Starting phenix.real_space_refine on Fri Oct 11 10:26:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/10_2024/8rt6_19480.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/10_2024/8rt6_19480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/10_2024/8rt6_19480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/10_2024/8rt6_19480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/10_2024/8rt6_19480.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/10_2024/8rt6_19480.cif" } resolution = 3.18 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= 0.026 sd= 0.073 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 542 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55802 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "a" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "d" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "g" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "j" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "m" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "p" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 24.78, per 1000 atoms: 0.44 Number of scatterers: 55802 At special positions: 0 Unit cell: (193.127, 195.261, 154.715, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 10556 8.00 N 10180 7.00 C 34862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS V 215 " - pdb=" SG CYS V 231 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 215 " - pdb=" SG CYS Y 231 " distance=2.03 Simple disulfide: pdb=" SG CYS b 215 " - pdb=" SG CYS b 231 " distance=2.03 Simple disulfide: pdb=" SG CYS e 215 " - pdb=" SG CYS e 231 " distance=2.03 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.03 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 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: 9.78 Conformation dependent library (CDL) restraints added in 5.3 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: 90 helices and 144 sheets defined 17.0% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 305 through 329 removed outlier: 5.258A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.505A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.730A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 305 through 329 removed outlier: 5.475A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.541A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 150 removed outlier: 3.757A pdb=" N ARG E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'F' and resid 39 through 43 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: 5.554A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.753A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 151 removed outlier: 4.218A pdb=" N ARG H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 169 Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'J' and resid 305 through 329 removed outlier: 5.638A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.592A pdb=" N ASN J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 151 removed outlier: 3.965A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.588A 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 180 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 5.564A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.336A 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: 3.922A pdb=" N GLN N 131 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 4.010A 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 'P' and resid 136 through 148 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 329 removed outlier: 5.407A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 359 Processing helix chain 'Q' and resid 127 through 151 removed outlier: 3.922A pdb=" N ARG Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 169 Processing helix chain 'S' and resid 136 through 148 Processing helix chain 'S' and resid 180 through 187 Processing helix chain 'S' and resid 305 through 329 removed outlier: 5.564A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 Processing helix chain 'T' and resid 127 through 151 removed outlier: 3.630A pdb=" N ALA T 138 " --> pdb=" O GLN T 134 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'V' and resid 182 through 187 Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.355A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA V 313 " --> pdb=" O ARG V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 359 Processing helix chain 'W' and resid 127 through 150 removed outlier: 3.772A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN W 139 " --> pdb=" O THR W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 169 Processing helix chain 'X' and resid 39 through 43 Processing helix chain 'Y' and resid 136 through 148 Processing helix chain 'Y' and resid 180 through 187 Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.392A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.289A 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: 4.217A 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 305 through 329 removed outlier: 5.405A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 Processing helix chain 'c' and resid 127 through 151 removed outlier: 4.247A 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 'e' and resid 136 through 148 Processing helix chain 'e' and resid 180 through 187 Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.499A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.672A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 151 removed outlier: 3.619A pdb=" N GLN f 131 " --> pdb=" O TYR f 127 " (cutoff:3.500A) removed outlier: 4.034A 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: 3.536A pdb=" N ILE g 42 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 Processing helix chain 'h' and resid 180 through 187 Processing helix chain 'h' and resid 305 through 329 removed outlier: 5.404A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.556A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) removed outlier: 4.109A 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 'k' and resid 136 through 148 Processing helix chain 'k' and resid 180 through 187 removed outlier: 3.510A pdb=" N GLU k 185 " --> pdb=" O GLY k 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.694A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 removed outlier: 3.559A pdb=" N ASN k 357 " --> pdb=" O GLU k 353 " (cutoff:3.500A) Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.854A 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 removed outlier: 3.530A pdb=" N ILE m 42 " --> pdb=" O PRO m 39 " (cutoff:3.500A) 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: 5.446A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 Processing helix chain 'o' and resid 127 through 151 removed outlier: 3.952A pdb=" N ARG o 151 " --> pdb=" O ALA o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing helix chain 'p' and resid 39 through 43 removed outlier: 3.544A pdb=" N ILE p 42 " --> pdb=" O PRO p 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'y' and resid 136 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.646A 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: 3.531A pdb=" N VAL D 282 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL D 270 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.531A pdb=" N VAL D 282 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 254 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 275 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS D 252 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 227 " --> pdb=" O TYR D 