Starting phenix.real_space_refine on Wed Sep 25 15:51:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/09_2024/8rt8_19482.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/09_2024/8rt8_19482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/09_2024/8rt8_19482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/09_2024/8rt8_19482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/09_2024/8rt8_19482.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/09_2024/8rt8_19482.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 34862 2.51 5 N 10180 2.21 5 O 10556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 454 residue(s): 0.14s 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: 26.90, per 1000 atoms: 0.48 Number of scatterers: 55802 At special positions: 0 Unit cell: (192.06, 195.261, 156.849, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 10556 8.00 N 10180 7.00 C 34862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS M 215 " - pdb=" SG CYS M 231 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 231 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 231 " distance=2.04 Simple disulfide: pdb=" SG CYS V 215 " - pdb=" SG CYS V 231 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 215 " - pdb=" SG CYS Y 231 " distance=2.03 Simple disulfide: pdb=" SG CYS b 215 " - pdb=" SG CYS b 231 " distance=2.03 Simple disulfide: pdb=" SG CYS e 215 " - pdb=" SG CYS e 231 " distance=2.04 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.05 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 5.4 seconds 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13052 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 144 sheets defined 17.7% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.95 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 305 through 329 removed outlier: 6.043A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.685A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.675A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 306 through 329 removed outlier: 5.873A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.593A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 151 removed outlier: 3.980A pdb=" N ALA E 138 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN E 139 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.540A pdb=" N ILE F 42 " --> pdb=" O PRO F 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 148 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 305 through 329 removed outlier: 5.829A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.814A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 150 Processing helix chain 'H' and resid 166 through 169 Processing helix chain 'I' and resid 39 through 43 Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'J' and resid 306 through 329 removed outlier: 6.298A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 358 Processing helix chain 'K' and resid 127 through 151 removed outlier: 4.380A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'L' and resid 39 through 43 removed outlier: 3.633A pdb=" N ILE L 42 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'M' and resid 182 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 6.165A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ALA M 313 " --> pdb=" O ARG M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 359 Processing helix chain 'N' and resid 127 through 151 removed outlier: 3.830A pdb=" N ARG N 151 " --> pdb=" O ALA N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 169 Processing helix chain 'O' and resid 39 through 43 Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 330 removed outlier: 5.425A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY P 330 " --> pdb=" O ALA P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 358 Processing helix chain 'Q' and resid 127 through 151 removed outlier: 3.790A pdb=" N ARG Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 169 Processing helix chain 'R' and resid 39 through 43 Processing helix chain 'S' and resid 136 through 148 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 186 Processing helix chain 'S' and resid 305 through 329 removed outlier: 6.266A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 removed outlier: 3.554A pdb=" N ASN S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 151 removed outlier: 3.508A pdb=" N GLU T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 169 Processing helix chain 'U' and resid 39 through 43 Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'V' and resid 180 through 186 removed outlier: 3.688A pdb=" N ALA V 184 " --> pdb=" O GLY V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.692A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA V 313 " --> pdb=" O ARG V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 359 Processing helix chain 'W' and resid 71 through 75 removed outlier: 3.811A pdb=" N TYR W 75 " --> pdb=" O SER W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 150 removed outlier: 3.502A pdb=" N ARG W 136 " --> pdb=" O ALA W 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 169 Processing helix chain 'Y' and resid 136 through 148 Processing helix chain 'Y' and resid 180 through 187 Processing helix chain 'Y' and resid 202 through 204 No H-bonds generated for 'chain 'Y' and resid 202 through 204' Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.750A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA Y 313 " --> pdb=" O ARG Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 359 Processing helix chain 'Z' and resid 127 through 150 removed outlier: 4.198A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 306 through 329 removed outlier: 6.045A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 removed outlier: 3.771A pdb=" N ASN b 357 " --> pdb=" O GLU b 353 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 151 removed outlier: 3.744A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU c 137 " --> pdb=" O ARG c 133 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 169 Processing helix chain 'd' and resid 39 through 43 Processing helix chain 'e' and resid 136 through 148 Processing helix chain 'e' and resid 180 through 186 Processing helix chain 'e' and resid 202 through 204 No H-bonds generated for 'chain 'e' and resid 202 through 204' Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.756A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.646A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 135 Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.772A pdb=" N ARG f 151 " --> pdb=" O ALA f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 169 Processing helix chain 'g' and resid 39 through 43 removed outlier: 3.547A pdb=" N ILE g 42 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 removed outlier: 3.653A pdb=" N LEU h 140 " --> pdb=" O THR h 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 182 through 187 Processing helix chain 'h' and resid 305 through 330 removed outlier: 5.609A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY h 330 " --> pdb=" O ALA h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.575A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 169 Processing helix chain 'j' and resid 39 through 43 Processing helix chain 'k' and resid 136 through 148 Processing helix chain 'k' and resid 180 through 187 Processing helix chain 'k' and resid 202 through 204 No H-bonds generated for 'chain 'k' and resid 202 through 204' Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.941A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.888A pdb=" N ARG l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'm' and resid 39 through 43 Processing helix chain 'n' and resid 136 through 148 Processing helix chain 'n' and resid 180 through 186 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.201A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 removed outlier: 3.694A pdb=" N ASN n 357 " --> pdb=" O GLU n 353 " (cutoff:3.500A) Processing helix chain 'o' and resid 127 through 150 removed outlier: 3.588A pdb=" N ASN o 139 " --> pdb=" O THR o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'v' and resid 71 through 75 removed outlier: 3.589A pdb=" N TYR v 75 " --> pdb=" O SER v 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 148 Processing helix chain 'z' and resid 71 through 73 No H-bonds generated for 'chain 'z' and resid 71 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.866A pdb=" N SER A 195 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.520A pdb=" N ILE D 283 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.707A pdb=" N ASP A 382 " --> pdb=" O ALA n 197 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ARG n 199 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 282 " --> pdb=" O GLY n 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 217 removed outlier: 3.584A pdb=" N GLY A 255 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 256 " --> pdb=" O TRP A 272 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP A 272 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 