Starting phenix.real_space_refine on Wed Sep 25 12:50:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/09_2024/8rt7_19481.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/09_2024/8rt7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/09_2024/8rt7_19481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/09_2024/8rt7_19481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/09_2024/8rt7_19481.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/09_2024/8rt7_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): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55802 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "a" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "d" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "g" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "j" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "m" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "p" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 26.07, per 1000 atoms: 0.47 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: 10.65 Conformation dependent library (CDL) restraints added in 5.6 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: 9.15 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: 30.29 Time building geometry restraints manager: 12.82 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: 0.00 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: 1.570 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: 0.070 Extract box with map and model: 1.800 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 114.090 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.780 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 842 time to evaluate : 5.237 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: 1.8560 time to fit residues: 1880.1783 Evaluate side-chains 507 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 503 time to evaluate : 5.134 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 fitting. rotamer outliers: 59 poor density : 590 time to evaluate : 5.067 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: D 138 TYR cc_start: 0.7962 (t80) cc_final: 0.7641 (t80) REVERT: H 134 GLN cc_start: 0.7626 (mp10) cc_final: 0.7266 (mm110) REVERT: X 28 ASP cc_start: 0.6734 (t0) cc_final: 0.6530 (t0) REVERT: Y 138 TYR cc_start: 0.7701 (t80) cc_final: 0.7422 (t80) REVERT: Y 142 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7930 (mtm180) REVERT: b 138 TYR cc_start: 0.7782 (t80) cc_final: 0.7547 (t80) REVERT: k 205 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5757 (mmt) REVERT: n 146 LEU cc_start: 0.8330 (mm) cc_final: 0.7925 (mm) REVERT: u 140 LEU cc_start: 0.9091 (mt) cc_final: 0.8838 (pp) REVERT: v 57 MET cc_start: 0.6725 (mmm) cc_final: 0.6171 (mmm) REVERT: z 36 VAL cc_start: 0.8077 (p) cc_final: 0.7812 (p) REVERT: z 47 ASP cc_start: 0.7001 (p0) cc_final: 0.6795 (p0) REVERT: z 102 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7971 (p0) REVERT: z 115 ASP cc_start: 0.7941 (p0) cc_final: 0.7526 (p0) outliers start: 59 outliers final: 14 residues processed: 619 average time/residue: 1.9007 time to fit residues: 1408.5926 Evaluate side-chains 489 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 473 time to evaluate : 5.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 134 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 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 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 350 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 524 optimal weight: 9.9990 chunk 429 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 631 optimal weight: 9.9990 chunk 682 optimal weight: 2.9990 chunk 562 optimal weight: 6.9990 chunk 626 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 506 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN 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 a 25 GLN c 111 GLN ** f 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 67 HIS z 63 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 56894 Z= 0.424 Angle : 0.653 11.383 77036 Z= 0.337 Chirality : 0.045 0.283 8370 Planarity : 0.005 0.074 10228 Dihedral : 4.506 22.627 7998 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 12.55 % Favored : 85.90 % 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: 0.00 (0.10), residues: 7036 helix: 1.96 (0.16), residues: 1130 sheet: -0.27 (0.12), residues: 1891 loop : -0.38 (0.09), residues: 4015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 301 HIS 0.006 0.001 HIS i 67 PHE 0.026 0.001 PHE Z 195 TYR 0.021 0.001 TYR M 138 ARG 0.010 0.001 ARG u 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 601 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 510 time to evaluate : 5.117 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: G 146 LEU cc_start: 0.8826 (mm) cc_final: 0.8439 (mm) REVERT: K 89 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: X 28 ASP cc_start: 0.6759 (t0) cc_final: 0.6534 (t0) REVERT: n 146 LEU cc_start: 0.8403 (mm) cc_final: 0.7935 (mm) REVERT: v 57 MET cc_start: 0.7004 (mmm) cc_final: 0.6334 (mmm) REVERT: y 140 LEU cc_start: 0.8942 (pp) cc_final: 0.8442 (pp) REVERT: z 115 ASP cc_start: 0.8002 (p0) cc_final: 0.7724 (p0) outliers start: 91 outliers final: 26 residues processed: 562 average time/residue: 1.7517 time to fit residues: 1197.6840 Evaluate side-chains 470 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 443 time to evaluate : 5.