.9046 (tm-30) REVERT: K 120 MET cc_start: 0.9246 (ptm) cc_final: 0.8456 (ppp) REVERT: K 131 GLN cc_start: 0.9496 (tp40) cc_final: 0.9132 (tp40) REVERT: K 134 GLN cc_start: 0.8841 (pp30) cc_final: 0.8497 (pp30) REVERT: K 161 MET cc_start: 0.9361 (mmm) cc_final: 0.9002 (mmm) REVERT: K 162 MET cc_start: 0.9543 (OUTLIER) cc_final: 0.7940 (ptp) REVERT: L 32 GLU cc_start: 0.9222 (pt0) cc_final: 0.8730 (pm20) REVERT: M 140 LEU cc_start: 0.9792 (mm) cc_final: 0.9574 (mm) REVERT: M 146 LEU cc_start: 0.9293 (mm) cc_final: 0.9041 (mm) REVERT: M 315 MET cc_start: 0.9060 (tpp) cc_final: 0.8725 (tmm) REVERT: M 371 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8259 (mt-10) REVERT: M 390 GLU cc_start: 0.8257 (pp20) cc_final: 0.8034 (pp20) REVERT: N 63 GLN cc_start: 0.9360 (tp-100) cc_final: 0.8854 (tm-30) REVERT: P 147 ARG cc_start: 0.9624 (ttp-110) cc_final: 0.9256 (mtm110) REVERT: Q 63 GLN cc_start: 0.9421 (tm-30) cc_final: 0.8920 (tm-30) REVERT: Q 120 MET cc_start: 0.8039 (tpp) cc_final: 0.7817 (tpp) REVERT: Q 131 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8859 (tp-100) REVERT: Q 150 GLN cc_start: 0.9385 (tp-100) cc_final: 0.9019 (tp-100) REVERT: Q 161 MET cc_start: 0.9246 (mmm) cc_final: 0.8857 (mmm) REVERT: S 147 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.9103 (mtm110) REVERT: S 276 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8741 (tm-30) REVERT: S 374 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8574 (t0) REVERT: S 390 GLU cc_start: 0.8005 (pp20) cc_final: 0.7780 (pp20) REVERT: T 89 GLN cc_start: 0.8997 (mt0) cc_final: 0.8617 (mp10) REVERT: T 120 MET cc_start: 0.8221 (tmm) cc_final: 0.7829 (tmm) REVERT: T 263 LYS cc_start: 0.9316 (ttmt) cc_final: 0.9083 (ttpp) REVERT: U 32 GLU cc_start: 0.9279 (pt0) cc_final: 0.8830 (pm20) REVERT: V 182 GLU cc_start: 0.8846 (tt0) cc_final: 0.8567 (tt0) REVERT: V 185 GLU cc_start: 0.8984 (pp20) cc_final: 0.8693 (pp20) REVERT: W 57 MET cc_start: 0.8637 (mmm) cc_final: 0.8424 (mmm) REVERT: W 120 MET cc_start: 0.7689 (tpp) cc_final: 0.7444 (tpp) REVERT: W 137 GLU cc_start: 0.9393 (mp0) cc_final: 0.9176 (mp0) REVERT: W 227 MET cc_start: 0.9346 (tpp) cc_final: 0.9082 (tpp) REVERT: X 32 GLU cc_start: 0.9039 (pt0) cc_final: 0.8346 (pm20) REVERT: Y 138 TYR cc_start: 0.9400 (t80) cc_final: 0.9097 (t80) REVERT: Y 142 ARG cc_start: 0.9667 (mtm180) cc_final: 0.9424 (mtm180) REVERT: Y 143 GLU cc_start: 0.9684 (mm-30) cc_final: 0.9483 (mm-30) REVERT: Y 205 MET cc_start: 0.9375 (mpp) cc_final: 0.9008 (mpp) REVERT: Y 276 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8671 (tm-30) REVERT: Y 308 GLU cc_start: 0.8735 (mp0) cc_final: 0.8533 (mp0) REVERT: Y 371 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: Z 57 MET cc_start: 0.9041 (mtm) cc_final: 0.8675 (mmm) REVERT: Z 63 GLN cc_start: 0.9152 (mp10) cc_final: 0.8668 (mp10) REVERT: Z 89 GLN cc_start: 0.9531 (mt0) cc_final: 0.9166 (mm-40) REVERT: Z 150 GLN cc_start: 0.9268 (pp30) cc_final: 0.8992 (pp30) REVERT: Z 161 MET cc_start: 0.9301 (mmm) cc_final: 0.9020 (mmm) REVERT: b 136 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9011 (t) REVERT: b 139 GLU cc_start: 0.9415 (pt0) cc_final: 0.8994 (pp20) REVERT: b 143 GLU cc_start: 0.9753 (mm-30) cc_final: 0.9503 (mm-30) REVERT: b 205 MET cc_start: 0.9387 (mpp) cc_final: 0.9036 (mpp) REVERT: b 353 GLU cc_start: 0.8844 (tp30) cc_final: 0.8301 (tp30) REVERT: b 357 ASN cc_start: 0.8654 (m110) cc_final: 0.8138 (m-40) REVERT: b 371 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8493 (mt-10) REVERT: b 390 GLU cc_start: 0.8277 (pp20) cc_final: 0.7969 (pp20) REVERT: c 45 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.8947 (tm-30) REVERT: c 80 LYS cc_start: 0.9757 (tppt) cc_final: 0.9384 (tttt) REVERT: c 120 MET cc_start: 0.9469 (ttp) cc_final: 0.9203 (ttp) REVERT: c 159 LYS cc_start: 0.9085 (mppt) cc_final: 0.8740 (mppt) REVERT: c 161 MET cc_start: 0.9458 (mmm) cc_final: 0.9043 (mmm) REVERT: e 139 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9288 (pp20) REVERT: e 205 MET cc_start: 0.9540 (mmt) cc_final: 0.8979 (mpp) REVERT: e 218 GLU cc_start: 0.9387 (tt0) cc_final: 0.8989 (tt0) REVERT: e 371 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8398 (mt-10) REVERT: f 89 GLN cc_start: 0.9574 (mt0) cc_final: 0.9195 (mm110) REVERT: f 263 LYS cc_start: 0.9549 (ttmt) cc_final: 0.9196 (ttpp) REVERT: g 32 GLU cc_start: 0.9159 (pt0) cc_final: 0.8696 (pm20) REVERT: i 63 GLN cc_start: 0.9320 (tp-100) cc_final: 0.9106 (tp-100) REVERT: i 80 LYS cc_start: 0.9714 (tppp) cc_final: 0.9399 (tptm) REVERT: i 120 MET cc_start: 0.8011 (mmm) cc_final: 0.7749 (mmm) REVERT: i 131 GLN cc_start: 0.9081 (pp30) cc_final: 0.8871 (pp30) REVERT: i 161 MET cc_start: 0.9079 (mmm) cc_final: 0.8608 (mmm) REVERT: i 225 LYS cc_start: 0.9394 (tttt) cc_final: 0.9167 (tttm) REVERT: j 32 GLU cc_start: 0.9383 (pt0) cc_final: 0.8909 (pm20) REVERT: k 139 GLU cc_start: 0.8697 (pp20) cc_final: 0.8447 (pp20) REVERT: k 147 ARG cc_start: 0.9123 (ttp80) cc_final: 0.8821 (ttp-110) REVERT: k 205 MET cc_start: 0.9560 (OUTLIER) cc_final: 0.8532 (mmt) REVERT: k 218 GLU cc_start: 0.9183 (tt0) cc_final: 0.8793 (tt0) REVERT: k 308 GLU cc_start: 0.8699 (mp0) cc_final: 0.8361 (mp0) REVERT: k 371 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: l 63 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8871 (mm-40) REVERT: l 80 LYS cc_start: 0.9742 (tppt) cc_final: 0.9539 (mmmm) REVERT: l 134 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9105 (mm-40) REVERT: l 150 GLN cc_start: 0.9415 (tp-100) cc_final: 0.9108 (tp-100) REVERT: l 161 MET cc_start: 0.9162 (mmm) cc_final: 0.8931 (mmm) REVERT: n 146 LEU cc_start: 0.9524 (mm) cc_final: 0.8937 (mm) REVERT: n 147 ARG cc_start: 0.9545 (ttp-110) cc_final: 0.9070 (mtm110) REVERT: n 371 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: o 57 MET cc_start: 0.9288 (tpt) cc_final: 0.8967 (mmm) REVERT: o 89 GLN cc_start: 0.8976 (pt0) cc_final: 0.8643 (pm20) REVERT: o 112 MET cc_start: 0.8968 (tpp) cc_final: 0.8758 (tpp) REVERT: o 120 MET cc_start: 0.9598 (mtp) cc_final: 0.8847 (tpp) REVERT: o 131 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: v 57 MET cc_start: 0.7540 (mmm) cc_final: 0.6545 (mmm) REVERT: v 59 GLU cc_start: 0.8508 (tt0) cc_final: 0.8152 (pt0) REVERT: v 63 GLN cc_start: 0.9835 (mm-40) cc_final: 0.9525 (tp-100) REVERT: v 80 LYS cc_start: 0.9531 (ttmm) cc_final: 0.9281 (ttmt) REVERT: v 125 PHE cc_start: 0.8549 (m-80) cc_final: 0.8114 (t80) REVERT: y 139 GLU cc_start: 0.9505 (pt0) cc_final: 0.9245 (pp20) REVERT: y 140 LEU cc_start: 0.9856 (pp) cc_final: 0.9597 (pp) REVERT: y 146 LEU cc_start: 0.9473 (mm) cc_final: 0.9103 (mm) REVERT: z 22 ASP cc_start: 0.8898 (t0) cc_final: 0.8570 (t0) REVERT: z 50 LEU cc_start: 0.9375 (tp) cc_final: 0.9051 (tp) REVERT: z 57 MET cc_start: 0.9106 (tpt) cc_final: 0.8894 (mmm) REVERT: z 59 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.9058 (mt-10) REVERT: z 91 GLU cc_start: 0.9365 (tp30) cc_final: 0.8756 (tp30) REVERT: z 92 LEU cc_start: 0.9648 (mt) cc_final: 0.9361 (mm) REVERT: z 115 ASP cc_start: 0.9646 (p0) cc_final: 0.9416 (p0) outliers start: 81 outliers final: 22 residues processed: 610 average time/residue: 1.7838 time to fit residues: 1315.5667 Evaluate side-chains 531 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 496 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 374 ASN Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 131 GLN Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 98 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 59 GLU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 619 optimal weight: 9.9990 chunk 416 optimal weight: 30.0000 chunk 263 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 658 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 339 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 chunk 458 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 HIS ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 131 GLN a 25 GLN b 374 ASN ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 201 ASN n 188 GLN n 305 HIS n 357 ASN z 63 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.032514 restraints weight = 229844.608| |-----------------------------------------------------------------------------| r_work (start): 0.2514 rms_B_bonded: 3.56 r_work: 0.2375 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 56894 Z= 0.294 Angle : 0.599 12.395 77036 Z= 0.307 Chirality : 0.044 0.253 8370 Planarity : 0.004 0.051 10228 Dihedral : 4.208 22.262 7998 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 13.47 % Favored : 84.89 % 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: 0.14 (0.10), residues: 7036 helix: 2.13 (0.16), residues: 1130 sheet: -0.25 (0.12), residues: 1895 loop : -0.26 (0.09), residues: 4011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 301 HIS 0.008 0.001 HIS H 55 PHE 0.025 0.001 PHE c 195 TYR 0.020 0.001 TYR A 387 ARG 0.013 0.000 ARG e 147 *********************** 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 647 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 551 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.9311 (mtt) cc_final: 0.9090 (ttm) REVERT: A 252 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9276 (ttpp) REVERT: B 22 ASP cc_start: 0.8259 (m-30) cc_final: 0.7818 (m-30) REVERT: D 185 GLU cc_start: 0.8857 (pp20) cc_final: 0.8545 (pp20) REVERT: E 89 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: E 120 MET cc_start: 0.9444 (ttp) cc_final: 0.8959 (ttm) REVERT: E 131 GLN cc_start: 0.9165 (mp10) cc_final: 0.8925 (mm-40) REVERT: E 145 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9019 (mm-30) REVERT: G 139 GLU cc_start: 0.9525 (pt0) cc_final: 0.9296 (pp20) REVERT: G 146 LEU cc_start: 0.9389 (mm) cc_final: 0.8882 (mm) REVERT: G 371 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8829 (mm-30) REVERT: H 134 GLN cc_start: 0.8896 (mp10) cc_final: 0.8394 (mm110) REVERT: H 137 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9000 (pt0) REVERT: H 161 MET cc_start: 0.9375 (mmm) cc_final: 0.8939 (mmm) REVERT: J 185 GLU cc_start: 0.9309 (tm-30) cc_final: 0.9049 (tm-30) REVERT: K 89 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: K 120 MET cc_start: 0.9254 (ptm) cc_final: 0.8373 (ppp) REVERT: K 131 GLN cc_start: 0.9493 (tp40) cc_final: 0.9159 (tp40) REVERT: K 134 GLN cc_start: 0.8900 (pp30) cc_final: 0.8680 (pp30) REVERT: K 161 MET cc_start: 0.9436 (mmm) cc_final: 0.9089 (mmm) REVERT: K 162 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.8143 (ptp) REVERT: L 32 GLU cc_start: 0.9291 (pt0) cc_final: 0.8787 (pm20) REVERT: M 135 LYS cc_start: 0.8061 (tptp) cc_final: 0.6790 (tptp) REVERT: M 139 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9354 (tm-30) REVERT: M 276 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8634 (tm-30) REVERT: M 371 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8235 (mt-10) REVERT: N 63 GLN cc_start: 0.9378 (tp-100) cc_final: 0.8846 (tm-30) REVERT: N 89 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: P 205 MET cc_start: 0.9587 (mmt) cc_final: 0.9177 (mpp) REVERT: Q 63 GLN cc_start: 0.9454 (tm-30) cc_final: 0.8946 (tm-30) REVERT: Q 120 MET cc_start: 0.8188 (tpp) cc_final: 0.7871 (tpp) REVERT: Q 131 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8932 (tp-100) REVERT: Q 150 GLN cc_start: 0.9437 (tp-100) cc_final: 0.9014 (tp-100) REVERT: Q 161 MET cc_start: 0.9305 (mmm) cc_final: 0.8878 (mmm) REVERT: S 147 ARG cc_start: 0.9373 (ttp-110) cc_final: 0.9108 (mtm110) REVERT: S 182 GLU cc_start: 0.8616 (tt0) cc_final: 0.8373 (tt0) REVERT: S 276 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8719 (tm-30) REVERT: S 371 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8458 (mt-10) REVERT: S 390 GLU cc_start: 0.8059 (pp20) cc_final: 0.7763 (pp20) REVERT: T 89 GLN cc_start: 0.8907 (mt0) cc_final: 0.8514 (mp10) REVERT: T 120 MET cc_start: 0.8189 (tmm) cc_final: 0.7747 (tmm) REVERT: T 161 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8949 (mmm) REVERT: T 263 LYS cc_start: 0.9279 (ttmt) cc_final: 0.9070 (ttpp) REVERT: U 24 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (ttpp) REVERT: U 32 GLU cc_start: 0.9359 (pt0) cc_final: 0.8760 (pm20) REVERT: V 145 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8764 (mpp) REVERT: V 182 GLU cc_start: 0.8868 (tt0) cc_final: 0.8648 (tt0) REVERT: V 185 GLU cc_start: 0.9042 (pp20) cc_final: 0.8814 (pp20) REVERT: V 308 GLU cc_start: 0.8766 (mp0) cc_final: 0.8477 (mp0) REVERT: W 57 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8425 (mmm) REVERT: W 120 MET cc_start: 0.7960 (tpp) cc_final: 0.7597 (tpp) REVERT: W 137 GLU cc_start: 0.9414 (mp0) cc_final: 0.9163 (mp0) REVERT: W 227 MET cc_start: 0.9344 (tpp) cc_final: 0.9049 (tpp) REVERT: X 32 GLU cc_start: 0.9069 (pt0) cc_final: 0.8564 (pm20) REVERT: Y 143 GLU cc_start: 0.9681 (mm-30) cc_final: 0.9472 (mp0) REVERT: Y 205 MET cc_start: 0.9399 (mpp) cc_final: 0.9014 (mpp) REVERT: Y 276 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8630 (tm-30) REVERT: Y 371 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: Y 390 GLU cc_start: 0.8017 (pp20) cc_final: 0.7686 (pp20) REVERT: Z 57 MET cc_start: 0.9152 (mtm) cc_final: 0.8791 (mmm) REVERT: Z 150 GLN cc_start: 0.9296 (pp30) cc_final: 0.9008 (pp30) REVERT: Z 161 MET cc_start: 0.9287 (mmm) cc_final: 0.9022 (mmm) REVERT: b 136 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9062 (t) REVERT: b 139 GLU cc_start: 0.9491 (pt0) cc_final: 0.8854 (pp20) REVERT: b 143 GLU cc_start: 0.9746 (mm-30) cc_final: 0.9427 (mp0) REVERT: b 145 MET cc_start: 0.9452 (mtp) cc_final: 0.8886 (ttm) REVERT: b 185 GLU cc_start: 0.8784 (pp20) cc_final: 0.8555 (pp20) REVERT: b 205 MET cc_start: 0.9410 (mpp) cc_final: 0.9045 (mpp) REVERT: b 218 GLU cc_start: 0.9262 (tt0) cc_final: 0.8808 (tt0) REVERT: b 353 GLU cc_start: 0.8839 (tp30) cc_final: 0.8203 (tp30) REVERT: b 357 ASN cc_start: 0.8687 (m110) cc_final: 0.8117 (m-40) REVERT: b 371 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8520 (mt-10) REVERT: b 390 GLU cc_start: 0.8345 (pp20) cc_final: 0.7952 (pp20) REVERT: c 107 LYS cc_start: 0.9314 (ptpp) cc_final: 0.9101 (ptmm) REVERT: c 120 MET cc_start: 0.9468 (ttp) cc_final: 0.9150 (ttp) REVERT: c 159 LYS cc_start: 0.9178 (mppt) cc_final: 0.8899 (mppt) REVERT: c 161 MET cc_start: 0.9420 (mmm) cc_final: 0.8986 (mmm) REVERT: e 139 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9245 (pp20) REVERT: e 147 ARG cc_start: 0.9538 (ttp-110) cc_final: 0.9018 (ptp-170) REVERT: e 185 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8632 (pp20) REVERT: e 218 GLU cc_start: 0.9404 (tt0) cc_final: 0.9030 (tt0) REVERT: e 276 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8838 (tm-30) REVERT: e 371 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8433 (mt-10) REVERT: f 64 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8909 (t80) REVERT: f 89 GLN cc_start: 0.9559 (mt0) cc_final: 0.9213 (mm110) REVERT: f 263 LYS cc_start: 0.9534 (ttmt) cc_final: 0.9190 (ttpp) REVERT: g 32 GLU cc_start: 0.9154 (pt0) cc_final: 0.8832 (pm20) REVERT: h 139 GLU cc_start: 0.9282 (pt0) cc_final: 0.8994 (pp20) REVERT: h 218 GLU cc_start: 0.9122 (tt0) cc_final: 0.8799 (tt0) REVERT: h 276 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8722 (tm-30) REVERT: h 371 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8262 (mt-10) REVERT: i 63 GLN cc_start: 0.9340 (tp-100) cc_final: 0.9124 (tp-100) REVERT: i 120 MET cc_start: 0.8393 (mmm) cc_final: 0.8038 (mmm) REVERT: i 161 MET cc_start: 0.9096 (mmm) cc_final: 0.8517 (mmm) REVERT: i 225 LYS cc_start: 0.9399 (tttt) cc_final: 0.9178 (tttm) REVERT: i 263 LYS cc_start: 0.9337 (ptmm) cc_final: 0.9087 (ttpp) REVERT: j 32 GLU cc_start: 0.9436 (pt0) cc_final: 0.8960 (pm20) REVERT: k 185 GLU cc_start: 0.9356 (tm-30) cc_final: 0.9083 (pp20) REVERT: k 205 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.8612 (mmt) REVERT: k 218 GLU cc_start: 0.9205 (tt0) cc_final: 0.8805 (tt0) REVERT: k 308 GLU cc_start: 0.8773 (mp0) cc_final: 0.8402 (mp0) REVERT: k 371 GLU cc_start: 0.8509 (mp0) cc_final: 0.7853 (mp0) REVERT: l 63 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8883 (mm-40) REVERT: l 134 GLN cc_start: 0.9433 (mm-40) cc_final: 0.9167 (mm-40) REVERT: l 150 GLN cc_start: 0.9447 (tp-100) cc_final: 0.9145 (tp-100) REVERT: l 161 MET cc_start: 0.9264 (mmm) cc_final: 0.8999 (mmm) REVERT: l 263 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8752 (ttpp) REVERT: n 146 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.8932 (mm) REVERT: n 147 ARG cc_start: 0.9543 (ttp-110) cc_final: 0.9070 (mtm110) REVERT: n 371 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: o 57 MET cc_start: 0.9285 (tpt) cc_final: 0.9002 (mmm) REVERT: o 112 MET cc_start: 0.9089 (tpp) cc_final: 0.8833 (tpp) REVERT: o 120 MET cc_start: 0.9591 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: o 161 MET cc_start: 0.9306 (mmm) cc_final: 0.9058 (mmm) REVERT: v 22 ASP cc_start: 0.8228 (m-30) cc_final: 0.7844 (m-30) REVERT: v 57 MET cc_start: 0.7760 (mmm) cc_final: 0.6735 (mmm) REVERT: v 59 GLU cc_start: 0.8518 (tt0) cc_final: 0.8176 (pt0) REVERT: v 63 GLN cc_start: 0.9840 (mm-40) cc_final: 0.9624 (tp-100) REVERT: v 80 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9283 (ttpp) REVERT: v 125 PHE cc_start: 0.8655 (m-80) cc_final: 0.8198 (t80) REVERT: y 139 GLU cc_start: 0.9565 (pt0) cc_final: 0.9298 (pp20) REVERT: z 22 ASP cc_start: 0.8951 (t0) cc_final: 0.8622 (t0) REVERT: z 50 LEU cc_start: 0.9333 (tp) cc_final: 0.8987 (tp) REVERT: z 54 THR cc_start: 0.9615 (m) cc_final: 0.9212 (p) REVERT: z 59 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (mt-10) REVERT: z 60 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8972 (mm-30) REVERT: z 91 GLU cc_start: 0.9414 (tp30) cc_final: 0.9054 (tp30) outliers start: 96 outliers final: 31 residues processed: 615 average time/residue: 1.7591 time to fit residues: 1309.1669 Evaluate side-chains 553 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 504 time to evaluate : 4.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain U residue 24 LYS Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 64 TYR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 59 GLU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 584 optimal weight: 0.9990 chunk 659 optimal weight: 6.9990 chunk 205 optimal weight: 0.0370 chunk 417 optimal weight: 9.9990 chunk 687 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 602 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 512 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 445 optimal weight: 1.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 ASN ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 188 GLN k 360 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.032707 restraints weight = 229591.383| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 3.56 r_work: 0.2385 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56894 Z= 0.242 Angle : 0.595 12.637 77036 Z= 0.303 Chirality : 0.044 0.338 8370 Planarity : 0.004 0.073 10228 Dihedral : 4.094 21.164 7998 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.42 % Allowed : 14.73 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.10), residues: 7036 helix: 2.15 (0.16), residues: 1130 sheet: -0.22 (0.12), residues: 1899 loop : -0.20 (0.09), residues: 4007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 301 HIS 0.006 0.001 HIS v 67 PHE 0.024 0.001 PHE c 195 TYR 0.020 0.001 TYR A 387 ARG 0.016 0.000 ARG A 147 *********************** 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 629 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 546 time to evaluate : 5.042 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 145 MET cc_start: 0.9343 (mtt) cc_final: 0.9129 (ttm) REVERT: A 147 ARG cc_start: 0.9176 (mtm110) cc_final: 0.8821 (mtm110) REVERT: A 252 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9274 (ttpp) REVERT: B 22 ASP cc_start: 0.8199 (m-30) cc_final: 0.7735 (m-30) REVERT: B 57 MET cc_start: 0.8400 (mmm) cc_final: 0.8018 (mmp) REVERT: B 159 LYS cc_start: 0.9193 (mppt) cc_final: 0.8943 (mppt) REVERT: D 185 GLU cc_start: 0.8911 (pp20) cc_final: 0.8615 (pp20) REVERT: E 89 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: E 112 MET cc_start: 0.8508 (tpp) cc_final: 0.8203 (tpp) REVERT: E 120 MET cc_start: 0.9469 (ttp) cc_final: 0.9116 (OUTLIER) REVERT: E 131 GLN cc_start: 0.9248 (mp10) cc_final: 0.8987 (mm-40) REVERT: E 145 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9033 (mm-30) REVERT: G 139 GLU cc_start: 0.9526 (pt0) cc_final: 