287 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.629A pdb=" N LEU A 247 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 391 removed outlier: 3.520A pdb=" N SER A 388 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 390 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.685A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 87 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.668A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 5.014A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB4, first strand: chain 'B' and resid 258 through 261 removed outlier: 3.759A pdb=" N GLU n 390 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 195 through 196 removed outlier: 7.012A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.610A pdb=" N VAL G 282 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 283 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE G 256 " --> pdb=" O TRP G 272 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP G 272 " --> pdb=" O PHE G 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB8, first strand: chain 'D' and resid 237 through 238 removed outlier: 6.933A pdb=" N VAL D 237 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 388 through 391 Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.936A pdb=" N ALA E 124 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL E 36 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 49 Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 3.559A pdb=" N VAL E 196 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.515A pdb=" N ASN E 172 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.408A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 198 through 199 removed outlier: 3.817A pdb=" N VAL J 282 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER J 273 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER J 287 " --> pdb=" O GLN J 271 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN J 271 " --> pdb=" O SER J 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 257 " --> pdb=" O GLY J 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 227 " --> pdb=" O TYR J 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 198 through 199 removed outlier: 3.817A pdb=" N VAL J 282 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS J 231 " --> pdb=" O VAL J 253 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 257 " --> pdb=" O GLY J 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 227 " --> pdb=" O TYR J 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'G' and resid 237 through 238 removed outlier: 6.868A pdb=" N VAL G 237 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AD2, first strand: chain 'G' and resid 387 through 391 removed outlier: 3.761A pdb=" N GLU G 390 " --> pdb=" O ARG K 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.845A pdb=" N ARG H 34 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.600A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG H 113 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR H 48 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN H 96 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE H 69 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE H 98 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS H 67 " --> pdb=" O ILE H 98 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL H 100 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 202 through 203 removed outlier: 3.580A pdb=" N VAL H 196 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.539A pdb=" N THR H 180 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.691A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 198 through 199 removed outlier: 3.771A pdb=" N LEU M 376 " --> pdb=" O PRO M 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY M 227 " --> pdb=" O TYR M 257 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE M 256 " --> pdb=" O TRP M 272 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP M 272 " --> pdb=" O PHE M 256 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG M 274 " --> pdb=" O LEU M 285 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU M 285 " --> pdb=" O ARG M 274 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU M 276 " --> pdb=" O ILE M 283 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE M 283 " --> pdb=" O GLU M 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AE1, first strand: chain 'J' and resid 237 through 238 removed outlier: 7.108A pdb=" N VAL J 237 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AE3, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AE4, first strand: chain 'K' and resid 25 through 26 removed outlier: 4.367A pdb=" N ARG K 34 " --> pdb=" O GLU K 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA K 124 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE K 125 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS K 83 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS K 80 " --> pdb=" O HIS K 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 44 through 49 removed outlier: 7.215A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 46 " --> pdb=" O GLN K 111 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG K 113 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR K 48 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.817A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AE8, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.561A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 198 through 199 removed outlier: 3.573A pdb=" N VAL P 282 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU P 376 " --> pdb=" O PRO P 288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN P 374 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY P 227 " --> pdb=" O TYR P 257 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG P 274 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU P 285 " --> pdb=" O ARG P 274 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU P 276 " --> pdb=" O ILE P 283 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE P 283 " --> pdb=" O GLU P 276 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'M' and resid 237 through 238 removed outlier: 7.016A pdb=" N VAL M 237 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AF4, first strand: chain 'M' and resid 388 through 391 Processing sheet with id=AF5, first strand: chain 'N' and resid 25 through 26 removed outlier: 6.639A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS N 83 " --> pdb=" O LYS N 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.631A pdb=" N VAL N 44 " --> pdb=" O ARG N 109 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN N 111 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL N 46 " --> pdb=" O GLN N 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 160 through 164 removed outlier: 5.103A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL N 196 " --> pdb=" O LYS N 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 172 through 175 removed outlier: 3.561A pdb=" N ASN N 172 " --> pdb=" O LYS N 183 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 206 through 207 removed outlier: 7.204A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE S 283 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER S 287 " --> pdb=" O TRP S 272 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU S 376 " --> pdb=" O PRO S 288 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY S 255 " --> pdb=" O THR S 229 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AG2, first strand: chain 'P' and resid 237 through 238 removed outlier: 6.898A pdb=" N VAL P 237 " --> pdb=" O LEU P 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 267 through 268 Processing sheet with id=AG4, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AG5, first strand: chain 'Q' and resid 25 through 26 removed outlier: 3.805A pdb=" N ARG Q 34 " --> pdb=" O GLU Q 122 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Q 124 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 44 through 49 removed outlier: 6.504A pdb=" N VAL Q 44 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLN Q 111 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL Q 46 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG Q 113 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR Q 48 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 202 through 203 removed outlier: 3.761A pdb=" N ARG Q 229 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 172 through 175 removed outlier: 3.566A pdb=" N ASN Q 172 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP Q 174 " --> pdb=" O TYR Q 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 195 through 196 removed outlier: 7.069A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AH2, first strand: chain 'S' and resid 237 through 238 removed outlier: 6.910A pdb=" N VAL S 237 " --> pdb=" O LEU S 246 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 387 through 391 removed outlier: 3.803A pdb=" N GLU S 390 " --> pdb=" O ARG W 259 