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 89 GLN 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 V residue 145 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 h residue 228 MET Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain u residue 136 THR 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 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 623 optimal weight: 0.0050 chunk 474 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 chunk 69 optimal weight: 0.0670 chunk 301 optimal weight: 2.9990 chunk 423 optimal weight: 2.9990 chunk 633 optimal weight: 7.9990 chunk 670 optimal weight: 7.9990 chunk 331 optimal weight: 5.9990 chunk 600 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 131 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 201 ASN k 374 ASN n 357 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56894 Z= 0.176 Angle : 0.610 13.418 77036 Z= 0.312 Chirality : 0.045 0.298 8370 Planarity : 0.004 0.057 10228 Dihedral : 4.263 21.764 7998 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.47 % Allowed : 13.91 % Favored : 84.62 % 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: 0.06 (0.10), residues: 7036 helix: 1.96 (0.16), residues: 1130 sheet: -0.30 (0.12), residues: 1899 loop : -0.28 (0.09), residues: 4007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 307 HIS 0.007 0.001 HIS Z 55 PHE 0.027 0.001 PHE c 195 TYR 0.019 0.001 TYR P 138 ARG 0.013 0.000 ARG J 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 624 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 538 time to evaluate : 5.162 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: B 120 MET cc_start: 0.6610 (tpt) cc_final: 0.6272 (tpp) REVERT: G 146 LEU cc_start: 0.8700 (mm) cc_final: 0.8451 (mm) REVERT: M 140 LEU cc_start: 0.8804 (mm) cc_final: 0.8474 (mm) REVERT: W 57 MET cc_start: 0.7493 (mmm) cc_final: 0.7275 (mmm) REVERT: X 28 ASP cc_start: 0.6675 (t0) cc_final: 0.6430 (t0) REVERT: Y 138 TYR cc_start: 0.7673 (t80) cc_final: 0.6291 (t80) REVERT: n 146 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7900 (mm) REVERT: u 140 LEU cc_start: 0.9138 (mt) cc_final: 0.8886 (mm) REVERT: v 57 MET cc_start: 0.7014 (mmm) cc_final: 0.6346 (mmm) REVERT: y 146 LEU cc_start: 0.8204 (mm) cc_final: 0.7947 (mm) outliers start: 86 outliers final: 26 residues processed: 595 average time/residue: 1.7295 time to fit residues: 1254.0278 Evaluate side-chains 483 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 456 time to evaluate : 5.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain S residue 136 THR 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 Z residue 99 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain h residue 147 ARG Chi-restraints excluded: chain i residue 23 VAL 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 7.9990 chunk 380 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 572 optimal weight: 8.9990 chunk 463 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 342 optimal weight: 9.9990 chunk 602 optimal weight: 30.0000 chunk 169 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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** G 374 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 HIS ** W 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 ** 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 305 HIS n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 56894 Z= 0.508 Angle : 0.699 10.900 77036 Z= 0.354 Chirality : 0.045 0.279 8370 Planarity : 0.005 0.057 10228 Dihedral : 4.341 23.952 7998 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.69 % Allowed : 15.04 % Favored : 83.27 % 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: 1.96 (0.16), residues: 1130 sheet: -0.14 (0.12), residues: 1889 loop : -0.28 (0.09), residues: 4017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 301 HIS 0.006 0.001 HIS H 83 PHE 0.023 0.002 PHE c 195 TYR 0.021 0.002 TYR M 138 ARG 0.017 0.001 ARG Y 142 *********************** 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 589 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 490 time to evaluate : 5.062 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: G 146 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8532 (mm) REVERT: G 205 MET cc_start: 0.6456 (mmm) cc_final: 0.5618 (mmm) REVERT: W 57 MET cc_start: 0.7968 (mmm) cc_final: 0.7322 (mmm) REVERT: X 28 ASP cc_start: 0.6719 (t0) cc_final: 0.6441 (t0) REVERT: e 143 GLU cc_start: 0.8007 (pp20) cc_final: 0.7801 (pp20) REVERT: y 146 LEU cc_start: 0.8448 (mm) cc_final: 0.8126 (mm) outliers start: 99 outliers final: 41 residues processed: 559 average time/residue: 1.6636 time to fit residues: 1136.8365 Evaluate side-chains 492 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 450 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL 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 K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 37 THR 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 319 ILE 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 l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL 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 66 THR 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 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 225 optimal weight: 9.9990 chunk 604 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 393 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 671 optimal weight: 3.9990 chunk 557 optimal weight: 10.0000 