0.9296 (pp20) REVERT: G 146 LEU cc_start: 0.9360 (mm) cc_final: 0.8911 (mm) REVERT: G 371 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8842 (mm-30) REVERT: H 134 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8347 (mm110) REVERT: H 137 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8982 (pt0) REVERT: H 161 MET cc_start: 0.9404 (mmm) cc_final: 0.8994 (mmm) REVERT: J 185 GLU cc_start: 0.9280 (tm-30) cc_final: 0.9041 (tm-30) REVERT: J 308 GLU cc_start: 0.8772 (mp0) cc_final: 0.8181 (mp0) REVERT: K 89 GLN cc_start: 0.9433 (pt0) cc_final: 0.9013 (mp10) REVERT: K 120 MET cc_start: 0.9219 (ptm) cc_final: 0.8371 (ppp) REVERT: K 131 GLN cc_start: 0.9512 (tp40) cc_final: 0.9169 (tp40) REVERT: K 134 GLN cc_start: 0.8911 (pp30) cc_final: 0.8652 (pp30) REVERT: K 161 MET cc_start: 0.9446 (mmm) cc_final: 0.9094 (mmm) REVERT: K 162 MET cc_start: 0.9592 (OUTLIER) cc_final: 0.8052 (ptp) REVERT: L 32 GLU cc_start: 0.9310 (pt0) cc_final: 0.8787 (pm20) REVERT: M 135 LYS cc_start: 0.7967 (tptp) cc_final: 0.6557 (tptp) REVERT: M 139 GLU cc_start: 0.9585 (mt-10) cc_final: 0.9263 (tm-30) REVERT: M 252 LYS cc_start: 0.9507 (ttpt) cc_final: 0.9263 (ttpt) REVERT: M 276 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8655 (tm-30) REVERT: M 371 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8287 (mt-10) REVERT: M 390 GLU cc_start: 0.8327 (pp20) cc_final: 0.8080 (pp20) REVERT: N 50 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9248 (pt) REVERT: N 63 GLN cc_start: 0.9417 (tp40) cc_final: 0.8910 (tm-30) REVERT: N 89 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: P 145 MET cc_start: 0.8953 (mtm) cc_final: 0.8717 (ptp) REVERT: P 205 MET cc_start: 0.9564 (mmt) cc_final: 0.9212 (mpp) REVERT: Q 22 ASP cc_start: 0.8597 (t0) cc_final: 0.8234 (p0) REVERT: Q 63 GLN cc_start: 0.9458 (tm-30) cc_final: 0.8926 (tm-30) REVERT: Q 120 MET cc_start: 0.8216 (tpp) cc_final: 0.7863 (tpp) REVERT: Q 131 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8864 (tp-100) REVERT: Q 150 GLN cc_start: 0.9449 (tp-100) cc_final: 0.9010 (tp-100) REVERT: Q 161 MET cc_start: 0.9348 (mmm) cc_final: 0.8968 (mmm) REVERT: R 24 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8910 (ttmt) REVERT: S 182 GLU cc_start: 0.8588 (tt0) cc_final: 0.8342 (tt0) REVERT: S 276 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8729 (tm-30) REVERT: S 390 GLU cc_start: 0.8094 (pp20) cc_final: 0.7725 (pp20) REVERT: T 89 GLN cc_start: 0.8867 (mt0) cc_final: 0.8572 (mp10) REVERT: T 120 MET cc_start: 0.8331 (tmm) cc_final: 0.7855 (tmm) REVERT: T 161 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8971 (mmm) REVERT: U 32 GLU cc_start: 0.9352 (pt0) cc_final: 0.8748 (pm20) REVERT: V 145 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8930 (mpp) REVERT: V 185 GLU cc_start: 0.9063 (pp20) cc_final: 0.8847 (pp20) REVERT: V 308 GLU cc_start: 0.8761 (mp0) cc_final: 0.8444 (mp0) REVERT: W 57 MET cc_start: 0.8790 (mmm) cc_final: 0.8398 (mmm) REVERT: W 120 MET cc_start: 0.8095 (tpp) cc_final: 0.7546 (tpp) REVERT: W 137 GLU cc_start: 0.9488 (mp0) cc_final: 0.9265 (mp0) REVERT: W 227 MET cc_start: 0.9345 (tpp) cc_final: 0.9056 (tpp) REVERT: X 32 GLU cc_start: 0.9074 (pt0) cc_final: 0.8354 (pm20) REVERT: Y 138 TYR cc_start: 0.9363 (t80) cc_final: 0.8899 (t80) REVERT: Y 142 ARG cc_start: 0.9655 (mmm160) cc_final: 0.9206 (ttm110) REVERT: Y 205 MET cc_start: 0.9398 (mpp) cc_final: 0.9009 (mpp) REVERT: Y 218 GLU cc_start: 0.9087 (tt0) cc_final: 0.8672 (tt0) REVERT: Y 276 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8605 (tm-30) REVERT: Y 308 GLU cc_start: 0.8799 (mp0) cc_final: 0.8553 (mp0) REVERT: Y 371 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: Z 57 MET cc_start: 0.9159 (mtm) cc_final: 0.8868 (mmm) REVERT: Z 150 GLN cc_start: 0.9289 (pp30) cc_final: 0.8967 (pp30) REVERT: Z 161 MET cc_start: 0.9303 (mmm) cc_final: 0.8985 (mmm) REVERT: b 136 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.9081 (t) REVERT: b 139 GLU cc_start: 0.9498 (pt0) cc_final: 0.9005 (pp20) REVERT: b 143 GLU cc_start: 0.9735 (mm-30) cc_final: 0.9492 (mm-30) REVERT: b 218 GLU cc_start: 0.9245 (tt0) cc_final: 0.8800 (tt0) REVERT: b 357 ASN cc_start: 0.8711 (m110) cc_final: 0.8219 (m-40) REVERT: b 371 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8521 (mt-10) REVERT: b 390 GLU cc_start: 0.8389 (pp20) cc_final: 0.8024 (pp20) REVERT: c 80 LYS cc_start: 0.9745 (tppt) cc_final: 0.9445 (tttm) REVERT: c 120 MET cc_start: 0.9477 (ttp) cc_final: 0.9163 (ttp) REVERT: c 159 LYS cc_start: 0.9173 (mppt) cc_final: 0.8878 (mppt) REVERT: c 161 MET cc_start: 0.9411 (mmm) cc_final: 0.8990 (mmm) REVERT: e 147 ARG cc_start: 0.9540 (ttp-110) cc_final: 0.8883 (mtm110) REVERT: e 185 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8664 (pp20) REVERT: e 218 GLU cc_start: 0.9384 (tt0) cc_final: 0.8980 (tt0) REVERT: e 276 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8830 (tm-30) REVERT: e 371 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8478 (mt-10) REVERT: f 64 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8873 (t80) REVERT: f 89 GLN cc_start: 0.9506 (mt0) cc_final: 0.9142 (mp10) REVERT: f 263 LYS cc_start: 0.9553 (ttmt) cc_final: 0.9247 (ttpp) REVERT: g 32 GLU cc_start: 0.9147 (pt0) cc_final: 0.8774 (pm20) REVERT: h 139 GLU cc_start: 0.9286 (pt0) cc_final: 0.8968 (pp20) REVERT: h 218 GLU cc_start: 0.9058 (tt0) cc_final: 0.8642 (tt0) REVERT: h 276 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8687 (tm-30) REVERT: i 63 GLN cc_start: 0.9375 (tp-100) cc_final: 0.9156 (tp-100) REVERT: i 80 LYS cc_start: 0.9714 (tppp) cc_final: 0.9410 (tptm) REVERT: i 120 MET cc_start: 0.8458 (mmm) cc_final: 0.8066 (mmm) REVERT: i 161 MET cc_start: 0.9101 (mmm) cc_final: 0.8498 (mmm) REVERT: i 162 MET cc_start: 0.9635 (ptt) cc_final: 0.8762 (ptp) REVERT: j 32 GLU cc_start: 0.9449 (pt0) cc_final: 0.8988 (pm20) REVERT: k 218 GLU cc_start: 0.9172 (tt0) cc_final: 0.8745 (tt0) REVERT: k 308 GLU cc_start: 0.8806 (mp0) cc_final: 0.8414 (mp0) REVERT: k 371 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: l 134 GLN cc_start: 0.9508 (mm-40) cc_final: 0.9216 (mm-40) REVERT: l 150 GLN cc_start: 0.9460 (tp-100) cc_final: 0.9178 (tp-100) REVERT: l 161 MET cc_start: 0.9261 (mmm) cc_final: 0.8977 (mmm) REVERT: l 225 LYS cc_start: 0.9298 (tttm) cc_final: 0.9034 (tppp) REVERT: l 263 LYS cc_start: 0.9179 (ptmm) cc_final: 0.8839 (ttpp) REVERT: n 146 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.8905 (mm) REVERT: n 371 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: o 57 MET cc_start: 0.9296 (tpt) cc_final: 0.9047 (mmm) REVERT: o 87 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8681 (ttmt) REVERT: o 112 MET cc_start: 0.9142 (tpp) cc_final: 0.8821 (tpp) REVERT: o 120 MET cc_start: 0.9576 (mtp) cc_final: 0.8996 (mmm) REVERT: o 161 MET cc_start: 0.9272 (mmm) cc_final: 0.8870 (mmm) REVERT: u 147 ARG cc_start: 0.9505 (ttp80) cc_final: 0.9283 (ttp80) REVERT: v 22 ASP cc_start: 0.8202 (m-30) cc_final: 0.7828 (m-30) REVERT: v 59 GLU cc_start: 0.8527 (tt0) cc_final: 0.8195 (pt0) REVERT: v 63 GLN cc_start: 0.9833 (mm-40) cc_final: 0.9592 (tp40) REVERT: v 65 LEU cc_start: 0.9631 (mm) cc_final: 0.9330 (pp) REVERT: v 73 GLU cc_start: 0.8452 (pm20) cc_final: 0.8114 (pm20) REVERT: v 80 LYS cc_start: 0.9526 (ttmm) cc_final: 0.9228 (ttmt) REVERT: v 125 PHE cc_start: 0.8684 (m-80) cc_final: 0.8229 (t80) REVERT: y 139 GLU cc_start: 0.9599 (pt0) cc_final: 0.9337 (pp20) REVERT: y 146 LEU cc_start: 0.9534 (mm) cc_final: 0.9216 (mm) REVERT: z 22 ASP cc_start: 0.8972 (t0) cc_final: 0.8613 (t0) REVERT: z 50 LEU cc_start: 0.9331 (tp) cc_final: 0.8995 (tp) REVERT: z 91 GLU cc_start: 0.9446 (tp30) cc_final: 0.9130 (tp30) outliers start: 83 outliers final: 34 residues processed: 605 average time/residue: 1.7304 time to fit residues: 1268.4048 Evaluate side-chains 551 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 501 time to evaluate : 4.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 64 TYR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 389 optimal weight: 9.9990 chunk 459 optimal weight: 30.0000 chunk 357 optimal weight: 3.9990 chunk 384 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 543 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 360 optimal weight: 20.0000 chunk 293 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN L 25 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.031747 restraints weight = 232786.802| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 3.56 r_work: 0.2354 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 56894 Z= 0.394 Angle : 0.644 13.634 77036 Z= 0.326 Chirality : 0.044 0.270 8370 Planarity : 0.004 0.056 10228 Dihedral : 4.119 23.073 7998 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.84 % Allowed : 15.26 % Favored : 82.90 % 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: 0.25 (0.10), residues: 7036 helix: 2.14 (0.16), residues: 1131 sheet: -0.18 (0.11), residues: 1911 loop : -0.16 (0.09), residues: 3994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP n 301 HIS 0.007 0.001 HIS v 67 PHE 0.023 0.001 PHE Z 195 TYR 0.025 0.001 TYR A 138 ARG 0.014 0.000 ARG G 147 *********************** 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 640 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 532 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.9202 (mtm110) cc_final: 0.8860 (mtm110) REVERT: A 252 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9247 (ttpp) REVERT: B 22 ASP cc_start: 0.8135 (m-30) cc_final: 0.7688 (m-30) REVERT: B 57 MET cc_start: 0.8497 (mmm) cc_final: 0.8269 (mmm) REVERT: B 159 LYS cc_start: 0.9226 (mppt) cc_final: 0.8962 (mppt) REVERT: B 227 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9106 (tpt) REVERT: D 147 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.8772 (mtm110) REVERT: D 185 GLU cc_start: 0.8975 (pp20) cc_final: 0.8672 (pp20) REVERT: E 89 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: E 112 MET cc_start: 0.8522 (tpp) cc_final: 0.8213 (tpp) REVERT: E 120 MET cc_start: 0.9453 (ttp) cc_final: 0.9037 (OUTLIER) REVERT: E 131 GLN cc_start: 0.9295 (mp10) cc_final: 0.9084 (mm-40) REVERT: E 145 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.9047 (mm-30) REVERT: G 146 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8938 (mm) REVERT: G 205 MET cc_start: 0.9603 (mmm) cc_final: 0.7880 (mmm) REVERT: G 371 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8837 (mm-30) REVERT: H 134 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8512 (mm110) REVERT: H 137 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8999 (pt0) REVERT: H 161 MET cc_start: 0.9386 (mmm) cc_final: 0.8857 (mmm) REVERT: J 185 GLU cc_start: 0.9295 (tm-30) cc_final: 0.9053 (tm-30) REVERT: K 89 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8987 (pm20) REVERT: K 120 MET cc_start: 0.9310 (ptm) cc_final: 0.8740 (tmm) REVERT: K 131 GLN cc_start: 0.9500 (tp40) cc_final: 0.9134 (tp40) REVERT: K 134 GLN cc_start: 0.8927 (pp30) cc_final: 0.8632 (pp30) REVERT: K 161 MET cc_start: 0.9457 (mmm) cc_final: 0.9055 (mmm) REVERT: K 162 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.8107 (ptp) REVERT: L 32 GLU cc_start: 0.9384 (pt0) cc_final: 0.8924 (pm20) REVERT: M 135 LYS cc_start: 0.7946 (tptp) cc_final: 0.6439 (tptp) REVERT: M 139 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9284 (tm-30) REVERT: M 182 GLU cc_start: 0.9087 (tt0) cc_final: 0.8801 (tt0) REVERT: M 252 LYS cc_start: 0.9520 (ttpt) cc_final: 0.9241 (ttpt) REVERT: M 276 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8663 (tm-30) REVERT: M 371 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8290 (mt-10) REVERT: N 50 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9236 (pt) REVERT: N 63 GLN cc_start: 0.9465 (tp40) cc_final: 0.8947 (tm-30) REVERT: N 89 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8664 (mp10) REVERT: N 150 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8592 (tp-100) REVERT: P 145 MET cc_start: 0.8956 (mtm) cc_final: 0.8709 (ptp) REVERT: P 205 MET cc_start: 0.9562 (mmt) cc_final: 0.9203 (mpp) REVERT: Q 22 ASP cc_start: 0.8664 (t0) cc_final: 0.8284 (p0) REVERT: Q 63 GLN cc_start: 0.9495 (tm-30) cc_final: 0.8957 (tm-30) REVERT: Q 120 MET cc_start: 0.8374 (tpp) cc_final: 0.7978 (tpp) REVERT: Q 131 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8850 (tp-100) REVERT: Q 150 GLN cc_start: 0.9463 (tp-100) cc_final: 0.9048 (tp-100) REVERT: Q 161 MET cc_start: 0.9322 (mmm) cc_final: 0.8890 (mmm) REVERT: S 182 GLU cc_start: 0.8723 (tt0) cc_final: 0.8514 (tt0) REVERT: S 276 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8782 (tm-30) REVERT: S 371 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8405 (mt-10) REVERT: S 390 GLU cc_start: 0.8140 (pp20) cc_final: 0.7784 (pp20) REVERT: T 87 LYS cc_start: 0.8367 (tppt) cc_final: 0.7923 (tptm) REVERT: T 89 GLN cc_start: 0.8751 (mt0) cc_final: 0.8301 (mp10) REVERT: T 120 MET cc_start: 0.8285 (tmm) cc_final: 0.7805 (tmm) REVERT: T 161 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9025 (mmm) REVERT: U 32 GLU cc_start: 0.9384 (pt0) cc_final: 0.8956 (pm20) REVERT: V 308 GLU cc_start: 0.8774 (mp0) cc_final: 0.8433 (mp0) REVERT: W 57 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8595 (mmm) REVERT: W 120 MET cc_start: 0.8268 (tpp) cc_final: 0.7621 (tpp) REVERT: W 137 GLU cc_start: 0.9512 (mp0) cc_final: 0.9288 (mp0) REVERT: W 227 MET cc_start: 0.9325 (tpp) cc_final: 0.9038 (tpp) REVERT: Y 138 TYR cc_start: 0.9405 (t80) cc_final: 0.8956 (t80) REVERT: Y 142 ARG cc_start: 0.9663 (mmm160) cc_final: 0.9228 (ttm110) REVERT: Y 143 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9448 (mp0) REVERT: Y 205 MET cc_start: 0.9438 (mpp) cc_final: 0.9043 (mpp) REVERT: Y 218 GLU cc_start: 0.9127 (tt0) cc_final: 0.8706 (tt0) REVERT: Y 276 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8603 (tm-30) REVERT: Y 308 GLU cc_start: 0.8817 (mp0) cc_final: 0.8574 (mp0) REVERT: Y 371 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: Y 390 GLU cc_start: 0.8154 (pp20) cc_final: 0.7952 (pp20) REVERT: Z 57 MET cc_start: 0.9338 (mtm) cc_final: 0.9012 (mmm) REVERT: Z 150 GLN cc_start: 0.9312 (pp30) cc_final: 0.8982 (pp30) REVERT: Z 161 MET cc_start: 0.9288 (mmm) cc_final: 0.8938 (mmm) REVERT: b 136 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9135 (t) REVERT: b 139 GLU cc_start: 0.9505 (pt0) cc_final: 0.9008 (pp20) REVERT: b 143 GLU cc_start: 0.9751 (mm-30) cc_final: 0.9500 (mm-30) REVERT: b 145 MET cc_start: 0.9386 (mtp) cc_final: 0.9080 (ttm) REVERT: b 185 GLU cc_start: 0.8810 (pp20) cc_final: 0.8561 (pp20) REVERT: b 218 GLU cc_start: 0.9276 (tt0) cc_final: 0.8845 (tt0) REVERT: b 371 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8461 (mt-10) REVERT: b 390 GLU cc_start: 0.8444 (pp20) cc_final: 0.8166 (pp20) REVERT: c 80 LYS cc_start: 0.9752 (tppt) cc_final: 0.9530 (mmmm) REVERT: c 120 MET cc_start: 0.9486 (ttp) cc_final: 0.9137 (ttp) REVERT: c 159 LYS cc_start: 0.9171 (mppt) cc_final: 0.8905 (mppt) REVERT: c 161 MET cc_start: 0.9396 (mmm) cc_final: 0.8937 (mmm) REVERT: e 218 GLU cc_start: 0.9402 (tt0) cc_final: 0.8989 (tt0) REVERT: e 276 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8835 (tm-30) REVERT: e 371 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8445 (mt-10) REVERT: f 89 GLN cc_start: 0.9497 (mt0) cc_final: 0.9180 (mm110) REVERT: f 263 LYS cc_start: 0.9526 (ttmt) cc_final: 0.9212 (ttpp) REVERT: g 32 GLU cc_start: 0.9184 (pt0) cc_final: 0.8676 (pm20) REVERT: h 139 GLU cc_start: 0.9268 (pt0) cc_final: 0.8956 (pp20) REVERT: h 218 GLU cc_start: 0.9128 (tt0) cc_final: 0.8711 (tt0) REVERT: h 276 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8741 (tm-30) REVERT: h 308 GLU cc_start: 0.8626 (mp0) cc_final: 0.8329 (mp0) REVERT: h 371 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8294 (mt-10) REVERT: i 120 MET cc_start: 0.8617 (mmm) cc_final: 0.8212 (mmm) REVERT: i 161 MET cc_start: 0.9138 (mmm) cc_final: 0.8525 (mmm) REVERT: j 32 GLU cc_start: 0.9445 (pt0) cc_final: 0.9014 (pm20) REVERT: k 147 ARG cc_start: 0.9161 (tmm-80) cc_final: 0.8918 (tmm-80) REVERT: k 185 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9004 (pp20) REVERT: k 218 GLU cc_start: 0.9231 (tt0) cc_final: 0.8835 (tt0) REVERT: k 308 GLU cc_start: 0.8878 (mp0) cc_final: 0.8462 (mp0) REVERT: k 371 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: l 63 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8848 (mm-40) REVERT: l 134 GLN cc_start: 0.9520 (mm-40) cc_final: 0.9224 (mm-40) REVERT: l 150 GLN cc_start: 0.9485 (tp-100) cc_final: 0.9221 (tp-100) REVERT: l 161 MET cc_start: 0.9307 (mmm) cc_final: 0.8995 (mmm) REVERT: l 225 LYS cc_start: 0.9316 (tttm) cc_final: 0.9037 (tppp) REVERT: l 263 LYS cc_start: 0.9168 (ptmm) cc_final: 0.8842 (ttpp) REVERT: n 147 ARG cc_start: 0.9557 (ttp-110) cc_final: 0.9027 (mtm110) REVERT: n 371 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: o 112 MET cc_start: 0.9163 (tpp) cc_final: 0.8798 (tpp) REVERT: o 120 MET cc_start: 0.9583 (mtp) cc_final: 0.8947 (mmm) REVERT: o 161 MET cc_start: 0.9204 (mmm) cc_final: 0.8584 (mmm) REVERT: v 22 ASP cc_start: 0.8228 (m-30) cc_final: 0.7864 (m-30) REVERT: v 59 GLU cc_start: 0.8443 (tt0) cc_final: 0.8032 (pt0) REVERT: v 63 GLN cc_start: 0.9839 (mm-40) cc_final: 0.9618 (tp40) REVERT: v 125 PHE cc_start: 0.8651 (m-80) cc_final: 0.8182 (t80) REVERT: y 139 GLU cc_start: 0.9603 (pt0) cc_final: 0.9338 (pp20) REVERT: y 146 LEU cc_start: 0.9537 (mm) cc_final: 0.9144 (mm) REVERT: z 22 ASP cc_start: 0.9002 (t0) cc_final: 0.8639 (t0) REVERT: z 46 VAL cc_start: 0.9329 (t) cc_final: 0.8964 (p) REVERT: z 47 ASP cc_start: 0.8460 (p0) cc_final: 0.7652 (p0) REVERT: z 50 LEU cc_start: 0.9291 (tp) cc_final: 0.9015 (tp) REVERT: z 54 THR cc_start: 0.9636 (m) cc_final: 0.9212 (p) REVERT: z 91 GLU cc_start: 0.9450 (tp30) cc_final: 0.9083 (tp30) REVERT: z 120 MET cc_start: 0.9113 (mtm) cc_final: 0.8102 (mpt) outliers start: 108 outliers final: 42 residues processed: 613 average time/residue: 1.6836 time to fit residues: 1254.6841 Evaluate side-chains 548 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 491 time to evaluate : 4.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 208 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 556 optimal weight: 9.9990 chunk 580 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 350 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 142 optimal weight: 0.0570 chunk 277 optimal weight: 5.9990 chunk 397 optimal weight: 2.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 55 HIS i 83 HIS k 360 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 188 GLN n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.032487 restraints weight = 229916.334| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 3.55 r_work: 0.2380 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 56894 Z= 0.237 Angle : 0.635 14.101 77036 Z= 0.319 Chirality : 0.044 0.294 8370 Planarity : 0.004 0.066 10228 Dihedral : 4.031 21.352 7998 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.54 % Allowed : 16.17 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.29 (0.10), residues: 7036 helix: 2.11 (0.16), residues: 1131 sheet: -0.19 (0.12), residues: 1895 loop : -0.10 (0.09), residues: 4010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 307 HIS 0.007 0.001 HIS v 67 PHE 0.022 0.001 PHE Z 195 TYR 0.018 0.001 TYR T 29 ARG 0.018 0.000 ARG e 147 *********************** 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 631 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 541 time to evaluate : 4.