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.658A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.436A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.436A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 202 through 203 removed outlier: 3.577A pdb=" N ARG T 229 " --> pdb=" O SER T 192 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL T 196 " --> pdb=" O LYS T 225 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'T' and resid 172 through 175 removed outlier: 3.595A pdb=" N ILE T 216 " --> pdb=" O VAL T 210 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.657A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 198 through 199 removed outlier: 3.720A pdb=" N VAL Y 282 " --> pdb=" O GLY V 198 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY Y 255 " --> pdb=" O THR Y 229 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Y 257 " --> pdb=" O GLY Y 227 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Y 227 " --> pdb=" O TYR Y 257 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 212 through 213 removed outlier: 3.633A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 376 " --> pdb=" O PRO V 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER V 287 " --> pdb=" O TRP V 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR V 257 " --> pdb=" O GLY V 227 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY V 227 " --> pdb=" O TYR V 257 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 212 through 213 removed outlier: 3.633A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 376 " --> pdb=" O PRO V 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER V 287 " --> pdb=" O TRP V 272 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI5, first strand: chain 'V' and resid 237 through 238 removed outlier: 6.820A pdb=" N VAL V 237 " --> pdb=" O LEU V 246 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 388 through 391 Processing sheet with id=AI7, first strand: chain 'W' and resid 25 through 26 removed outlier: 3.749A pdb=" N ARG W 34 " --> pdb=" O GLU W 122 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'W' and resid 44 through 49 removed outlier: 6.825A pdb=" N VAL W 44 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN W 111 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL W 46 " --> pdb=" O GLN W 111 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG W 113 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR W 48 " --> pdb=" O ARG W 113 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL W 99 " --> pdb=" O TYR W 106 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.657A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ2, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.725A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Y' and resid 198 through 199 removed outlier: 3.531A pdb=" N ILE b 283 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE b 275 " --> pdb=" O ILE b 283 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU b 376 " --> pdb=" O PRO b 288 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE b 256 " --> pdb=" O TRP b 272 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TRP b 272 " --> pdb=" O PHE b 256 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Y' and resid 231 through 233 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 221 through 222 removed outlier: 3.521A pdb=" N THR Y 364 " --> pdb=" O ASP Y 303 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP Y 303 " --> pdb=" O THR Y 364 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 237 through 238 removed outlier: 7.040A pdb=" N VAL Y 237 " --> pdb=" O LEU Y 246 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 25 through 26 removed outlier: 3.627A pdb=" N ARG Z 34 " --> pdb=" O GLU Z 122 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Z 124 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR Z 54 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Z 86 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Z 87 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 44 through 49 removed outlier: 6.620A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG Z 113 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR Z 48 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 202 through 203 removed outlier: 4.480A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AK3, first strand: chain 'b' and resid 197 through 199 removed outlier: 7.765A pdb=" N ILE e 283 " --> pdb=" O GLU e 276 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU e 276 " --> pdb=" O ILE e 283 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU e 285 " --> pdb=" O ARG e 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG e 274 " --> pdb=" O LEU e 285 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP e 272 " --> pdb=" O PHE e 256 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE e 256 " --> pdb=" O TRP e 272 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY e 227 " --> pdb=" O TYR e 257 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 197 through 199 removed outlier: 3.698A pdb=" N LEU e 376 " --> pdb=" O PRO e 288 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AK6, first strand: chain 'b' and resid 237 through 238 removed outlier: 6.990A pdb=" N VAL b 237 " --> pdb=" O LEU b 246 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AK8, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.999A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'c' and resid 44 through 49 removed outlier: 6.787A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG c 113 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR c 48 " --> pdb=" O ARG c 113 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'c' and resid 202 through 203 removed outlier: 3.664A pdb=" N VAL c 196 " --> pdb=" O LYS c 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 172 through 175 removed outlier: 3.671A pdb=" N THR c 180 " --> pdb=" O VAL c 219 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.417A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'e' and resid 198 through 199 removed outlier: 3.646A pdb=" N LEU h 376 " --> pdb=" O PRO h 288 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY h 227 " --> pdb=" O TYR h 257 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE h 256 " --> pdb=" O TRP h 272 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP h 272 " --> pdb=" O PHE h 256 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'e' and resid 206 through 207 Processing sheet with id=AL6, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AL7, first strand: chain 'e' and resid 237 through 238 removed outlier: 6.991A pdb=" N VAL e 237 " --> pdb=" O LEU e 246 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'e' and resid 267 through 268 Processing sheet with id=AL9, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AM1, first strand: chain 'f' and resid 25 through 26 removed outlier: 3.511A pdb=" N ALA f 124 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'f' and resid 44 through 48 removed outlier: 6.728A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 202 through 203 removed outlier: 3.825A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AM5, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.474A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'h' and resid 198 through 199 removed outlier: 3.656A pdb=" N VAL k 282 " --> pdb=" O GLY h 198 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER k 287 " --> pdb=" O TRP k 272 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'h' and resid 198 through 199 removed outlier: 3.656A pdb=" N VAL k 282 " --> pdb=" O GLY h 198 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY k 227 " --> pdb=" O TYR k 257 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM9, first strand: chain 'h' and resid 237 through 238 removed outlier: 6.726A pdb=" N VAL h 237 " --> pdb=" O LEU h 246 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AN2, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN3, first strand: chain 'i' and resid 25 through 26 removed outlier: 7.048A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA i 78 " --> pdb=" O PHE i 85 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 44 through 48 removed outlier: 3.583A pdb=" N GLN i 111 " --> pdb=" O VAL i 46 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR i 48 " --> pdb=" O GLN i 111 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE i 98 " --> pdb=" O HIS i 67 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS i 67 " --> pdb=" O ILE i 98 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL i 100 " --> pdb=" O LEU i 65 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'i' and resid 202 through 203 removed outlier: 4.332A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN7, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.779A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'k' and resid 198 through 199 removed outlier: 3.707A pdb=" N LEU n 376 " --> pdb=" O PRO n 288 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'k' and resid 198 through 199 removed outlier: 