chunk 310 optimal weight: 0.0870 chunk 55 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 374 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** v 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3038 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= 0.250 Angle : 0.653 13.616 77036 Z= 0.328 Chirality : 0.044 0.223 8370 Planarity : 0.004 0.067 10228 Dihedral : 4.208 22.005 7998 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.55 % Allowed : 16.11 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.10), residues: 7036 helix: 1.99 (0.16), residues: 1131 sheet: -0.26 (0.12), residues: 1885 loop : -0.18 (0.09), residues: 4020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 307 HIS 0.009 0.001 HIS E 55 PHE 0.024 0.001 PHE c 195 TYR 0.029 0.001 TYR Y 138 ARG 0.015 0.000 ARG P 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 594 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 503 time to evaluate : 5.057 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: B 120 MET cc_start: 0.6902 (tpp) cc_final: 0.6683 (tpt) REVERT: G 205 MET cc_start: 0.6290 (mmm) cc_final: 0.5679 (mmm) REVERT: W 57 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7214 (mmm) REVERT: W 120 MET cc_start: 0.7229 (tpp) cc_final: 0.6635 (tpp) REVERT: X 28 ASP cc_start: 0.6733 (t0) cc_final: 0.6417 (t0) REVERT: e 143 GLU cc_start: 0.7865 (pp20) cc_final: 0.7497 (pp20) REVERT: k 205 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5714 (mmt) REVERT: n 146 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8046 (mm) REVERT: u 140 LEU cc_start: 0.9159 (mt) cc_final: 0.8956 (mm) REVERT: v 57 MET cc_start: 0.6598 (mmm) cc_final: 0.5676 (mmm) REVERT: v 94 ASN cc_start: 0.8629 (m-40) cc_final: 0.8321 (m-40) REVERT: y 144 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7995 (tmm-80) REVERT: y 146 LEU cc_start: 0.8266 (mm) cc_final: 0.8000 (mm) REVERT: z 47 ASP cc_start: 0.7203 (p0) cc_final: 0.6932 (p0) REVERT: z 91 GLU cc_start: 0.7903 (tp30) cc_final: 0.7673 (tp30) outliers start: 91 outliers final: 37 residues processed: 564 average time/residue: 1.6672 time to fit residues: 1149.5343 Evaluate side-chains 494 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 453 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain P residue 138 TYR Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 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 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 l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU 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 66 THR 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 144 ARG Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 49 VAL 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 647 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 382 optimal weight: 20.0000 chunk 490 optimal weight: 9.9990 chunk 379 optimal weight: 8.9990 chunk 565 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 668 optimal weight: 5.9990 chunk 418 optimal weight: 4.9990 chunk 407 optimal weight: 3.9990 chunk 308 optimal weight: 0.3980 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 ASN ** 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 360 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 56894 Z= 0.300 Angle : 0.687 14.950 77036 Z= 0.341 Chirality : 0.045 0.279 8370 Planarity : 0.004 0.056 10228 Dihedral : 4.173 21.859 7998 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.45 % Allowed : 17.33 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.10), residues: 7036 helix: 1.94 (0.16), residues: 1131 sheet: -0.29 (0.12), residues: 1893 loop : -0.14 (0.09), residues: 4012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 301 HIS 0.007 0.001 HIS W 83 PHE 0.023 0.001 PHE c 195 TYR 0.020 0.001 TYR A 387 ARG 0.012 0.000 ARG y 142 *********************** 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 575 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 490 time to evaluate : 5.038 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: B 120 MET cc_start: 0.6965 (tpp) cc_final: 0.6743 (tpt) REVERT: W 57 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7760 (mmm) REVERT: W 120 MET cc_start: 0.7268 (tpp) cc_final: 0.6772 (tpp) REVERT: X 28 ASP cc_start: 0.6670 (t0) cc_final: 0.6363 (t0) REVERT: f 120 MET cc_start: 0.7466 (mmm) cc_final: 0.7117 (mmp) REVERT: k 205 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5774 (mmt) REVERT: n 146 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8089 (mm) REVERT: v 57 MET cc_start: 0.6908 (mmm) cc_final: 0.6019 (mmm) REVERT: v 94 ASN cc_start: 0.8640 (m-40) cc_final: 0.8307 (m-40) REVERT: y 146 LEU cc_start: 0.8298 (mm) cc_final: 0.8029 (mm) outliers start: 85 outliers final: 46 residues processed: 553 average time/residue: 1.6747 time to fit residues: 1131.8321 Evaluate side-chains 492 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 443 time to evaluate : 5.