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.9301 (mtt) cc_final: 0.9015 (ttm) REVERT: A 252 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9288 (ttpt) REVERT: B 22 ASP cc_start: 0.8124 (m-30) cc_final: 0.7659 (m-30) REVERT: B 159 LYS cc_start: 0.9237 (mppt) cc_final: 0.8971 (mppt) REVERT: B 183 LYS cc_start: 0.9518 (tttt) cc_final: 0.9292 (ttmm) REVERT: B 227 MET cc_start: 0.9510 (OUTLIER) cc_final: 0.9122 (tpt) REVERT: D 147 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.8933 (mtm110) REVERT: D 182 GLU cc_start: 0.8760 (tt0) cc_final: 0.8389 (tt0) REVERT: D 185 GLU cc_start: 0.9009 (pp20) cc_final: 0.8729 (pp20) REVERT: E 89 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8319 (mp10) REVERT: E 112 MET cc_start: 0.8560 (tpp) cc_final: 0.8263 (tpp) REVERT: E 120 MET cc_start: 0.9434 (ttp) cc_final: 0.9046 (ttp) REVERT: E 145 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.9048 (mm-30) REVERT: G 146 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8979 (mm) REVERT: G 371 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8843 (mm-30) REVERT: H 71 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: H 80 LYS cc_start: 0.9426 (ttpt) cc_final: 0.9200 (ptmt) REVERT: H 134 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8572 (mm110) REVERT: H 137 GLU cc_start: 0.9320 (mt-10) cc_final: 0.9022 (pt0) REVERT: H 161 MET cc_start: 0.9418 (mmm) cc_final: 0.8752 (mmm) REVERT: J 185 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9038 (tm-30) REVERT: J 205 MET cc_start: 0.9676 (mmm) cc_final: 0.8119 (mmm) REVERT: K 80 LYS cc_start: 0.9475 (ttpt) cc_final: 0.9255 (ptpt) REVERT: K 89 GLN cc_start: 0.9467 (pt0) cc_final: 0.9266 (pm20) REVERT: K 120 MET cc_start: 0.9278 (ptm) cc_final: 0.8636 (ppp) REVERT: K 131 GLN cc_start: 0.9489 (tp40) cc_final: 0.9079 (tp40) REVERT: K 134 GLN cc_start: 0.8899 (pp30) cc_final: 0.8585 (pp30) REVERT: K 161 MET cc_start: 0.9468 (mmm) cc_final: 0.9155 (mmm) REVERT: K 162 MET cc_start: 0.9592 (OUTLIER) cc_final: 0.8079 (ptp) REVERT: L 32 GLU cc_start: 0.9388 (pt0) cc_final: 0.8929 (pm20) REVERT: M 135 LYS cc_start: 0.8036 (tptp) cc_final: 0.6700 (tptp) REVERT: M 139 GLU cc_start: 0.9593 (mt-10) cc_final: 0.9251 (tm-30) REVERT: M 182 GLU cc_start: 0.9040 (tt0) cc_final: 0.8782 (tt0) REVERT: M 205 MET cc_start: 0.9744 (mmm) cc_final: 0.8424 (mmm) REVERT: M 252 LYS cc_start: 0.9506 (ttpt) cc_final: 0.9211 (ttpt) REVERT: M 371 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8283 (mt-10) REVERT: M 390 GLU cc_start: 0.8325 (pp20) cc_final: 0.8066 (pp20) REVERT: N 63 GLN cc_start: 0.9468 (tp40) cc_final: 0.8945 (tm-30) REVERT: N 80 LYS cc_start: 0.9650 (ttmt) cc_final: 0.9428 (ttpt) REVERT: N 89 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: P 205 MET cc_start: 0.9566 (mmt) cc_final: 0.9209 (mpp) REVERT: Q 22 ASP cc_start: 0.8678 (t0) cc_final: 0.8296 (p0) REVERT: Q 63 GLN cc_start: 0.9527 (tm-30) cc_final: 0.8989 (tm-30) REVERT: Q 120 MET cc_start: 0.8270 (tpp) cc_final: 0.7981 (tpp) REVERT: Q 131 GLN cc_start: 0.9229 (tp-100) cc_final: 0.8901 (tp-100) REVERT: Q 150 GLN cc_start: 0.9451 (tp-100) cc_final: 0.9021 (tp-100) REVERT: Q 161 MET cc_start: 0.9355 (mmm) cc_final: 0.8958 (mmm) REVERT: S 147 ARG cc_start: 0.9450 (ttp-110) cc_final: 0.9126 (mtm110) REVERT: S 182 GLU cc_start: 0.8650 (tt0) cc_final: 0.8415 (tt0) REVERT: S 276 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8768 (tm-30) REVERT: S 390 GLU cc_start: 0.8135 (pp20) cc_final: 0.7735 (OUTLIER) REVERT: T 89 GLN cc_start: 0.8757 (mt0) cc_final: 0.8550 (mt0) REVERT: T 120 MET cc_start: 0.8334 (tmm) cc_final: 0.7819 (tmm) REVERT: T 159 LYS cc_start: 0.9255 (mppt) cc_final: 0.8929 (mppt) REVERT: T 161 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9047 (mmm) REVERT: T 162 MET cc_start: 0.9550 (ptt) cc_final: 0.8425 (ptp) REVERT: U 32 GLU cc_start: 0.9402 (pt0) cc_final: 0.8733 (pm20) REVERT: V 218 GLU cc_start: 0.9083 (tt0) cc_final: 0.8423 (pt0) REVERT: V 371 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8526 (mt-10) REVERT: W 57 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8522 (mmm) REVERT: W 120 MET cc_start: 0.8231 (tpp) cc_final: 0.7787 (tpp) REVERT: W 137 GLU cc_start: 0.9529 (mp0) cc_final: 0.9316 (mp0) REVERT: W 227 MET cc_start: 0.9325 (tpp) cc_final: 0.9081 (tpp) REVERT: Y 138 TYR cc_start: 0.9398 (t80) cc_final: 0.8863 (t80) REVERT: Y 142 ARG cc_start: 0.9670 (mmm160) cc_final: 0.9166 (ttm110) REVERT: Y 185 GLU cc_start: 0.9316 (tm-30) cc_final: 0.9095 (pp20) REVERT: Y 186 LYS cc_start: 0.9604 (mttp) cc_final: 0.9382 (mttp) REVERT: Y 205 MET cc_start: 0.9426 (mpp) cc_final: 0.9046 (mpp) REVERT: Y 218 GLU cc_start: 0.9113 (tt0) cc_final: 0.8673 (tt0) REVERT: Y 276 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8586 (tm-30) REVERT: Y 308 GLU cc_start: 0.8817 (mp0) cc_final: 0.8556 (mp0) REVERT: Z 57 MET cc_start: 0.9280 (mtm) cc_final: 0.9005 (mmm) REVERT: Z 150 GLN cc_start: 0.9304 (pp30) cc_final: 0.8963 (pp30) REVERT: Z 161 MET cc_start: 0.9318 (mmm) cc_final: 0.9005 (mmm) REVERT: b 143 GLU cc_start: 0.9740 (mm-30) cc_final: 0.9530 (mm-30) REVERT: b 145 MET cc_start: 0.9352 (mtp) cc_final: 0.9014 (ttt) REVERT: b 185 GLU cc_start: 0.8856 (pp20) cc_final: 0.8630 (pp20) REVERT: b 218 GLU cc_start: 0.9271 (tt0) cc_final: 0.8858 (tt0) REVERT: b 371 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8485 (mt-10) REVERT: b 390 GLU cc_start: 0.8478 (pp20) cc_final: 0.8141 (pp20) REVERT: c 107 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9159 (ptpp) REVERT: c 120 MET cc_start: 0.9475 (ttp) cc_final: 0.9119 (ttp) REVERT: c 159 LYS cc_start: 0.9167 (mppt) cc_final: 0.8902 (mppt) REVERT: c 161 MET cc_start: 0.9398 (mmm) cc_final: 0.8918 (mmm) REVERT: e 139 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9126 (tm-30) REVERT: e 218 GLU cc_start: 0.9368 (tt0) cc_final: 0.8921 (tt0) REVERT: e 276 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8852 (tm-30) REVERT: e 371 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8503 (mt-10) REVERT: f 89 GLN cc_start: 0.9467 (mt0) cc_final: 0.9187 (mm110) REVERT: f 120 MET cc_start: 0.8010 (mmm) cc_final: 0.7572 (mmp) REVERT: f 263 LYS cc_start: 0.9517 (ttmt) cc_final: 0.9076 (ttpp) REVERT: g 32 GLU cc_start: 0.9122 (pt0) cc_final: 0.8729 (pm20) REVERT: h 139 GLU cc_start: 0.9293 (pt0) cc_final: 0.8987 (pp20) REVERT: h 218 GLU cc_start: 0.9125 (tt0) cc_final: 0.8721 (tt0) REVERT: h 276 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8704 (tm-30) REVERT: h 371 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8345 (mt-10) REVERT: i 120 MET cc_start: 0.8675 (mmm) cc_final: 0.8238 (mmm) REVERT: i 161 MET cc_start: 0.9175 (mmm) cc_final: 0.8533 (mmm) REVERT: i 162 MET cc_start: 0.9650 (ptt) cc_final: 0.8888 (ptp) REVERT: j 32 GLU cc_start: 0.9463 (pt0) cc_final: 0.9025 (pm20) REVERT: k 147 ARG cc_start: 0.9240 (tmm-80) cc_final: 0.8867 (ptt-90) REVERT: k 185 GLU cc_start: 0.9297 (tm-30) cc_final: 0.9009 (pp20) REVERT: k 205 MET cc_start: 0.9674 (OUTLIER) cc_final: 0.8739 (mmp) REVERT: k 218 GLU cc_start: 0.9201 (tt0) cc_final: 0.8817 (tt0) REVERT: k 308 GLU cc_start: 0.8903 (mp0) cc_final: 0.8475 (mp0) REVERT: k 371 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: l 63 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8818 (mm-40) REVERT: l 134 GLN cc_start: 0.9529 (mm-40) cc_final: 0.9211 (mm-40) REVERT: l 150 GLN cc_start: 0.9482 (tp-100) cc_final: 0.9230 (tp-100) REVERT: l 161 MET cc_start: 0.9305 (mmm) cc_final: 0.8965 (mmm) REVERT: l 225 LYS cc_start: 0.9312 (tttm) cc_final: 0.9056 (tppp) REVERT: n 146 LEU cc_start: 0.9423 (mm) cc_final: 0.8866 (mm) REVERT: n 147 ARG cc_start: 0.9549 (ttp-110) cc_final: 0.9066 (mtm110) REVERT: n 371 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: o 112 MET cc_start: 0.9202 (tpp) cc_final: 0.8760 (tpp) REVERT: o 120 MET cc_start: 0.9576 (mtp) cc_final: 0.8965 (mmm) REVERT: o 159 LYS cc_start: 0.9041 (mppt) cc_final: 0.8801 (mppt) REVERT: v 22 ASP cc_start: 0.8179 (m-30) cc_final: 0.7904 (m-30) REVERT: v 59 GLU cc_start: 0.8520 (tt0) cc_final: 0.8171 (pt0) REVERT: v 63 GLN cc_start: 0.9836 (mm-40) cc_final: 0.9572 (tp40) REVERT: v 65 LEU cc_start: 0.9575 (mm) cc_final: 0.9366 (pt) REVERT: v 71 ASP cc_start: 0.8240 (t0) cc_final: 0.7859 (t0) REVERT: v 80 LYS cc_start: 0.9489 (ttmm) cc_final: 0.9197 (ttpp) REVERT: v 125 PHE cc_start: 0.8662 (m-80) cc_final: 0.8235 (t80) REVERT: y 139 GLU cc_start: 0.9623 (pt0) cc_final: 0.9372 (pp20) REVERT: y 146 LEU cc_start: 0.9521 (mm) cc_final: 0.9148 (mm) REVERT: z 22 ASP cc_start: 0.9045 (t0) cc_final: 0.8695 (t0) REVERT: z 46 VAL cc_start: 0.9337 (t) cc_final: 0.8953 (p) REVERT: z 47 ASP cc_start: 0.8506 (p0) cc_final: 0.7734 (p0) REVERT: z 50 LEU cc_start: 0.9294 (tp) cc_final: 0.8938 (tp) REVERT: z 54 THR cc_start: 0.9646 (m) cc_final: 0.9218 (p) REVERT: z 73 GLU cc_start: 0.8393 (pm20) cc_final: 0.8174 (pm20) REVERT: z 120 MET cc_start: 0.9098 (mtm) cc_final: 0.8113 (mpt) outliers start: 90 outliers final: 46 residues processed: 606 average time/residue: 1.7174 time to fit residues: 1265.0411 Evaluate side-chains 566 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 507 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 102 ASP 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 e residue 231 CYS Chi-restraints excluded: chain e residue 319 ILE Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 236 optimal weight: 8.9990 chunk 448 optimal weight: 8.9990 chunk 447 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 551 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 519 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.031761 restraints weight = 232594.881| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 3.54 r_work: 0.2359 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 56894 Z= 0.364 Angle : 0.679 17.049 77036 Z= 0.339 Chirality : 0.044 0.310 8370 Planarity : 0.004 0.070 10228 Dihedral : 4.079 21.592 7998 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.54 % Allowed : 17.09 % Favored : 81.38 % 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: 0.28 (0.10), residues: 7036 helix: 2.00 (0.16), residues: 1131 sheet: -0.18 (0.12), residues: 1895 loop : -0.08 (0.10), residues: 4010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP k 301 HIS 0.007 0.001 HIS B 55 PHE 0.021 0.001 PHE c 195 TYR 0.027 0.001 TYR A 138 ARG 0.013 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 609 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 519 time to evaluate : 5.068 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 145 MET cc_start: 0.9210 (mtt) cc_final: 0.8899 (ttm) REVERT: A 146 LEU cc_start: 0.9532 (mm) cc_final: 0.9259 (mm) REVERT: A 252 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9274 (ttpt) REVERT: B 22 ASP cc_start: 0.8085 (m-30) cc_final: 0.7639 (m-30) REVERT: B 159 LYS cc_start: 0.9255 (mppt) cc_final: 0.8983 (mppt) REVERT: B 227 MET cc_start: 0.9511 (OUTLIER) cc_final: 0.9197 (tpt) REVERT: D 185 GLU cc_start: 0.9036 (pp20) cc_final: 0.8744 (pp20) REVERT: E 87 LYS cc_start: 0.8913 (tppt) cc_final: 0.8657 (tppt) REVERT: E 89 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: E 112 MET cc_start: 0.8524 (tpp) cc_final: 0.8207 (tpp) REVERT: E 120 MET cc_start: 0.9415 (ttp) cc_final: 