8.011A pdb=" N ILE n 283 " --> pdb=" O GLU n 276 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU n 276 " --> pdb=" O ILE n 283 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU n 285 " --> pdb=" O ARG n 274 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG n 274 " --> pdb=" O LEU n 285 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER n 287 " --> pdb=" O TRP n 272 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY n 255 " --> pdb=" O THR n 229 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AO2, first strand: chain 'k' and resid 237 through 238 removed outlier: 6.759A pdb=" N VAL k 237 " --> pdb=" O LEU k 246 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AO4, first strand: chain 'k' and resid 387 through 391 removed outlier: 4.239A pdb=" N GLU k 390 " --> pdb=" O ARG o 259 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 25 through 27 removed outlier: 6.221A pdb=" N ILE l 33 " --> pdb=" O SER l 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA l 78 " --> pdb=" O PHE l 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS l 87 " --> pdb=" O ALA l 76 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'l' and resid 44 through 49 removed outlier: 6.537A pdb=" N VAL l 44 " --> pdb=" O ARG l 109 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN l 111 " --> pdb=" O VAL l 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL l 46 " --> pdb=" O GLN l 111 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG l 113 " --> pdb=" O VAL l 46 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR l 48 " --> pdb=" O ARG l 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR l 95 " --> pdb=" O LEU l 110 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'l' and resid 202 through 203 removed outlier: 3.643A pdb=" N ARG l 229 " --> pdb=" O SER l 192 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL l 196 " --> pdb=" O LYS l 225 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AO9, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AP1, first strand: chain 'n' and resid 237 through 238 removed outlier: 6.720A pdb=" N VAL n 237 " --> pdb=" O LEU n 246 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 25 through 26 removed outlier: 3.991A pdb=" N ARG o 34 " --> pdb=" O GLU o 122 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE o 125 " --> pdb=" O MET o 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS o 83 " --> pdb=" O LYS o 80 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA o 78 " --> pdb=" O PHE o 85 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'o' and resid 44 through 49 removed outlier: 3.556A pdb=" N VAL o 99 " --> pdb=" O TYR o 106 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'o' and resid 202 through 204 removed outlier: 3.759A pdb=" N VAL o 196 " --> pdb=" O LYS o 225 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'o' and resid 172 through 175 removed outlier: 3.529A pdb=" N ASN o 172 " --> pdb=" O LYS o 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP o 174 " --> pdb=" O TYR o 181 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'v' and resid 25 through 26 removed outlier: 7.005A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'v' and resid 44 through 49 removed outlier: 6.195A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN v 111 " --> pdb=" O VAL v 44 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL v 46 " --> pdb=" O GLN v 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG v 113 " --> pdb=" O VAL v 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR v 48 " --> pdb=" O ARG v 113 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'z' and resid 25 through 26 removed outlier: 3.503A pdb=" N ARG z 34 " --> pdb=" O GLU z 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA z 124 " --> pdb=" O ARG z 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS z 83 " --> pdb=" O LYS z 80 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS z 87 " --> pdb=" O ALA z 76 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'z' and resid 44 through 48 removed outlier: 3.564A pdb=" N VAL z 46 " --> pdb=" O ARG z 109 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL z 99 " --> pdb=" O TYR z 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR z 66 " --> pdb=" O VAL z 100 " (cutoff:3.500A) 2000 hydrogen bonds defined for protein. 5220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 32.12 Time building geometry restraints manager: 13.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 19002 1.33 - 1.45: 9177 1.45 - 1.57: 28349 1.57 - 1.69: 0 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" CA ASP n 286 " pdb=" CB ASP n 286 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.51e-02 4.39e+03 6.97e+00 bond pdb=" C GLU Y 276 " pdb=" N THR Y 277 " ideal model delta sigma weight residual 1.330 1.295 0.036 1.37e-02 5.33e+03 6.83e+00 bond pdb=" CA GLN M 329 " pdb=" C GLN M 329 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.38e-02 5.25e+03 5.80e+00 bond pdb=" CA ASP S 286 " pdb=" CB ASP S 286 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.51e-02 4.39e+03 5.42e+00 bond pdb=" CA ASP k 286 " pdb=" CB ASP k 286 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.70e-02 3.46e+03 5.17e+00 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 76920 4.75 - 9.51: 101 9.51 - 14.26: 6 14.26 - 19.02: 8 19.02 - 23.77: 1 Bond angle restraints: 77036 Sorted by residual: angle pdb=" O GLN F 43 " pdb=" C GLN F 43 " pdb=" N ARG F 44 " ideal model delta sigma weight residual 122.41 98.64 23.77 1.34e+00 5.57e-01 3.15e+02 angle pdb=" O GLN O 43 " pdb=" C GLN O 43 " pdb=" N ARG O 44 " ideal model delta sigma weight residual 122.41 104.63 17.78 1.34e+00 5.57e-01 1.76e+02 angle pdb=" O GLN a 43 " pdb=" C GLN a 43 " pdb=" N ARG a 44 " ideal model delta sigma weight residual 122.41 106.18 16.23 1.34e+00 5.57e-01 1.47e+02 angle pdb=" O GLN m 43 " pdb=" C GLN m 43 " pdb=" N ARG m 44 " ideal model delta sigma weight residual 122.41 106.51 15.90 1.34e+00 5.57e-01 1.41e+02 angle pdb=" O GLN g 43 " pdb=" C GLN g 43 " pdb=" N ARG g 44 " ideal model delta sigma weight residual 122.41 107.16 15.25 1.34e+00 5.57e-01 1.30e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 31071 18.10 - 36.20: 2627 36.20 - 54.30: 349 54.30 - 72.40: 90 72.40 - 90.50: 53 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA MET f 57 " pdb=" C MET f 57 " pdb=" N LEU f 58 " pdb=" CA LEU f 58 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU f 137 " pdb=" C GLU f 137 " pdb=" N ALA f 138 " pdb=" CA ALA f 138 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY V 180 " pdb=" C GLY V 180 " pdb=" N GLY V 181 " pdb=" CA GLY V 181 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 6258 0.049 - 0.097: 1653 0.097 - 0.146: 441 0.146 - 0.195: 16 0.195 - 0.243: 2 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB VAL J 253 " pdb=" CA VAL J 253 " pdb=" CG1 VAL J 253 " pdb=" CG2 VAL J 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE W 33 " pdb=" CA ILE W 33 " pdb=" CG1 ILE W 33 " pdb=" CG2 ILE W 33 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CG LEU N 50 " pdb=" CB LEU N 50 " pdb=" CD1 LEU N 50 " pdb=" CD2 LEU N 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 43 " -0.098 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" C GLN F 43 " 0.296 2.00e-02 2.50e+03 pdb=" O GLN F 43 " -0.108 2.00e-02 2.50e+03 pdb=" N ARG F 44 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN p 43 " -0.086 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C GLN p 43 " 0.269 2.00e-02 2.50e+03 pdb=" O GLN p 43 " -0.099 2.00e-02 2.50e+03 pdb=" N ARG p 44 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN O 43 " 0.084 2.00e-02 2.50e+03 1.53e-01 2.34e+02 pdb=" C GLN O 43 " -0.265 2.00e-02 2.50e+03 pdb=" O GLN O 43 " 0.098 2.00e-02 2.50e+03 pdb=" N ARG O 44 " 0.082 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 742 2.56 - 3.14: 46585 3.14 - 3.73: 87124 3.73 - 4.31: 119120 4.31 - 4.90: 199609 Nonbonded interactions: 453180 Sorted by model distance: nonbonded pdb=" OE1 GLU N 137 " pdb=" NH1 ARG N 141 " model vdw 1.973 3.120 nonbonded pdb=" O GLU D 218 " pdb=" OH TYR E 194 " model vdw 1.998 3.040 nonbonded pdb=" O GLU A 218 " pdb=" OH TYR B 194 " model vdw 2.021 3.040 nonbonded pdb=" O GLU Y 218 " pdb=" OH TYR Z 194 " model vdw 2.044 3.040 nonbonded pdb=" O ARG h 243 " pdb=" OG1 THR l 253 " model vdw 2.059 3.040 ... (remaining 453175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.890 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: 0.090 Extract box with map and model: 1.850 Check model and map are aligned: 0.330 Set scattering table: 0.440 Process input model: 117.430 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.750 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 56894 Z= 0.424 Angle : 0.809 23.773 77036 Z= 0.476 Chirality : 0.046 0.243 8370 Planarity : 0.007 0.171 10228 Dihedral : 13.745 90.502 21096 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.10), residues: 7036 helix: 0.72 (0.16), residues: 1102 sheet: -0.65 (0.11), residues: 2048 loop : -0.89 (0.09), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 307 HIS 0.012 0.002 HIS T 67 PHE 0.025 0.002 PHE o 195 TYR 0.031 0.002 TYR z 127 ARG 0.013 0.001 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 936 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8561 (ttp) cc_final: 0.8298 (tpp) REVERT: D 186 LYS cc_start: 0.9157 (mttm) cc_final: 0.8828 (mttm) REVERT: D 353 GLU cc_start: 0.8792 (tp30) cc_final: 0.8398 (tp30) REVERT: E 120 MET cc_start: 0.7727 (mtm) cc_final: 0.6828 (mmt) REVERT: E 131 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9010 (pt0) REVERT: E 227 MET cc_start: 0.8323 (tpp) cc_final: 0.8042 (tpt) REVERT: H 133 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9209 (tpm170) REVERT: H 134 GLN cc_start: 0.8718 (pp30) cc_final: 0.8462 (pp30) REVERT: J 353 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8000 (tp30) REVERT: K 84 ILE cc_start: 0.8984 (mt) cc_final: 0.8783 (mm) REVERT: K 107 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8146 (mttm) REVERT: M 138 TYR cc_start: 0.8954 (t80) cc_final: 0.8739 (t80) REVERT: M 353 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8077 (tp30) REVERT: N 63 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8672 (mm-40) REVERT: N 98 ILE cc_start: 0.8246 (mm) cc_final: 0.8021 (tp) REVERT: P 353 GLU cc_start: 0.8440 (tp30) cc_final: 0.7926 (tp30) REVERT: Q 120 MET cc_start: 0.6316 (mtt) cc_final: 0.5815 (mtt) REVERT: Q 129 ASP cc_start: 0.8754 (p0) cc_final: 0.8514 (p0) REVERT: V 145 MET cc_start: 0.9010 (ttt) cc_final: 0.8484 (ttt) REVERT: W 67 HIS cc_start: 0.8874 (p-80) cc_final: 0.8580 (p-80) REVERT: W 183 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8914 (ttmm) REVERT: Y 357 ASN cc_start: 0.8855 (m-40) cc_final: 0.8640 (m110) REVERT: Z 108 PHE cc_start: 0.8789 (m-10) cc_final: 0.8584 (m-10) REVERT: e 353 GLU cc_start: 0.8253 (tp30) cc_final: 0.7732 (tp30) REVERT: k 145 MET cc_start: 0.8694 (ttt) cc_final: 0.8223 (tpp) REVERT: k 186 LYS cc_start: 0.9222 (mttm) cc_final: 0.8990 (mtpt) REVERT: l 111 GLN cc_start: 0.8145 (mm110) cc_final: 0.7914 (mp10) REVERT: l 120 MET cc_start: 0.8182 (ptm) cc_final: 0.7726 (tmm) REVERT: l 129 ASP cc_start: 0.8889 (p0) cc_final: 0.8482 (p0) REVERT: n 308 GLU cc_start: 0.8035 (tp30) cc_final: 0.7802 (mm-30) REVERT: u 142 ARG cc_start: 0.9172 (mpt180) cc_final: 0.8888 (mpt180) REVERT: u 145 MET cc_start: 0.9086 (mtt) cc_final: 0.8780 (mmt) REVERT: v 50 LEU cc_start: 0.8479 (tp) cc_final: 0.7556 (tp) REVERT: v 108 PHE cc_start: 0.8775 (m-10) cc_final: 0.8442 (m-80) REVERT: v 115 ASP cc_start: 0.9207 (p0) cc_final: 0.8947 (p0) REVERT: v 117 ASN cc_start: 0.8996 (m110) cc_final: 0.8674 (m-40) REVERT: z 25 SER cc_start: 0.9466 (m) cc_final: 0.9174 (p) REVERT: z 35 TYR cc_start: 0.8895 (m-80) cc_final: 0.8458 (m-80) REVERT: z 89 GLN cc_start: 0.9397 (mp10) cc_final: 0.8870 (mp10) REVERT: z 94 ASN cc_start: 0.8815 (m-40) cc_final: 0.8248 (m-40) REVERT: z 120 MET cc_start: 0.6709 (mtm) cc_final: 0.5909 (mtm) outliers start: 4 outliers final: 0 residues processed: 939 average time/residue: 0.6140 time to fit residues: 923.7012 Evaluate side-chains 530 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 5.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 7.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 354 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 543 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 404 optimal weight: 3.9990 chunk 630 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN E 214 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 ASN ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 GLN P 305 HIS P 357 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 201 ASN ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 ASN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 172 ASN Z 220 HIS c 89 GLN c 249 ASN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN n 360 ASN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 56894 Z= 0.272 Angle : 0.643 10.893 77036 Z= 0.336 Chirality : 0.045 0.184 8370 Planarity : 0.005 0.054 10228 Dihedral : 4.600 22.562 7996 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.01 % Allowed : 8.30 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.10), residues: 7036 helix: 1.53 (0.16), residues: 1108 sheet: -0.36 (0.11), residues: 2125 loop : -0.50 (0.10), residues: 3803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 272 HIS 0.007 0.001 HIS v 67 PHE 0.028 0.002 PHE o 195 TYR 0.023 0.002 TYR n 238 ARG 0.008 0.001 ARG J 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 675 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 616 time to evaluate : 5.020 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: B 161 MET cc_start: 0.8539 (mmm) cc_final: 0.8138 (mmm) REVERT: D 145 MET cc_start: 0.9099 (ttt) cc_final: 0.8689 (mtp) REVERT: D 188 GLN cc_start: 0.8125 (tt0) cc_final: 0.7858 (tm-30) REVERT: E 120 MET cc_start: 0.7315 (mtm) cc_final: 0.6342 (mmt) REVERT: E 131 GLN cc_start: 0.9456 (tm-30) cc_final: 0.9051 (pt0) REVERT: J 147 ARG cc_start: 0.9410 (mtm110) cc_final: 0.9188 (ptp90) REVERT: J 205 MET cc_start: 0.8238 (tpp) cc_final: 0.7942 (mmm) REVERT: K 86 ILE cc_start: 0.9477 (pt) cc_final: 0.9113 (mm) REVERT: K 123 LEU cc_start: 0.9276 (tp) cc_final: 0.9067 (tp) REVERT: K 162 MET cc_start: 0.8405 (ptp) cc_final: 0.7494 (ptp) REVERT: M 143 GLU cc_start: 0.9438 (pp20) cc_final: 0.9087 (pp20) REVERT: M 188 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7854 (tm-30) REVERT: M 371 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7954 (mp0) REVERT: N 98 ILE cc_start: 0.8425 (mm) cc_final: 0.8179 (tp) REVERT: Q 54 THR cc_start: 0.8794 (m) cc_final: 0.8435 (t) REVERT: Q 63 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8410 (mm110) REVERT: Q 129 ASP cc_start: 0.8830 (p0) cc_final: 0.8598 (p0) REVERT: Q 227 MET cc_start: 0.8798 (tpp) cc_final: 0.8559 (tpp) REVERT: T 120 MET cc_start: 0.8490 (tmm) cc_final: 0.8085 (tpt) REVERT: V 138 TYR cc_start: 0.9024 (t80) cc_final: 0.8072 (t80) REVERT: V 142 ARG cc_start: 0.9402 (mmm-85) cc_final: 0.8654 (ttm110) REVERT: V 371 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7982 (mt-10) REVERT: W 67 HIS cc_start: 0.9071 (p-80) cc_final: 0.8826 (p-80) REVERT: W 150 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8704 (tm-30) REVERT: X 30 ASN cc_start: 0.8271 (p0) cc_final: 0.7630 (p0) REVERT: Y 252 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8650 (ttpp) REVERT: Y 357 ASN cc_start: 0.8749 (m-40) cc_final: 0.8406 (m110) REVERT: Z 112 MET cc_start: 0.8384 (tpp) cc_final: 0.8117 (mmm) REVERT: Z 131 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8559 (tm-30) REVERT: e 185 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8178 (tm-30) REVERT: e 390 GLU cc_start: 0.7803 (pp20) cc_final: 0.7532 (pp20) REVERT: f 120 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7580 (tpp) REVERT: f 161 MET cc_start: 0.8619 (mmm) cc_final: 0.8311 (mmm) REVERT: f 263 LYS cc_start: 0.8953 (ptmm) cc_final: 0.8665 (ptmm) REVERT: k 145 MET cc_start: 0.8730 (ttt) cc_final: 0.8235 (mmt) REVERT: l 120 MET cc_start: 0.8079 (ptm) cc_final: 0.7702 (tmm) REVERT: l 129 ASP cc_start: 0.8799 (p0) cc_final: 0.8476 (p0) REVERT: o 120 MET cc_start: 0.8176 (mtm) cc_final: 0.7900 (mtm) REVERT: o 150 GLN cc_start: 0.8674 (pp30) cc_final: 0.8442 (pp30) REVERT: o 162 MET cc_start: 0.8581 (mtm) cc_final: 0.7735 (ptp) REVERT: u 145 MET cc_start: 0.9067 (mtt) cc_final: 0.8845 (mmm) REVERT: v 73 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8440 (pt0) REVERT: v 86 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8868 (mm) REVERT: v 89 GLN cc_start: 0.8743 (mp10) cc_final: 0.8430 (mp10) REVERT: v 108 PHE cc_start: 0.8758 (m-10) cc_final: 0.8453 (m-80) REVERT: v 115 ASP cc_start: 0.9212 (p0) cc_final: 0.8734 (p0) REVERT: v 117 ASN cc_start: 0.8981 (m110) cc_final: 0.8487 (m110) REVERT: z 67 HIS cc_start: 0.8173 (p-80) cc_final: 0.7574 (p-80) REVERT: z 89 GLN cc_start: 0.9428 (mp10) cc_final: 0.9164 (mp10) REVERT: z 111 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8662 (tm-30) outliers start: 59 outliers final: 23 residues processed: 647 average time/residue: 0.6564 time to fit residues: 704.3617 Evaluate side-chains 506 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 481 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain b residue 357 ASN Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain z residue 22 ASP Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 86 ILE Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 350 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 524 optimal weight: 8.9990 chunk 429 optimal weight: 0.0470 chunk 173 optimal weight: 30.0000 chunk 631 optimal weight: 5.9990 chunk 682 optimal weight: 40.0000 chunk 562 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 506 optimal weight: 7.