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL 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 S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 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 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 275 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 282 VAL 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 56 ILE Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 49 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 413 optimal weight: 20.0000 chunk 267 optimal weight: 30.0000 chunk 399 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 425 optimal weight: 0.9990 chunk 455 optimal weight: 30.0000 chunk 330 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 525 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 89 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 131 GLN ** 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 n 360 ASN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 56894 Z= 0.314 Angle : 0.713 19.127 77036 Z= 0.354 Chirality : 0.045 0.282 8370 Planarity : 0.004 0.056 10228 Dihedral : 4.169 22.973 7998 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.33 % Allowed : 18.33 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.10), residues: 7036 helix: 1.89 (0.16), residues: 1131 sheet: -0.36 (0.11), residues: 2013 loop : -0.09 (0.10), residues: 3892 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 0.022 0.001 PHE c 195 TYR 0.031 0.001 TYR A 138 ARG 0.011 0.000 ARG b 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 546 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 468 time to evaluate : 5.103 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: J 205 MET cc_start: 0.6230 (mmm) cc_final: 0.5487 (mmm) REVERT: K 112 MET cc_start: 0.7158 (tpp) cc_final: 0.6907 (tpt) REVERT: W 57 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7259 (mmm) REVERT: W 120 MET cc_start: 0.7319 (tpp) cc_final: 0.6867 (tpp) REVERT: X 28 ASP cc_start: 0.6675 (t0) cc_final: 0.6308 (t0) REVERT: f 120 MET cc_start: 0.7588 (mmm) cc_final: 0.7150 (mmp) REVERT: k 205 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5788 (mmt) REVERT: n 146 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (mm) REVERT: v 57 MET cc_start: 0.7185 (mmm) cc_final: 0.6171 (mmm) REVERT: v 94 ASN cc_start: 0.8550 (m-40) cc_final: 0.8303 (m-40) REVERT: y 146 LEU cc_start: 0.8241 (mm) cc_final: 0.7958 (mm) outliers start: 78 outliers final: 47 residues processed: 520 average time/residue: 1.6353 time to fit residues: 1042.7365 Evaluate side-chains 485 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 435 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN 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 319 ILE Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 225 LYS Chi-restraints excluded: chain g residue 37 THR 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 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 146 LEU Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain n residue 282 VAL 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 56 ILE Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 49 VAL 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 608 optimal weight: 20.0000 chunk 640 optimal weight: 5.9990 chunk 584 optimal weight: 5.9990 chunk 623 optimal weight: 2.9990 chunk 375 optimal weight: 0.9990 chunk 271 optimal weight: 30.0000 chunk 489 optimal weight: 9.9990 chunk 191 optimal weight: 0.3980 chunk 563 optimal weight: 1.9990 chunk 589 optimal weight: 9.9990 chunk 621 optimal weight: 0.0870 overall best weight: 1.2964 ------------------------------------------------------------------------------- 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** G 188 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 ASN M 271 GLN ** 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** ** f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 374 ASN ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56894 Z= 0.206 Angle : 0.728 15.387 77036 Z= 0.359 Chirality : 0.045 0.385 8370 Planarity : 0.004 0.074 10228 Dihedral : 4.086 23.915 7996 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.19 % Allowed : 18.71 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.10), residues: 7036 helix: 1.78 (0.17), residues: 1131 sheet: -0.35 (0.11), residues: 2019 loop : -0.08 (0.10), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 301 HIS 0.006 0.001 HIS v 67 PHE 0.021 0.001 PHE c 195 TYR 0.032 0.001 TYR N 64 ARG 0.017 0.000 ARG y 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 492 time to evaluate : 5.100 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: B 57 MET cc_start: 0.7249 (mmm) cc_final: 0.6981 (mmm) REVERT: J 205 MET cc_start: 0.6186 (mmm) cc_final: 0.5577 (mmm) REVERT: N 120 MET cc_start: 0.7350 (tpp) cc_final: 0.7092 (tpp) REVERT: S 205 MET cc_start: 0.6083 (mmm) cc_final: 0.5640 (mmm) REVERT: W 57 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7239 (mmm) REVERT: W 120 MET cc_start: 0.7142 (tpp) cc_final: 0.6745 (tpp) REVERT: X 28 ASP cc_start: 0.6729 (t0) cc_final: 0.6355 (t0) REVERT: f 120 MET cc_start: 0.7535 (mmm) cc_final: 0.7262 (mmp) REVERT: k 205 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5717 (mmt) REVERT: l 120 MET cc_start: 0.7217 (mmm) cc_final: 0.6653 (mmm) REVERT: n 146 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8008 (mm) REVERT: o 112 MET cc_start: 0.8066 (tpp) cc_final: 0.7862 (tpt) REVERT: u 145 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8079 (ppp) REVERT: v 57 MET cc_start: 0.7155 (mmm) cc_final: 0.6249 (mmm) REVERT: v 94 ASN cc_start: 0.8557 (m-40) cc_final: 0.8304 (m-40) REVERT: y 146 LEU cc_start: 0.8153 (mm) cc_final: 0.7887 (mm) outliers start: 70 outliers final: 42 residues processed: 541 average time/residue: 1.6894 time to fit residues: 1117.7850 Evaluate side-chains 489 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 443 time to evaluate : 5.