0.9011 (ttp) REVERT: E 145 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9051 (mm-30) REVERT: G 146 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8967 (mm) REVERT: G 147 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8629 (ptt90) REVERT: G 371 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8842 (mm-30) REVERT: H 71 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: H 80 LYS cc_start: 0.9401 (ttpt) cc_final: 0.9158 (ptmt) REVERT: H 134 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8600 (mm110) REVERT: H 137 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9035 (pt0) REVERT: H 161 MET cc_start: 0.9404 (mmm) cc_final: 0.8821 (mmm) REVERT: J 185 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9034 (tm-30) REVERT: K 80 LYS cc_start: 0.9493 (ttpt) cc_final: 0.9176 (ptpt) REVERT: K 89 GLN cc_start: 0.9326 (pt0) cc_final: 0.8943 (pm20) REVERT: K 120 MET cc_start: 0.9324 (ptm) cc_final: 0.8677 (ppp) REVERT: K 131 GLN cc_start: 0.9494 (tp40) cc_final: 0.9085 (tp40) REVERT: K 134 GLN cc_start: 0.8923 (pp30) cc_final: 0.8605 (pp30) REVERT: K 161 MET cc_start: 0.9454 (mmm) cc_final: 0.9082 (mmm) REVERT: K 162 MET cc_start: 0.9617 (OUTLIER) cc_final: 0.8106 (ptp) REVERT: L 32 GLU cc_start: 0.9415 (pt0) cc_final: 0.8952 (pm20) REVERT: M 182 GLU cc_start: 0.9093 (tt0) cc_final: 0.8838 (tt0) REVERT: M 205 MET cc_start: 0.9740 (mmm) cc_final: 0.8449 (mmm) REVERT: M 252 LYS cc_start: 0.9505 (ttpt) cc_final: 0.9234 (ttpt) REVERT: M 371 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8318 (mt-10) REVERT: M 390 GLU cc_start: 0.8337 (pp20) cc_final: 0.8080 (pp20) REVERT: N 63 GLN cc_start: 0.9482 (tp40) cc_final: 0.8948 (tm-30) REVERT: N 66 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9060 (p) REVERT: N 80 LYS cc_start: 0.9660 (ttmt) cc_final: 0.9414 (ttpt) REVERT: N 89 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: N 263 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8999 (ttpm) REVERT: P 205 MET cc_start: 0.9589 (mmt) cc_final: 0.9189 (mpp) REVERT: Q 22 ASP cc_start: 0.8691 (t0) cc_final: 0.8362 (p0) REVERT: Q 63 GLN cc_start: 0.9526 (tm-30) cc_final: 0.8968 (tm-30) REVERT: Q 120 MET cc_start: 0.8431 (tpp) cc_final: 0.8115 (tpp) REVERT: Q 131 GLN cc_start: 0.9254 (tp-100) cc_final: 0.8912 (tp-100) REVERT: Q 150 GLN cc_start: 0.9473 (tp-100) cc_final: 0.9052 (tp-100) REVERT: Q 161 MET cc_start: 0.9359 (mmm) cc_final: 0.8965 (mmm) REVERT: S 205 MET cc_start: 0.9632 (mmm) cc_final: 0.8261 (mmm) REVERT: S 276 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8778 (tm-30) REVERT: S 371 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8445 (mt-10) REVERT: S 390 GLU cc_start: 0.8148 (pp20) cc_final: 0.7777 (pp20) REVERT: T 87 LYS cc_start: 0.8642 (tppt) cc_final: 0.8063 (tptm) REVERT: T 89 GLN cc_start: 0.8647 (mt0) cc_final: 0.8157 (mp10) REVERT: T 120 MET cc_start: 0.8314 (tmm) cc_final: 0.7804 (tmm) REVERT: T 161 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9065 (mmm) REVERT: U 32 GLU cc_start: 0.9410 (pt0) cc_final: 0.8809 (pm20) REVERT: V 218 GLU cc_start: 0.9122 (tt0) cc_final: 0.8483 (pt0) REVERT: V 308 GLU cc_start: 0.8769 (mp0) cc_final: 0.8422 (mp0) REVERT: W 57 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8644 (mmm) REVERT: W 120 MET cc_start: 0.8281 (tpp) cc_final: 0.7104 (tpp) REVERT: W 227 MET cc_start: 0.9306 (tpp) cc_final: 0.9082 (tpp) REVERT: Y 138 TYR cc_start: 0.9429 (t80) cc_final: 0.9170 (t80) REVERT: Y 205 MET cc_start: 0.9432 (mpp) cc_final: 0.9052 (mpp) REVERT: Y 218 GLU cc_start: 0.9146 (tt0) cc_final: 0.8726 (tt0) REVERT: Y 276 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8593 (tm-30) REVERT: Y 308 GLU cc_start: 0.8824 (mp0) cc_final: 0.8549 (mp0) REVERT: Y 371 GLU cc_start: 0.8766 (mm-30) cc_final: 0.7771 (mp0) REVERT: Z 57 MET cc_start: 0.9363 (mtm) cc_final: 0.9059 (mmm) REVERT: Z 150 GLN cc_start: 0.9326 (pp30) cc_final: 0.8984 (pp30) REVERT: Z 161 MET cc_start: 0.9279 (mmm) cc_final: 0.8952 (mmm) REVERT: b 185 GLU cc_start: 0.8927 (pp20) cc_final: 0.8669 (pp20) REVERT: b 205 MET cc_start: 0.9610 (mmm) cc_final: 0.9377 (mpp) REVERT: b 218 GLU cc_start: 0.9248 (tt0) cc_final: 0.8798 (tt0) REVERT: b 371 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8469 (mt-10) REVERT: b 390 GLU cc_start: 0.8488 (pp20) cc_final: 0.8211 (pp20) REVERT: c 120 MET cc_start: 0.9463 (ttp) cc_final: 0.9115 (ttp) REVERT: c 159 LYS cc_start: 0.9172 (mppt) cc_final: 0.8899 (mppt) REVERT: c 161 MET cc_start: 0.9392 (mmm) cc_final: 0.8943 (mmm) REVERT: e 139 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9112 (tm-30) REVERT: e 205 MET cc_start: 0.9548 (mmt) cc_final: 0.9060 (mpp) REVERT: e 218 GLU cc_start: 0.9388 (tt0) cc_final: 0.8950 (tt0) REVERT: e 276 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8869 (tm-30) REVERT: e 371 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8491 (mt-10) REVERT: f 89 GLN cc_start: 0.9458 (mt0) cc_final: 0.9183 (mm110) REVERT: g 32 GLU cc_start: 0.9119 (pt0) cc_final: 0.8755 (pm20) REVERT: i 80 LYS cc_start: 0.9672 (tppp) cc_final: 0.9360 (tptm) REVERT: i 120 MET cc_start: 0.8666 (mmm) cc_final: 0.8210 (mmm) REVERT: i 161 MET cc_start: 0.9194 (mmm) cc_final: 0.8555 (mmm) REVERT: j 32 GLU cc_start: 0.9474 (pt0) cc_final: 0.9018 (pm20) REVERT: k 147 ARG cc_start: 0.9213 (tmm-80) cc_final: 0.8844 (ptt-90) REVERT: k 205 MET cc_start: 0.9702 (OUTLIER) cc_final: 0.8785 (mmp) REVERT: k 218 GLU cc_start: 0.9194 (tt0) cc_final: 0.8856 (tt0) REVERT: k 308 GLU cc_start: 0.8908 (mp0) cc_final: 0.8470 (mp0) REVERT: k 371 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: l 63 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8801 (mm-40) REVERT: l 89 GLN cc_start: 0.7996 (mm110) cc_final: 0.7635 (mm110) REVERT: l 134 GLN cc_start: 0.9544 (mm-40) cc_final: 0.9223 (mm-40) REVERT: l 150 GLN cc_start: 0.9496 (tp-100) cc_final: 0.9241 (tp-100) REVERT: l 161 MET cc_start: 0.9328 (mmm) cc_final: 0.8984 (mmm) REVERT: l 225 LYS cc_start: 0.9323 (tttm) cc_final: 0.9060 (tppp) REVERT: n 146 LEU cc_start: 0.9440 (mm) cc_final: 0.8916 (mm) REVERT: n 371 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: o 112 MET cc_start: 0.9191 (tpp) cc_final: 0.8713 (tpp) REVERT: o 120 MET cc_start: 0.9575 (mtp) cc_final: 0.8948 (mmm) REVERT: o 159 LYS cc_start: 0.9039 (mppt) cc_final: 0.8803 (mppt) REVERT: o 161 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8702 (mmm) REVERT: v 22 ASP cc_start: 0.8277 (m-30) cc_final: 0.7884 (m-30) REVERT: v 59 GLU cc_start: 0.8585 (tt0) cc_final: 0.8234 (pt0) REVERT: v 63 GLN cc_start: 0.9844 (mm-40) cc_final: 0.9551 (tp40) REVERT: v 65 LEU cc_start: 0.9574 (mm) cc_final: 0.9354 (pp) REVERT: v 80 LYS cc_start: 0.9490 (ttmm) cc_final: 0.9201 (ttpp) REVERT: v 100 VAL cc_start: 0.9117 (m) cc_final: 0.8092 (m) REVERT: v 125 PHE cc_start: 0.8732 (m-80) cc_final: 0.8241 (t80) REVERT: y 139 GLU cc_start: 0.9598 (pt0) cc_final: 0.9348 (pp20) REVERT: y 146 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9119 (mm) REVERT: z 22 ASP cc_start: 0.9056 (t0) cc_final: 0.8680 (t0) REVERT: z 46 VAL cc_start: 0.9275 (t) cc_final: 0.8864 (p) REVERT: z 47 ASP cc_start: 0.8579 (p0) cc_final: 0.7849 (p0) REVERT: z 50 LEU cc_start: 0.9270 (tp) cc_final: 0.8720 (tp) REVERT: z 91 GLU cc_start: 0.9204 (tp30) cc_final: 0.8860 (tp30) REVERT: z 120 MET cc_start: 0.9130 (mtm) cc_final: 0.8168 (mpt) outliers start: 90 outliers final: 46 residues processed: 583 average time/residue: 1.6589 time to fit residues: 1178.0849 Evaluate side-chains 552 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 488 time to evaluate : 4.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain e residue 319 ILE Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain m residue 42 ILE Chi-restraints excluded: chain n residue 282 VAL Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain o residue 161 MET Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 152 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 415 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 588 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 313 optimal weight: 30.0000 chunk 614 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 ASN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 188 GLN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN n 360 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.032016 restraints weight = 231994.727| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 3.54 r_work: 0.2370 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 56894 Z= 0.292 Angle : 0.691 16.710 77036 Z= 0.346 Chirality : 0.044 0.291 8370 Planarity : 0.004 0.057 10228 Dihedral : 4.059 22.935 7998 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.40 % Allowed : 17.63 % Favored : 80.97 % 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: 0.27 (0.10), residues: 7036 helix: 1.92 (0.16), residues: 1131 sheet: -0.17 (0.12), residues: 1895 loop : -0.06 (0.10), residues: 4010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 301 HIS 0.006 0.001 HIS v 67 PHE 0.021 0.001 PHE H 195 TYR 0.021 0.001 TYR A 387 ARG 0.015 0.000 ARG Y 147 *********************** 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 596 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 514 time to evaluate : 5.092 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 145 MET cc_start: 0.9218 (mtt) cc_final: 0.8924 (ttm) REVERT: A 146 LEU cc_start: 0.9518 (mm) cc_final: 0.9205 (mm) REVERT: A 252 LYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9284 (ttpt) REVERT: B 159 LYS cc_start: 0.9268 (mppt) cc_final: 0.8994 (mppt) REVERT: B 161 MET cc_start: 0.9189 (mmm) cc_final: 0.8946 (mmm) REVERT: B 183 LYS cc_start: 0.9521 (tttt) cc_final: 0.9291 (ttmm) REVERT: B 227 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.9194 (tpt) REVERT: D 147 ARG cc_start: 0.9380 (ttp-110) cc_final: 0.8930 (mtm110) REVERT: D 182 GLU cc_start: 0.8797 (tt0) cc_final: 0.8416 (tt0) REVERT: D 185 GLU cc_start: 0.9029 (pp20) cc_final: 0.8724 (pp20) REVERT: E 87 LYS cc_start: 0.8895 (tppt) cc_final: 0.8659 (tppt) REVERT: E 89 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8360 (mp10) REVERT: E 112 MET cc_start: 0.8571 (tpp) cc_final: 0.8268 (tpp) REVERT: E 120 MET cc_start: 0.9411 (ttp) cc_final: 0.8999 (ttp) REVERT: E 145 GLU