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS D 271 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 HIS ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 HIS V 209 GLN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 GLN ** v 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 56894 Z= 0.357 Angle : 0.623 12.833 77036 Z= 0.320 Chirality : 0.044 0.191 8370 Planarity : 0.004 0.051 10228 Dihedral : 4.361 21.826 7996 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.59 % Allowed : 10.93 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7036 helix: 1.80 (0.16), residues: 1114 sheet: -0.32 (0.11), residues: 2246 loop : -0.25 (0.10), residues: 3676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 272 HIS 0.006 0.001 HIS z 83 PHE 0.023 0.002 PHE B 195 TYR 0.025 0.002 TYR T 194 ARG 0.011 0.001 ARG D 235 *********************** 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 618 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 525 time to evaluate : 5.059 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: B 161 MET cc_start: 0.8635 (mmm) cc_final: 0.8340 (mmm) REVERT: D 145 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8701 (mtp) REVERT: E 120 MET cc_start: 0.7581 (mtm) cc_final: 0.6779 (mmt) REVERT: E 131 GLN cc_start: 0.9531 (tm-30) cc_final: 0.9024 (mt0) REVERT: G 308 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: H 145 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8886 (mp0) REVERT: J 357 ASN cc_start: 0.8683 (m110) cc_final: 0.8481 (m110) REVERT: K 63 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8736 (mm110) REVERT: K 112 MET cc_start: 0.8656 (tpp) cc_final: 0.7418 (mmm) REVERT: M 147 ARG cc_start: 0.9087 (ppt90) cc_final: 0.8613 (ppt170) REVERT: M 371 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7941 (mp0) REVERT: N 120 MET cc_start: 0.8439 (tpt) cc_final: 0.8151 (tpt) REVERT: N 134 GLN cc_start: 0.8933 (pp30) cc_final: 0.8724 (pp30) REVERT: O 28 ASP cc_start: 0.8857 (p0) cc_final: 0.8444 (t0) REVERT: Q 54 THR cc_start: 0.8930 (m) cc_final: 0.8444 (t) REVERT: Q 112 MET cc_start: 0.8694 (tpt) cc_final: 0.7471 (mmm) REVERT: S 188 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8514 (mm-40) REVERT: T 120 MET cc_start: 0.8521 (tmm) cc_final: 0.8107 (tmm) REVERT: W 67 HIS cc_start: 0.9240 (p-80) cc_final: 0.8972 (p-80) REVERT: W 150 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8632 (tm-30) REVERT: W 183 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8747 (ttmm) REVERT: X 30 ASN cc_start: 0.8229 (p0) cc_final: 0.7590 (p0) REVERT: X 32 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: Y 357 ASN cc_start: 0.8707 (m-40) cc_final: 0.8346 (m110) REVERT: Z 66 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.8629 (m) REVERT: Z 131 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8488 (tm-30) REVERT: b 190 MET cc_start: 0.8843 (ttp) cc_final: 0.8487 (ttp) REVERT: e 218 GLU cc_start: 0.7942 (tt0) cc_final: 0.7718 (tt0) REVERT: e 390 GLU cc_start: 0.8068 (pp20) cc_final: 0.7745 (pp20) REVERT: h 205 MET cc_start: 0.8892 (tpp) cc_final: 0.8600 (mpp) REVERT: k 145 MET cc_start: 0.8818 (ttt) cc_final: 0.8206 (mmt) REVERT: l 120 MET cc_start: 0.8202 (ptm) cc_final: 0.7937 (tmm) REVERT: l 129 ASP cc_start: 0.8793 (p0) cc_final: 0.8328 (p0) REVERT: n 371 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7973 (mt-10) REVERT: o 120 MET cc_start: 0.8492 (mtm) cc_final: 0.8241 (mtm) REVERT: o 150 GLN cc_start: 0.8733 (pp30) cc_final: 0.8513 (pp30) REVERT: u 147 ARG cc_start: 0.9346 (ptt-90) cc_final: 0.9102 (ptt-90) REVERT: v 73 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8413 (pt0) REVERT: v 86 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9091 (mm) REVERT: v 91 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8843 (tp30) REVERT: v 108 PHE cc_start: 0.8918 (m-10) cc_final: 0.8635 (m-80) REVERT: v 115 ASP cc_start: 0.9210 (p0) cc_final: 0.8903 (p0) REVERT: v 117 ASN cc_start: 0.9025 (m110) cc_final: 0.8567 (m-40) REVERT: z 29 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7349 (t80) REVERT: z 63 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8345 (mm-40) REVERT: z 67 HIS cc_start: 0.8553 (p-80) cc_final: 0.7843 (p-80) REVERT: z 89 GLN cc_start: 0.9591 (mt0) cc_final: 0.9256 (mp10) REVERT: z 111 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8806 (tm-30) outliers start: 93 outliers final: 45 residues processed: 590 average time/residue: 0.5730 time to fit residues: 564.3465 Evaluate side-chains 507 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 454 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain z residue 22 ASP Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 623 optimal weight: 8.9990 chunk 474 optimal weight: 0.7980 chunk 327 optimal weight: 0.0570 chunk 69 optimal weight: 8.9990 chunk 301 optimal weight: 0.5980 chunk 423 optimal weight: 1.9990 chunk 633 optimal weight: 4.9990 chunk 670 optimal weight: 9.9990 chunk 331 optimal weight: 9.9990 chunk 600 optimal weight: 50.0000 chunk 180 optimal weight: 6.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS H 220 HIS K 45 GLN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 284 ASN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 220 HIS ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 258 GLN i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 56894 Z= 0.172 Angle : 0.559 11.728 77036 Z= 0.286 Chirality : 0.043 0.196 8370 Planarity : 0.004 0.058 10228 Dihedral : 4.087 23.611 7996 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.74 % Allowed : 12.50 % Favored : 85.76 % 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: 1.85 (0.16), residues: 1124 sheet: -0.10 (0.12), residues: 2105 loop : -0.22 (0.10), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 272 HIS 0.003 0.001 HIS Q 83 PHE 0.025 0.001 PHE B 195 TYR 0.015 0.001 TYR T 194 ARG 0.011 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 524 time to evaluate : 5.022 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: B 161 MET cc_start: 0.8629 (mmm) cc_final: 0.8372 (mmm) REVERT: D 145 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8793 (mtp) REVERT: E 65 LEU cc_start: 0.9328 (mm) cc_final: 0.9108 (mt) REVERT: E 120 MET cc_start: 0.7581 (mtm) cc_final: 0.6779 (mmt) REVERT: G 139 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8696 (pp20) REVERT: G 308 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: H 145 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: H 150 GLN cc_start: 0.8715 (pp30) cc_final: 0.8486 (pp30) REVERT: J 145 MET cc_start: 0.9109 (ttt) cc_final: 0.8685 (ppp) REVERT: J 205 MET cc_start: 0.8247 (tpp) cc_final: 0.7961 (mmm) REVERT: K 63 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8713 (mm110) REVERT: K 112 MET cc_start: 0.8673 (tpp) cc_final: 0.8422 (tpt) REVERT: K 123 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9088 (tp) REVERT: N 134 GLN cc_start: 0.8967 (pp30) cc_final: 0.8734 (pp30) REVERT: P 371 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7723 (mt-10) REVERT: Q 54 THR cc_start: 0.8835 (m) cc_final: 0.8615 (p) REVERT: Q 112 MET cc_start: 0.8856 (tpt) cc_final: 0.7264 (mmm) REVERT: V 185 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: W 67 HIS cc_start: 0.9154 (p-80) cc_final: 0.8896 (p-80) REVERT: W 150 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8439 (tm-30) REVERT: W 162 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8246 (ptm) REVERT: X 30 ASN cc_start: 0.8220 (p0) cc_final: 0.7581 (p0) REVERT: X 32 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: Y 357 ASN cc_start: 0.8640 (m-40) cc_final: 0.8277 (m110) REVERT: b 190 MET cc_start: 0.8745 (ttp) cc_final: 0.8431 (ttp) REVERT: e 390 GLU cc_start: 0.8057 (pp20) cc_final: 0.7744 (pp20) REVERT: h 205 MET cc_start: 0.8748 (tpp) cc_final: 0.8469 (mpp) REVERT: i 57 MET cc_start: 0.8176 (tpt) cc_final: 0.7760 (tpt) REVERT: i 162 MET cc_start: 0.8466 (ptp) cc_final: 0.7057 (ptm) REVERT: k 145 MET cc_start: 0.8746 (ttt) cc_final: 0.8149 (mmt) REVERT: k 147 ARG cc_start: 0.9176 (ptt90) cc_final: 0.8949 (ptt90) REVERT: l 120 MET cc_start: 0.8185 (ptm) cc_final: 0.7961 (tmm) REVERT: l 162 MET cc_start: 0.8620 (ptp) cc_final: 0.8183 (ptp) REVERT: n 371 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7641 (mt-10) REVERT: o 150 GLN cc_start: 0.8743 (pp30) cc_final: 0.8485 (pp30) REVERT: u 142 ARG cc_start: 0.9023 (mpt180) cc_final: 0.8741 (mmt-90) REVERT: u 144 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8884 (ttp80) REVERT: v 73 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8356 (pt0) REVERT: v 86 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9100 (mm) REVERT: v 91 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8839 (tp30) REVERT: v 108 PHE cc_start: 0.8960 (m-10) cc_final: 0.8733 (m-80) REVERT: v 115 ASP cc_start: 0.9182 (p0) cc_final: 0.8448 (p0) REVERT: v 117 ASN cc_start: 0.9014 (m110) cc_final: 0.8364 (m-40) REVERT: z 47 ASP cc_start: 0.8480 (p0) cc_final: 0.8236 (p0) REVERT: z 57 MET cc_start: 0.7613 (mpp) cc_final: 0.7196 (mmm) REVERT: z 63 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8122 (mm-40) REVERT: z 67 HIS cc_start: 0.8479 (p-80) cc_final: 0.7683 (p-80) REVERT: z 89 GLN cc_start: 0.9595 (mt0) cc_final: 0.9180 (mp10) REVERT: z 111 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8758 (tm-30) outliers start: 102 outliers final: 50 residues processed: 600 average time/residue: 0.5479 time to fit residues: 553.0411 Evaluate side-chains 513 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 454 time to evaluate : 4.