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 143 GLU 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 S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain Y residue 139 GLU 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 f residue 23 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 205 MET 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 146 LEU Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain o residue 66 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 145 MET Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain v residue 98 ILE Chi-restraints excluded: chain v residue 99 VAL 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 49 VAL 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 409 optimal weight: 8.9990 chunk 659 optimal weight: 8.9990 chunk 402 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 458 optimal weight: 7.9990 chunk 691 optimal weight: 8.9990 chunk 636 optimal weight: 9.9990 chunk 550 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** E 111 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 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** e 271 GLN ** 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** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 134 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3431 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= 0.410 Angle : 0.784 16.697 77036 Z= 0.389 Chirality : 0.046 0.318 8370 Planarity : 0.004 0.060 10228 Dihedral : 4.180 28.490 7996 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.04 % Allowed : 19.19 % Favored : 79.77 % 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: 0.16 (0.10), residues: 7036 helix: 1.74 (0.17), residues: 1131 sheet: -0.28 (0.11), residues: 2051 loop : -0.07 (0.10), residues: 3854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 325 HIS 0.006 0.001 HIS v 67 PHE 0.021 0.001 PHE c 195 TYR 0.035 0.001 TYR Y 138 ARG 0.020 0.000 ARG A 147 ********************** 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 509 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 448 time to evaluate : 5.065 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: A 146 LEU cc_start: 0.8428 (mm) cc_final: 0.8045 (mm) REVERT: B 120 MET cc_start: 0.6957 (tpp) cc_final: 0.6660 (tpt) REVERT: G 146 LEU cc_start: 0.8572 (mm) cc_final: 0.8285 (mm) REVERT: G 147 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7904 (ptp90) REVERT: J 205 MET cc_start: 0.6260 (mmm) cc_final: 0.5516 (mmm) REVERT: K 112 MET cc_start: 0.6988 (tpp) cc_final: 0.6745 (tpt) REVERT: S 205 MET cc_start: 0.6182 (mmm) cc_final: 0.5675 (mmm) REVERT: W 57 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7374 (mmm) REVERT: W 120 MET cc_start: 0.7248 (tpp) cc_final: 0.6831 (tpp) REVERT: Y 138 TYR cc_start: 0.7732 (t80) cc_final: 0.7355 (t80) REVERT: Y 142 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8346 (ttm110) REVERT: f 134 GLN cc_start: 0.7448 (pp30) cc_final: 0.7138 (pp30) REVERT: k 205 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5818 (mmt) REVERT: n 146 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8101 (mm) REVERT: u 144 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8078 (tmm-80) REVERT: v 57 MET cc_start: 0.7114 (mmm) cc_final: 0.6173 (mmm) REVERT: v 71 ASP cc_start: 0.8079 (t0) cc_final: 0.7773 (OUTLIER) REVERT: v 120 MET cc_start: 0.7179 (ptp) cc_final: 0.6950 (ptp) REVERT: y 146 LEU cc_start: 0.8266 (mm) cc_final: 0.7973 (mm) REVERT: z 57 MET cc_start: 0.7462 (mmm) cc_final: 0.7241 (mmm) outliers start: 61 outliers final: 45 residues processed: 492 average time/residue: 1.6386 time to fit residues: 990.7065 Evaluate side-chains 470 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 423 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 275 ILE Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL 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 205 MET 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 146 LEU Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain o residue 66 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 34 ARG Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 49 VAL 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 437 optimal weight: 3.9990 chunk 586 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 507 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 551 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 566 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 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** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 134 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.032027 restraints weight = 236525.226| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 3.56 r_work: 0.2364 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 56894 Z= 0.356 Angle : 0.786 16.608 77036 Z= 0.389 Chirality : 0.046 0.324 8370 Planarity : 0.005 0.069 10228 Dihedral : 4.237 31.321 7996 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.04 % Allowed : 19.24 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.15 (0.10), residues: 7036 helix: 1.70 (0.17), residues: 1131 sheet: -0.32 (0.11), residues: 1968 loop : -0.05 (0.10), residues: 3937 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 0.021 0.001 PHE c 195 TYR 0.028 0.001 TYR Y 138 ARG 0.019 0.000 ARG n 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17526.78 seconds wall clock time: 300 minutes 57.65 seconds (18057.65 seconds total)