cc_start: 0.9433 (OUTLIER) cc_final: 0.9066 (mm-30) REVERT: G 146 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8961 (mm) REVERT: G 371 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8842 (mm-30) REVERT: H 71 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: H 80 LYS cc_start: 0.9407 (ttpt) cc_final: 0.9144 (ptmt) REVERT: H 134 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8649 (mm110) REVERT: H 137 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9030 (pt0) REVERT: H 159 LYS cc_start: 0.9001 (mppt) cc_final: 0.8585 (mppt) REVERT: H 161 MET cc_start: 0.9395 (mmm) cc_final: 0.8787 (mmm) REVERT: J 185 GLU cc_start: 0.9287 (tm-30) cc_final: 0.9031 (tm-30) REVERT: J 205 MET cc_start: 0.9665 (mmm) cc_final: 0.8316 (mmm) REVERT: K 80 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9194 (ptpt) REVERT: K 89 GLN cc_start: 0.9250 (pt0) cc_final: 0.8878 (pm20) REVERT: K 120 MET cc_start: 0.9325 (ptm) cc_final: 0.8687 (ppp) REVERT: K 131 GLN cc_start: 0.9485 (tp40) cc_final: 0.9070 (tp40) REVERT: K 134 GLN cc_start: 0.8916 (pp30) cc_final: 0.8588 (pp30) REVERT: K 161 MET cc_start: 0.9464 (mmm) cc_final: 0.9104 (mmm) REVERT: K 162 MET cc_start: 0.9614 (OUTLIER) cc_final: 0.8115 (ptp) REVERT: L 32 GLU cc_start: 0.9423 (pt0) cc_final: 0.8966 (pm20) REVERT: M 182 GLU cc_start: 0.9084 (tt0) cc_final: 0.8778 (tt0) REVERT: M 205 MET cc_start: 0.9728 (mmm) cc_final: 0.8468 (mmm) REVERT: M 252 LYS cc_start: 0.9491 (ttpt) cc_final: 0.9215 (ttpt) REVERT: M 371 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8280 (mt-10) REVERT: N 63 GLN cc_start: 0.9481 (tp40) cc_final: 0.8927 (tm-30) REVERT: N 66 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9058 (p) REVERT: N 89 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8627 (mp10) REVERT: N 263 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8964 (ttpp) REVERT: P 205 MET cc_start: 0.9585 (mmt) cc_final: 0.9229 (mpp) REVERT: Q 22 ASP cc_start: 0.8708 (t0) cc_final: 0.8365 (p0) REVERT: Q 63 GLN cc_start: 0.9508 (tm-30) cc_final: 0.8916 (tm-30) REVERT: Q 120 MET cc_start: 0.8411 (tpp) cc_final: 0.8119 (tpp) REVERT: Q 131 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8919 (tp-100) REVERT: Q 150 GLN cc_start: 0.9470 (tp-100) cc_final: 0.9065 (tp-100) REVERT: Q 161 MET cc_start: 0.9370 (mmm) cc_final: 0.8965 (mmm) REVERT: S 276 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8781 (tm-30) REVERT: S 390 GLU cc_start: 0.8140 (pp20) cc_final: 0.7764 (pp20) REVERT: T 87 LYS cc_start: 0.8602 (tppt) cc_final: 0.7542 (tptm) REVERT: T 89 GLN cc_start: 0.8629 (mt0) cc_final: 0.8399 (mm110) REVERT: T 120 MET cc_start: 0.8320 (tmm) cc_final: 0.7776 (tmm) REVERT: T 159 LYS cc_start: 0.9232 (mppt) cc_final: 0.9004 (mppt) REVERT: T 161 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9080 (mmm) REVERT: T 162 MET cc_start: 0.9557 (ptt) cc_final: 0.8473 (ptp) REVERT: U 32 GLU cc_start: 0.9420 (pt0) cc_final: 0.8758 (pm20) REVERT: V 185 GLU cc_start: 0.8894 (pp20) cc_final: 0.8649 (pp20) REVERT: V 218 GLU cc_start: 0.9145 (tt0) cc_final: 0.8716 (pt0) REVERT: V 371 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8484 (mt-10) REVERT: W 57 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8620 (mmm) REVERT: W 120 MET cc_start: 0.8307 (tpp) cc_final: 0.7619 (tpp) REVERT: W 227 MET cc_start: 0.9320 (tpp) cc_final: 0.9093 (tpp) REVERT: Y 205 MET cc_start: 0.9422 (mpp) cc_final: 0.9041 (mpp) REVERT: Y 218 GLU cc_start: 0.9144 (tt0) cc_final: 0.8722 (tt0) REVERT: Y 276 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8581 (tm-30) REVERT: Y 308 GLU cc_start: 0.8826 (mp0) cc_final: 0.8581 (mp0) REVERT: Y 390 GLU cc_start: 0.8177 (pp20) cc_final: 0.7975 (pp20) REVERT: Z 57 MET cc_start: 0.9357 (mtm) cc_final: 0.9038 (mmm) REVERT: Z 150 GLN cc_start: 0.9333 (pp30) cc_final: 0.8972 (pp30) REVERT: Z 161 MET cc_start: 0.9310 (mmm) cc_final: 0.8980 (mmm) REVERT: b 143 GLU cc_start: 0.9588 (mm-30) cc_final: 0.9306 (mp0) REVERT: b 145 MET cc_start: 0.9228 (ttm) cc_final: 0.9007 (ttt) REVERT: c 120 MET cc_start: 0.9478 (ttp) cc_final: 0.9139 (ttp) REVERT: c 159 LYS cc_start: 0.9166 (mppt) cc_final: 0.8872 (mppt) REVERT: c 161 MET cc_start: 0.9393 (mmm) cc_final: 0.8928 (mmm) REVERT: e 138 TYR cc_start: 0.9549 (t80) cc_final: 0.9328 (t80) REVERT: e 147 ARG cc_start: 0.9320 (mtm110) cc_final: 0.8965 (ptt-90) REVERT: e 218 GLU cc_start: 0.9385 (tt0) cc_final: 0.8917 (tt0) REVERT: e 276 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8848 (tm-30) REVERT: e 371 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8504 (mt-10) REVERT: f 120 MET cc_start: 0.8103 (mmm) cc_final: 0.7681 (mmp) REVERT: f 263 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9076 (ttpp) REVERT: g 32 GLU cc_start: 0.9116 (pt0) cc_final: 0.8713 (pm20) REVERT: h 139 GLU cc_start: 0.9291 (pt0) cc_final: 0.8996 (pp20) REVERT: h 218 GLU cc_start: 0.9153 (tt0) cc_final: 0.8727 (tt0) REVERT: h 276 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8709 (tm-30) REVERT: h 371 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8404 (mt-10) REVERT: i 120 MET cc_start: 0.8687 (mmm) cc_final: 0.8209 (mmm) REVERT: i 161 MET cc_start: 0.9210 (mmm) cc_final: 0.8543 (mmm) REVERT: j 32 GLU cc_start: 0.9457 (pt0) cc_final: 0.9064 (pm20) REVERT: k 147 ARG cc_start: 0.9207 (tmm-80) cc_final: 0.8972 (tmm-80) REVERT: k 205 MET cc_start: 0.9691 (OUTLIER) cc_final: 0.8789 (mmp) REVERT: k 218 GLU cc_start: 0.9185 (tt0) cc_final: 0.8809 (tt0) REVERT: k 308 GLU cc_start: 0.8930 (mp0) cc_final: 0.8494 (mp0) REVERT: k 371 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: l 63 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8830 (mm-40) REVERT: l 89 GLN cc_start: 0.7995 (mm110) cc_final: 0.7628 (mm110) REVERT: l 134 GLN cc_start: 0.9543 (mm-40) cc_final: 0.9235 (mm-40) REVERT: l 150 GLN cc_start: 0.9505 (tp-100) cc_final: 0.9244 (tp-100) REVERT: l 161 MET cc_start: 0.9320 (mmm) cc_final: 0.8980 (mmm) REVERT: l 225 LYS cc_start: 0.9338 (tttm) cc_final: 0.9096 (tppp) REVERT: n 146 LEU cc_start: 0.9430 (mm) cc_final: 0.8901 (mm) REVERT: n 147 ARG cc_start: 0.9501 (ttp-110) cc_final: 0.8963 (mtm110) REVERT: n 371 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: o 112 MET cc_start: 0.9243 (tpp) cc_final: 0.8741 (tpp) REVERT: o 120 MET cc_start: 0.9578 (mtp) cc_final: 0.8950 (mmm) REVERT: o 159 LYS cc_start: 0.9050 (mppt) cc_final: 0.8820 (mppt) REVERT: o 161 MET cc_start: 0.9359 (mmm) cc_final: 0.8811 (mmm) REVERT: u 144 ARG cc_start: 0.9401 (ttp-110) cc_final: 0.8784 (ptm160) REVERT: u 145 MET cc_start: 0.9254 (ptm) cc_final: 0.8468 (tmt) REVERT: v 22 ASP cc_start: 0.8327 (m-30) cc_final: 0.7937 (m-30) REVERT: v 47 ASP cc_start: 0.8814 (t70) cc_final: 0.8485 (t70) REVERT: v 59 GLU cc_start: 0.8608 (tt0) cc_final: 0.8257 (pt0) REVERT: v 63 GLN cc_start: 0.9838 (mm-40) cc_final: 0.9536 (tp40) REVERT: v 71 ASP cc_start: 0.8597 (t0) cc_final: 0.7153 (t0) REVERT: v 73 GLU cc_start: 0.8775 (pm20) cc_final: 0.8463 (pm20) REVERT: v 80 LYS cc_start: 0.9507 (ttmm) cc_final: 0.9212 (ttpp) REVERT: v 120 MET cc_start: 0.8594 (mtm) cc_final: 0.8316 (tmm) REVERT: y 139 GLU cc_start: 0.9593 (pt0) cc_final: 0.9339 (pp20) REVERT: y 146 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9062 (mm) REVERT: z 22 ASP cc_start: 0.9078 (t0) cc_final: 0.8712 (t0) REVERT: z 46 VAL cc_start: 0.9298 (t) cc_final: 0.8918 (p) REVERT: z 47 ASP cc_start: 0.8672 (p0) cc_final: 0.7842 (p0) REVERT: z 50 LEU cc_start: 0.9258 (tp) cc_final: 0.8628 (tp) REVERT: z 91 GLU cc_start: 0.9178 (tp30) cc_final: 0.8848 (tp30) REVERT: z 120 MET cc_start: 0.9157 (mtm) cc_final: 0.8141 (mpt) outliers start: 82 outliers final: 51 residues processed: 571 average time/residue: 1.7071 time to fit residues: 1185.1972 Evaluate side-chains 553 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 485 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 143 GLU Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 231 CYS 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 e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain m residue 42 ILE Chi-restraints excluded: chain n residue 282 VAL Chi-restraints excluded: chain n residue 371 GLU Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 242 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 chunk 338 optimal weight: 0.0270 chunk 278 optimal weight: 9.9990 chunk 344 optimal weight: 1.9990 chunk 502 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 264 optimal weight: 8.9990 chunk 198 optimal weight: 0.0570 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 374 ASN ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032866 restraints weight = 229950.706| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.57 r_work: 0.2400 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 56894 Z= 0.193 Angle : 0.704 20.067 77036 Z= 0.349 Chirality : 0.045 0.309 8370 Planarity : 0.004 0.064 10228 Dihedral : 3.985 27.800 7996 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.26 % Allowed : 18.11 % Favored : 80.62 % 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: 1.85 (0.16), residues: 1131 sheet: -0.24 (0.11), residues: 1988 loop : -0.04 (0.10), residues: 3917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 301 HIS 0.007 0.001 HIS v 67 PHE 0.021 0.001 PHE H 195 TYR 0.026 0.001 TYR A 138 ARG 0.018 0.000 ARG u 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 600 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 526 time to evaluate : 5.504 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: A 138 TYR cc_start: 0.9397 (t80) cc_final: 0.9193 (t80) REVERT: A 145 MET cc_start: 0.9239 (mtt) cc_final: 0.8945 (ttm) REVERT: A 146 LEU cc_start: 0.9533 (mm) cc_final: 0.9248 (mm) REVERT: A 147 ARG cc_start: 0.9239 (mtm110) cc_final: 0.9027 (mtm110) REVERT: A 252 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9318 (ttpt) REVERT: B 22 ASP cc_start: 0.8078 (m-30) cc_final: 0.7618 (m-30) REVERT: B 159 LYS cc_start: 0.9278 (mppt) cc_final: 0.8989 (mppt) REVERT: B 161 MET cc_start: 0.9128 (mmm) cc_final: 0.8875 (mmm) REVERT: B 183 LYS cc_start: 0.9538 (tttt) cc_final: 0.9306 (ttmm) REVERT: B 227 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.9096 (tpt) REVERT: C 32 GLU cc_start: 0.9013 (pt0) cc_final: 0.8516 (pm20) REVERT: D 146 LEU cc_start: 