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 147 ARG Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 162 MET Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 22 ASP Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 54 THR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 20.0000 chunk 380 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 499 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 572 optimal weight: 5.9990 chunk 463 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 342 optimal weight: 10.0000 chunk 602 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS D 188 GLN E 134 GLN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 GLN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 188 GLN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 GLN o 134 GLN ** v 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 56894 Z= 0.300 Angle : 0.583 10.708 77036 Z= 0.297 Chirality : 0.043 0.186 8370 Planarity : 0.004 0.052 10228 Dihedral : 4.066 21.491 7996 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.89 % Allowed : 13.33 % Favored : 84.77 % 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: 0.28 (0.10), residues: 7036 helix: 1.95 (0.16), residues: 1127 sheet: -0.12 (0.12), residues: 2102 loop : -0.08 (0.10), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 272 HIS 0.004 0.001 HIS T 83 PHE 0.022 0.001 PHE B 195 TYR 0.026 0.001 TYR c 64 ARG 0.011 0.000 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 484 time to evaluate : 5.043 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: B 152 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8301 (t) REVERT: D 142 ARG cc_start: 0.9145 (mmt-90) cc_final: 0.8905 (mmp80) REVERT: D 145 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8846 (mtp) REVERT: D 188 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: E 120 MET cc_start: 0.7844 (mtm) cc_final: 0.7085 (mmt) REVERT: G 139 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8737 (pp20) REVERT: H 145 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: J 138 TYR cc_start: 0.8533 (t80) cc_final: 0.8174 (t80) REVERT: J 145 MET cc_start: 0.9057 (ttt) cc_final: 0.8636 (ppp) REVERT: M 147 ARG cc_start: 0.9553 (ptt90) cc_final: 0.8924 (ppt170) REVERT: N 63 GLN cc_start: 0.9357 (mm-40) cc_final: 0.9151 (mm-40) REVERT: N 120 MET cc_start: 0.8292 (mmm) cc_final: 0.7967 (tpt) REVERT: N 227 MET cc_start: 0.8844 (tpp) cc_final: 0.8619 (tpp) REVERT: O 28 ASP cc_start: 0.8814 (p0) cc_final: 0.8469 (t0) REVERT: P 371 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7726 (mt-10) REVERT: Q 54 THR cc_start: 0.8949 (m) cc_final: 0.8634 (p) REVERT: Q 112 MET cc_start: 0.8871 (tpt) cc_final: 0.7384 (mmm) REVERT: T 112 MET cc_start: 0.8033 (tpp) cc_final: 0.7326 (mmm) REVERT: V 145 MET cc_start: 0.8849 (ttt) cc_final: 0.8414 (ttt) REVERT: V 185 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: W 67 HIS cc_start: 0.9238 (p-80) cc_final: 0.8932 (p-80) REVERT: W 150 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8448 (tm-30) REVERT: W 162 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8196 (ptm) REVERT: X 30 ASN cc_start: 0.8323 (p0) cc_final: 0.7746 (p0) REVERT: X 32 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: Y 357 ASN cc_start: 0.8691 (m-40) cc_final: 0.8329 (m110) REVERT: b 190 MET cc_start: 0.8805 (ttp) cc_final: 0.8546 (ttp) REVERT: c 63 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8182 (tm-30) REVERT: e 145 MET cc_start: 0.8081 (ttt) cc_final: 0.7460 (tmt) REVERT: e 390 GLU cc_start: 0.8067 (pp20) cc_final: 0.7783 (pp20) REVERT: f 161 MET cc_start: 0.8622 (mmm) cc_final: 0.8268 (mmm) REVERT: h 205 MET cc_start: 0.8781 (tpp) cc_final: 0.8474 (mpp) REVERT: i 57 MET cc_start: 0.8386 (tpt) cc_final: 0.8185 (tpt) REVERT: i 137 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: k 145 MET cc_start: 0.8758 (ttt) cc_final: 0.8138 (mmt) REVERT: l 120 MET cc_start: 0.8402 (ptm) cc_final: 0.8096 (tmm) REVERT: n 371 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7693 (mt-10) REVERT: o 150 GLN cc_start: 0.8774 (pp30) cc_final: 0.8573 (pp30) REVERT: u 144 ARG cc_start: 0.9217 (ttp80) cc_final: 0.8882 (ttp80) REVERT: u 145 MET cc_start: 0.8745 (mmm) cc_final: 0.8438 (mmm) REVERT: u 147 ARG cc_start: 0.9336 (ptt-90) cc_final: 0.8982 (ptt90) REVERT: v 73 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8243 (mp0) REVERT: v 86 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9104 (mm) REVERT: v 108 PHE cc_start: 0.9032 (m-10) cc_final: 0.8828 (m-80) REVERT: v 115 ASP cc_start: 0.9216 (p0) cc_final: 0.8464 (p0) REVERT: v 117 ASN cc_start: 0.9092 (m110) cc_final: 0.8414 (m-40) REVERT: z 63 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8182 (mm-40) REVERT: z 89 GLN cc_start: 0.9668 (mt0) cc_final: 0.9243 (mp10) outliers start: 111 outliers final: 62 residues processed: 572 average time/residue: 0.5532 time to fit residues: 530.5555 Evaluate side-chains 505 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 433 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 147 ARG Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 190 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 162 MET Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain i residue 137 GLU Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain o residue 57 MET Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 225 optimal weight: 9.9990 chunk 604 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 671 optimal weight: 0.7980 chunk 557 optimal weight: 7.9990 chunk 310 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN i 134 GLN i 150 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 GLN ** v 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 56894 Z= 0.298 Angle : 0.578 11.550 77036 Z= 0.295 Chirality : 0.043 0.180 8370 Planarity : 0.004 0.052 10228 Dihedral : 4.042 22.795 7996 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.05 % Allowed : 14.22 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7036 helix: 1.94 (0.16), residues: 1127 sheet: -0.05 (0.12), residues: 2070 loop : -0.02 (0.10), residues: 3839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 272 HIS 0.004 0.001 HIS E 67 PHE 0.024 0.001 PHE D 269 TYR 0.025 0.001 TYR e 138 ARG 0.010 0.000 ARG K 259 *********************** 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 582 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 462 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8508 (t80) REVERT: A 142 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8012 (ttm110) REVERT: B 57 MET cc_start: 0.7365 (mmm) cc_final: 0.7163 (mmm) REVERT: B 134 GLN cc_start: 0.9102 (mp10) cc_final: 0.8711 (mm110) REVERT: D 145 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8837 (mtp) REVERT: E 120 MET cc_start: 0.7934 (mtm) cc_final: 0.7198 (mmt) REVERT: G 139 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8790 (pp20) REVERT: G 308 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: H 80 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9165 (tttm) REVERT: H 145 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8861 (mp0) REVERT: H 150 GLN cc_start: 0.8757 (pp30) cc_final: 0.8526 (pp30) REVERT: H 161 MET cc_start: 0.8569 (mmm) cc_final: 0.8275 (mmm) REVERT: J 145 MET cc_start: 0.9052 (ttt) cc_final: 0.8732 (ppp) REVERT: K 63 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8482 (mm-40) REVERT: M 357 ASN cc_start: 0.8647 (m110) cc_final: 0.8362 (m110) REVERT: N 120 MET cc_start: 0.8415 (mmm) cc_final: 0.7980 (tpt) REVERT: O 28 ASP cc_start: 0.8787 (p0) cc_final: 0.8433 (t0) REVERT: P 371 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7728 (mt-10) REVERT: Q 54 THR cc_start: 0.8992 (m) cc_final: 0.8665 (p) REVERT: Q 112 MET cc_start: 0.8819 (tpt) cc_final: 0.7340 (mmm) REVERT: Q 161 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: T 112 MET cc_start: 0.8045 (tpp) cc_final: 0.7290 (mmm) REVERT: T 161 MET cc_start: 0.8740 (mmm) cc_final: 0.8486 (mmm) REVERT: V 185 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: W 67 HIS cc_start: 0.9263 (p-80) cc_final: 0.8939 (p-80) REVERT: W 150 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8417 (tm-30) REVERT: W 162 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: X 30 ASN cc_start: 0.8274 (p0) cc_final: 0.7784 (p0) REVERT: X 32 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: Y 357 ASN cc_start: 0.8679 (m-40) cc_final: 0.8337 (m110) REVERT: b 190 MET cc_start: 0.8839 (ttp) cc_final: 0.8578 (ttp) REVERT: b 205 MET cc_start: 0.8816 (mmm) cc_final: 0.7997 (mmm) REVERT: c 111 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8323 (tm-30) REVERT: f 161 MET cc_start: 0.8701 (mmm) cc_final: 0.8364 (mmm) REVERT: h 205 MET cc_start: 0.8777 (tpp) cc_final: 0.8444 (mpp) REVERT: i 120 MET cc_start: 0.8577 (tpt) cc_final: 0.8263 (tpp) REVERT: k 145 MET cc_start: 0.8744 (ttt) cc_final: 0.8095 (mmt) REVERT: l 120 MET cc_start: 0.8529 (ptm) cc_final: 0.8249 (tmm) REVERT: n 371 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7792 (mt-10) REVERT: o 150 GLN cc_start: 0.8818 (pp30) cc_final: 0.8615 (pp30) REVERT: u 145 MET cc_start: 0.8719 (mmm) cc_final: 0.8269 (mmm) REVERT: u 147 ARG cc_start: 0.9325 (ptt-90) cc_final: 0.9018 (ptt90) REVERT: v 73 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8156 (mp0) REVERT: v 86 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9116 (mm) REVERT: v 91 GLU cc_start: 0.8959 (tp30) cc_final: 0.8678 (tp30) REVERT: v 115 ASP cc_start: 0.9209 (p0) cc_final: 0.8625 (p0) REVERT: v 117 ASN cc_start: 0.9112 (m110) cc_final: 0.8571 (m-40) REVERT: z 47 ASP cc_start: 0.8654 (p0) cc_final: 0.8002 (p0) REVERT: z 63 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8048 (mm-40) REVERT: z 77 PHE cc_start: 0.9135 (t80) cc_final: 0.8534 (t80) REVERT: z 89 GLN cc_start: 0.9678 (mt0) cc_final: 0.9082 (mp10) outliers start: 120 outliers final: 76 residues processed: 555 average time/residue: 0.5780 time to fit residues: 547.3008 Evaluate side-chains 521 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 434 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 67 HIS Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 190 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 218 GLU Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 161 MET Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 162 MET Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 32 GLU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 80 LYS Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain c residue 253 THR Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain i residue 150 GLN Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 54 THR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 647 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 382 optimal weight: 4.9990 chunk 490 optimal weight: 7.9990 chunk 379 optimal weight: 9.9990 chunk 565 optimal weight: 10.0000 chunk 374 optimal weight: 2.9990 chunk 668 optimal weight: 8.9990 chunk 418 optimal weight: 4.9990 chunk 407 optimal weight: 40.0000 chunk 308 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 271 GLN c 134 GLN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 56894 Z= 0.301 Angle : 0.596 12.549 77036 Z= 0.302 Chirality : 0.043 0.210 8370 Planarity : 0.004 0.051 10228 Dihedral : 4.055 27.406 7996 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.07 % Allowed : 14.60 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.10), residues: 7036 helix: 1.93 (0.16), residues: 1130 sheet: -0.07 (0.12), residues: 2103 loop : 0.00 (0.10), residues: 3803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 272 HIS 0.004 0.001 HIS Z 83 PHE 0.026 0.001 PHE V 383 TYR 0.026 0.001 TYR e 138 ARG 0.013 0.000 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 454 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8557 (t80) REVERT: A 142 ARG cc_start: 0.8369 (mmp80) cc_final: 0.8071 (ttm110) REVERT: B 134 GLN cc_start: 0.9136 (mp10) cc_final: 0.8766 (mm110) REVERT: D 145 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8893 (mtp) REVERT: E 120 MET cc_start: 0.7965 (mtm) cc_final: 0.7274 (mmt) REVERT: G 139 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8797 (pp20) REVERT: G 308 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: H 107 LYS cc_start: 0.7643 (pttt) cc_final: 0.7155 (pttt) REVERT: H 145 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8866 (mp0) REVERT: J 145 MET cc_start: 0.9051 (ttt) cc_final: 0.8741 (ppp) REVERT: K 63 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8521 (mm-40) REVERT: K 166 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.7348 (mttm) REVERT: M 357 ASN cc_start: 0.8639 (m110) cc_final: 0.8387 (m110) REVERT: N 57 MET cc_start: 0.8638 (mmm) cc_final: 0.8254 (mmm) REVERT: N 120 MET cc_start: 0.8547 (mmm) cc_final: 0.8098 (tpt) REVERT: O 28 ASP cc_start: 0.8760 (p0) cc_final: 0.8536 (t0) REVERT: P 371 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7763 (mt-10) REVERT: Q 54 THR cc_start: 0.9032 (m) cc_final: 0.8807 (p) REVERT: Q 120 MET cc_start: 0.7570 (mtt) cc_final: 0.6846 (mpp) REVERT: Q 161 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8277 (mmm) REVERT: T 112 MET cc_start: 0.8111 (tpp) cc_final: 0.7416 (mmm) REVERT: V 185 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: W 150 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8417 (tm-30) REVERT: Y 357 ASN cc_start: 0.8643 (m-40) cc_final: 0.8310 (m110) REVERT: Z 161 MET cc_start: 0.8843 (mmm) cc_final: 0.8613 (mmm) REVERT: b 182 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8263 (tm-30) REVERT: b 190 MET cc_start: 0.8809 (ttp) cc_final: 0.8542 (ttp) REVERT: c 86 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9063 (tp) REVERT: c 111 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8277 (tm-30) REVERT: h 205 MET cc_start: 0.8786 (tpp) cc_final: 0.8447 (mpp) REVERT: i 120 MET cc_start: 0.8571 (tpt) cc_final: 0.7976 (tpt) REVERT: k 145 MET cc_start: 0.8759 (ttt) cc_final: 0.8158 (mmm) REVERT: k 186 LYS cc_start: 0.9392 (mttm) cc_final: 0.9175 (mtpp) REVERT: l 120 MET cc_start: 0.8643 (ptm) cc_final: 0.8382 (tmm) REVERT: l 161 MET cc_start: 0.8644 (mmm) cc_final: 0.8148 (mmm) REVERT: n 371 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7832 (mt-10) REVERT: o 150 GLN cc_start: 0.8882 (pp30) cc_final: 0.8646 (pp30) REVERT: u 145 MET cc_start: 0.8657 (mmm) cc_final: 0.8228 (mmm) REVERT: v 73 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8250 (mp0) REVERT: v 86 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9165 (mm) REVERT: v 91 GLU cc_start: 0.8951 (tp30) cc_final: 0.8680 (tp30) REVERT: v 115 ASP cc_start: 0.9239 (p0) cc_final: 0.8673 (p0) REVERT: v 117 ASN cc_start: 0.9145 (m110) cc_final: 0.8587 (m-40) REVERT: z 29 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7345 (t80) REVERT: z 47 ASP cc_start: 0.8489 (p0) cc_final: 0.8251 (p0) REVERT: z 57 MET cc_start: 0.7285 (mmm) cc_final: 0.7065 (mmm) REVERT: z 63 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8014 (mm-40) REVERT: z 77 PHE cc_start: 0.9152 (t80) cc_final: 0.8667 (t80) REVERT: z 89 GLN cc_start: 0.9669 (mt0) cc_final: 0.9179 (mp10) outliers start: 121 outliers final: 84 residues processed: 548 average time/residue: 0.5641 time to fit residues: 523.4168 Evaluate side-chains 523 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 428 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 67 HIS Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 161 MET Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 80 LYS Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain c residue 253 THR Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain f residue 253 THR Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 205 VAL Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain o residue 253 THR Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 66 THR Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4158 > 50: distance: 32 - 158: 25.433 distance: 35 - 155: 23.277 distance: 93 - 99: 32.106 distance: 99 - 100: 31.880 distance: 100 - 101: 9.560 distance: 100 - 103: 26.537 distance: 101 - 102: 24.435 distance: 101 - 107: 12.544 distance: 103 - 104: 47.518 distance: 104 - 105: 13.477 distance: 104 - 106: 22.463 distance: 107 - 108: 6.215 distance: 108 - 109: 31.902 distance: 108 - 111: 4.349 distance: 109 - 110: 40.233 distance: 109 - 114: 31.369 distance: 111 - 112: 19.784 distance: 111 - 113: 19.674 distance: 114 - 115: 25.013 distance: 115 - 116: 12.775 distance: 116 - 117: 3.897 distance: 116 - 118: 17.125 distance: 118 - 119: 10.808 distance: 119 - 120: 16.926 distance: 119 - 122: 23.058 distance: 120 - 121: 20.170 distance: 120 - 125: 19.959 distance: 122 - 123: 18.486 distance: 122 - 124: 38.485 distance: 125 - 126: 56.198 distance: 126 - 127: 45.152 distance: 126 - 129: 42.216 distance: 127 - 128: 45.792 distance: 127 - 130: 29.308 distance: 130 - 131: 51.223 distance: 131 - 132: 48.270 distance: 131 - 134: 20.447 distance: 132 - 133: 45.542 distance: 132 - 136: 44.217 distance: 136 - 142: 14.582 distance: 137 - 138: 39.374 distance: 137 - 140: 20.143 distance: 138 - 139: 14.278 distance: 138 - 143: 34.445 distance: 140 - 141: 32.676 distance: 141 - 142: 41.518 distance: 143 - 144: 34.735 distance: 144 - 145: 42.926 distance: 144 - 147: 14.900 distance: 145 - 146: 43.602 distance: 145 - 148: 44.453 distance: 148 - 149: 15.077 distance: 149 - 150: 16.350 distance: 149 - 152: 30.392 distance: 150 - 151: 20.732 distance: 150 - 155: 11.060 distance: 152 - 153: 49.255 distance: 152 - 154: 43.310 distance: 155 - 156: 29.460 distance: 156 - 157: 45.136 distance: 156 - 159: 45.625 distance: 157 - 158: 41.139 distance: 157 - 166: 29.492 distance: 159 - 160: 19.976 distance: 160 - 161: 52.433 distance: 161 - 162: 31.928 distance: 162 - 163: 6.276 distance: 163 - 164: 22.663 distance: 163 - 165: 11.866