0.9194 (mm) cc_final: 0.8602 (mm) REVERT: D 147 ARG cc_start: 0.9385 (ttp-110) cc_final: 0.8911 (mtm110) REVERT: D 182 GLU cc_start: 0.8686 (tt0) cc_final: 0.8271 (tt0) REVERT: D 185 GLU cc_start: 0.8998 (pp20) cc_final: 0.8679 (pp20) REVERT: D 371 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8395 (mt-10) REVERT: E 87 LYS cc_start: 0.8916 (tppt) cc_final: 0.8705 (tppt) REVERT: E 89 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: E 112 MET cc_start: 0.8576 (tpp) cc_final: 0.8242 (tpp) REVERT: E 120 MET cc_start: 0.9400 (ttp) cc_final: 0.8980 (ttp) REVERT: E 145 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9057 (mm-30) REVERT: G 146 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8978 (mm) REVERT: G 371 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8819 (mm-30) REVERT: H 71 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: H 134 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8670 (mm110) REVERT: H 137 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9043 (pt0) REVERT: H 159 LYS cc_start: 0.8986 (mppt) cc_final: 0.8570 (mppt) REVERT: H 161 MET cc_start: 0.9396 (mmm) cc_final: 0.8775 (mmm) REVERT: J 185 GLU cc_start: 0.9226 (tm-30) cc_final: 0.9004 (tm-30) REVERT: J 205 MET cc_start: 0.9668 (mmm) cc_final: 0.8120 (mmm) REVERT: J 371 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8617 (mt-10) REVERT: K 80 LYS cc_start: 0.9522 (ttpt) cc_final: 0.9273 (ptmt) REVERT: K 89 GLN cc_start: 0.9172 (pt0) cc_final: 0.8812 (pm20) REVERT: K 120 MET cc_start: 0.9342 (ptm) cc_final: 0.8361 (ttt) REVERT: K 131 GLN cc_start: 0.9459 (tp40) cc_final: 0.9112 (mm110) REVERT: K 134 GLN cc_start: 0.8907 (pp30) cc_final: 0.8701 (pp30) REVERT: K 161 MET cc_start: 0.9500 (mmm) cc_final: 0.9186 (mmm) REVERT: K 162 MET cc_start: 0.9586 (OUTLIER) cc_final: 0.8011 (ptp) REVERT: L 32 GLU cc_start: 0.9426 (pt0) cc_final: 0.8976 (pm20) REVERT: M 182 GLU cc_start: 0.9016 (tt0) cc_final: 0.8442 (tt0) REVERT: M 185 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8913 (pp20) REVERT: M 205 MET cc_start: 0.9720 (mmm) cc_final: 0.8479 (mmm) REVERT: M 252 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9197 (ttpt) REVERT: M 371 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8325 (mt-10) REVERT: M 374 ASN cc_start: 0.9076 (m-40) cc_final: 0.8716 (t0) REVERT: M 390 GLU cc_start: 0.8316 (pp20) cc_final: 0.8047 (pp20) REVERT: N 63 GLN cc_start: 0.9494 (tp40) cc_final: 0.8946 (tm-30) REVERT: N 89 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: N 159 LYS cc_start: 0.8941 (mppt) cc_final: 0.8712 (mppt) REVERT: N 263 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.8998 (ttpp) REVERT: P 205 MET cc_start: 0.9556 (mmt) cc_final: 0.9239 (mpp) REVERT: Q 22 ASP cc_start: 0.8696 (t0) cc_final: 0.8356 (p0) REVERT: Q 63 GLN cc_start: 0.9504 (tm-30) cc_final: 0.8885 (tm-30) REVERT: Q 120 MET cc_start: 0.8264 (tpp) cc_final: 0.8005 (tpp) REVERT: Q 131 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8886 (tp-100) REVERT: Q 150 GLN cc_start: 0.9462 (tp-100) cc_final: 0.9068 (tp-100) REVERT: Q 159 LYS cc_start: 0.9001 (mppt) cc_final: 0.8376 (mppt) REVERT: Q 161 MET cc_start: 0.9380 (mmm) cc_final: 0.8970 (mmm) REVERT: S 205 MET cc_start: 0.9616 (mmm) cc_final: 0.8284 (mmm) REVERT: S 276 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8762 (tm-30) REVERT: S 371 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8381 (mt-10) REVERT: S 390 GLU cc_start: 0.8105 (pp20) cc_final: 0.7741 (pp20) REVERT: T 87 LYS cc_start: 0.8558 (tppt) cc_final: 0.7454 (tptm) REVERT: T 89 GLN cc_start: 0.8640 (mt0) cc_final: 0.8394 (mm110) REVERT: T 120 MET cc_start: 0.8301 (tmm) cc_final: 0.7705 (tmm) REVERT: T 159 LYS cc_start: 0.9249 (mppt) cc_final: 0.9006 (mppt) REVERT: T 161 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9108 (mmm) REVERT: T 162 MET cc_start: 0.9565 (ptt) cc_final: 0.8504 (ptp) REVERT: U 32 GLU cc_start: 0.9426 (pt0) cc_final: 0.8788 (pm20) REVERT: V 147 ARG cc_start: 0.9390 (mtm110) cc_final: 0.9159 (mtm110) REVERT: V 182 GLU cc_start: 0.8750 (tt0) cc_final: 0.8496 (tt0) REVERT: V 218 GLU cc_start: 0.9097 (tt0) cc_final: 0.8663 (pt0) REVERT: V 371 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8501 (mt-10) REVERT: W 57 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8540 (mmm) REVERT: W 120 MET cc_start: 0.8305 (tpp) cc_final: 0.7009 (tpp) REVERT: W 227 MET cc_start: 0.9330 (tpp) cc_final: 0.9095 (tpp) REVERT: Y 182 GLU cc_start: 0.8532 (tt0) cc_final: 0.8271 (tt0) REVERT: Y 185 GLU cc_start: 0.8569 (pp20) cc_final: 0.8350 (pp20) REVERT: Y 205 MET cc_start: 0.9374 (mpp) cc_final: 0.9024 (mpp) REVERT: Y 218 GLU cc_start: 0.9094 (tt0) cc_final: 0.8731 (tt0) REVERT: Y 276 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8545 (tm-30) REVERT: Y 308 GLU cc_start: 0.8811 (mp0) cc_final: 0.8567 (mp0) REVERT: Y 371 GLU cc_start: 0.8832 (mm-30) cc_final: 0.7827 (mp0) REVERT: Z 57 MET cc_start: 0.9349 (mtm) cc_final: 0.9035 (mmm) REVERT: Z 150 GLN cc_start: 0.9309 (pp30) cc_final: 0.8956 (pp30) REVERT: Z 159 LYS cc_start: 0.8897 (mppt) cc_final: 0.8667 (mppt) REVERT: Z 161 MET cc_start: 0.9328 (mmm) cc_final: 0.9027 (mmm) REVERT: a 32 GLU cc_start: 0.9226 (pt0) cc_final: 0.8618 (pm20) REVERT: b 143 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9296 (mp0) REVERT: b 145 MET cc_start: 0.9190 (ttm) cc_final: 0.8964 (ttt) REVERT: c 120 MET cc_start: 0.9489 (ttp) cc_final: 0.9137 (ttp) REVERT: c 159 LYS cc_start: 0.9171 (mppt) cc_final: 0.8898 (mppt) REVERT: c 161 MET cc_start: 0.9394 (mmm) cc_final: 0.8924 (mmm) REVERT: e 138 TYR cc_start: 0.9558 (t80) cc_final: 0.9320 (t80) REVERT: f 120 MET cc_start: 0.8080 (mmm) cc_final: 0.7580 (mmp) REVERT: f 159 LYS cc_start: 0.9139 (mppt) cc_final: 0.8655 (mppt) REVERT: g 32 GLU cc_start: 0.9099 (pt0) cc_final: 0.8747 (pm20) REVERT: i 57 MET cc_start: 0.9294 (mmm) cc_final: 0.8901 (mmm) REVERT: i 120 MET cc_start: 0.8692 (mmm) cc_final: 0.8230 (mmm) REVERT: i 161 MET cc_start: 0.9207 (mmm) cc_final: 0.8545 (mmm) REVERT: j 24 LYS cc_start: 0.9415 (tttt) cc_final: 0.9145 (ttpp) REVERT: j 32 GLU cc_start: 0.9477 (pt0) cc_final: 0.9033 (pm20) REVERT: k 205 MET cc_start: 0.9685 (OUTLIER) cc_final: 0.8774 (mmp) REVERT: k 218 GLU cc_start: 0.9190 (tt0) cc_final: 0.8827 (tt0) REVERT: k 308 GLU cc_start: 0.8922 (mp0) cc_final: 0.8486 (mp0) REVERT: k 371 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: l 63 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8819 (mm-40) REVERT: l 89 GLN cc_start: 0.7982 (mm110) cc_final: 0.7633 (mm110) REVERT: l 134 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9224 (mm-40) REVERT: l 150 GLN cc_start: 0.9516 (tp-100) cc_final: 0.9258 (tp-100) REVERT: l 161 MET cc_start: 0.9326 (mmm) cc_final: 0.9000 (mmm) REVERT: l 225 LYS cc_start: 0.9312 (tttm) cc_final: 0.9091 (tppp) REVERT: n 146 LEU cc_start: 0.9410 (mm) cc_final: 0.8897 (mm) REVERT: n 147 ARG cc_start: 0.9492 (ttp-110) cc_final: 0.8957 (mtm110) REVERT: o 120 MET cc_start: 0.9565 (mtp) cc_final: 0.8934 (mmm) REVERT: o 159 LYS cc_start: 0.9096 (mppt) cc_final: 0.8852 (mppt) REVERT: o 161 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9023 (mmm) REVERT: u 145 MET cc_start: 0.9232 (ptm) cc_final: 0.8600 (tmt) REVERT: v 22 ASP cc_start: 0.8318 (m-30) cc_final: 0.7580 (m-30) REVERT: v 42 ASP cc_start: 0.8098 (t0) cc_final: 0.7339 (t70) REVERT: v 47 ASP cc_start: 0.8832 (t70) cc_final: 0.8508 (OUTLIER) REVERT: v 59 GLU cc_start: 0.8620 (tt0) cc_final: 0.8276 (pt0) REVERT: v 63 GLN cc_start: 0.9793 (mm-40) cc_final: 0.9572 (tp40) REVERT: v 71 ASP cc_start: 0.8464 (t0) cc_final: 0.8257 (t0) REVERT: v 80 LYS cc_start: 0.9546 (ttmm) cc_final: 0.9272 (ttpp) REVERT: v 125 PHE cc_start: 0.8611 (m-80) cc_final: 0.8125 (t80) REVERT: y 139 GLU cc_start: 0.9618 (pt0) cc_final: 0.9329 (pp20) REVERT: y 146 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9108 (mm) REVERT: z 22 ASP cc_start: 0.9092 (t0) cc_final: 0.8717 (t0) REVERT: z 46 VAL cc_start: 0.9337 (t) cc_final: 0.8967 (p) REVERT: z 47 ASP cc_start: 0.8573 (p0) cc_final: 0.7738 (p0) REVERT: z 50 LEU cc_start: 0.9233 (tp) cc_final: 0.8677 (tp) REVERT: z 91 GLU cc_start: 0.9159 (tp30) cc_final: 0.8824 (tp30) REVERT: z 120 MET cc_start: 0.9186 (mtm) cc_final: 0.8091 (mpt) outliers start: 74 outliers final: 44 residues processed: 580 average time/residue: 1.7047 time to fit residues: 1201.1189 Evaluate side-chains 560 residues out of total 5886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 501 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 231 CYS Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain T residue 161 MET Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain Y residue 136 THR 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 e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 371 GLU Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 282 VAL Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 161 MET Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 139 GLU Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 177 optimal weight: 5.9990 chunk 633 optimal weight: 8.9990 chunk 563 optimal weight: 7.9990 chunk 577 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 596 optimal weight: 0.8980 chunk 460 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 600 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.050052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.032379 restraints weight = 232291.428| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 3.56 r_work: 0.2383 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 56894 Z= 0.261 Angle : 0.715 20.864 77036 Z= 0.356 Chirality : 0.044 0.322 8370 Planarity : 0.004 0.055 10228 Dihedral : 3.983 29.998 7996 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 18.47 % Favored : 80.39 % 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: 0.28 (0.10), residues: 7036 helix: 1.88 (0.17), residues: 1116 sheet: -0.23 (0.11), residues: 1984 loop : 0.01 (0.10), residues: 3936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 301 HIS 0.005 0.001 HIS v 67 PHE 0.020 0.001 PHE H 195 TYR 0.037 0.001 TYR Y 138 ARG 0.015 0.000 ARG W 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31826.51 seconds wall clock time: 545 minutes 35.62 seconds (32735.62 seconds total)