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA5, first strand: chain 'n' and resid 198 through 199 removed outlier: 3.547A pdb=" N VAL A 282 " --> pdb=" O GLY n 198 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 270 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 255 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS A 252 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE A 275 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 254 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 391 Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.515A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.990A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 64 through 69 Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 204 removed outlier: 4.619A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB5, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AB6, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.793A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 198 through 199 removed outlier: 4.652A pdb=" N VAL G 270 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS G 252 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE G 275 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL G 254 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB9, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AC1, first strand: chain 'D' and resid 387 through 391 Processing sheet with id=AC2, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.369A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 44 through 48 Processing sheet with id=AC4, first strand: chain 'E' and resid 202 through 204 removed outlier: 4.636A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 233 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AC6, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.526A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 198 through 199 removed outlier: 4.614A pdb=" N VAL J 270 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY J 255 " --> pdb=" O THR J 229 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (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 Processing sheet with id=AD1, first strand: chain 'G' and resid 387 through 391 Processing sheet with id=AD2, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.387A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.553A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG H 113 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR H 48 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 97 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 64 through 66 removed outlier: 7.177A 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 204 removed outlier: 3.589A pdb=" N VAL H 196 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.652A 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 Processing sheet with id=AD7, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.638A 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: 4.589A pdb=" N VAL M 270 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY M 255 " --> pdb=" O THR M 229 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS M 252 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE M 275 " --> pdb=" O LYS M 252 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL M 254 " --> pdb=" O SER M 273 " (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 Processing sheet with id=AE2, first strand: chain 'J' and resid 387 through 391 removed outlier: 3.677A pdb=" N GLU J 390 " --> pdb=" O ARG N 259 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 25 through 26 removed outlier: 6.689A pdb=" N HIS K 55 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N PHE K 125 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N MET K 57 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.896A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL K 46 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.523A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AE7, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.823A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 198 through 199 removed outlier: 4.647A pdb=" N VAL P 270 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY P 255 " --> pdb=" O THR P 229 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AF1, first strand: chain 'M' and resid 237 through 238 Processing sheet with id=AF2, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AF3, first strand: chain 'M' and resid 387 through 391 Processing sheet with id=AF4, first strand: chain 'N' and resid 25 through 26 removed outlier: 7.089A pdb=" N ARG N 34 " --> pdb=" O ALA N 124 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ARG N 126 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL N 36 " --> pdb=" O ARG N 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.479A pdb=" N VAL N 44 " --> pdb=" O ARG N 109 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN N 111 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL N 46 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR N 66 " --> pdb=" O VAL N 100 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 202 through 204 removed outlier: 4.472A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 172 through 175 Processing sheet with id=AF8, first strand: chain 'P' and resid 195 through 196 removed outlier: 6.706A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 198 through 199 removed outlier: 3.563A pdb=" N VAL S 282 " --> pdb=" O GLY P 198 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.569A 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: 6.746A 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: 3.630A pdb=" N ARG Q 34 " --> pdb=" O GLU Q 122 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE Q 125 " --> pdb=" O MET Q 57 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 47 through 48 removed outlier: 6.873A pdb=" N THR Q 48 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN Q 111 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR Q 95 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id=AG8, first strand: chain 'Q' and resid 202 through 204 removed outlier: 3.615A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 172 through 175 Processing sheet with id=AH1, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.607A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AH3, first strand: chain 'S' and resid 237 through 238 Processing sheet with id=AH4, first strand: chain 'S' and resid 267 through 268 Processing sheet with id=AH5, first strand: chain 'S' and resid 388 through 391 Processing sheet with id=AH6, first strand: chain 'T' and resid 25 through 26 removed outlier: 4.113A pdb=" N ARG T 34 " --> pdb=" O GLU T 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA T 124 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.499A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'T' and resid 64 through 69 Processing sheet with id=AH9, first strand: chain 'T' and resid 202 through 203 removed outlier: 3.525A pdb=" N VAL T 196 " --> pdb=" O LYS T 225 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'T' and resid 172 through 175 Processing sheet with id=AI2, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.805A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 198 through 199 removed outlier: 3.529A pdb=" N VAL Y 282 " --> pdb=" O GLY V 198 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL Y 270 " --> pdb=" O GLY Y 289 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY Y 255 " --> pdb=" O THR Y 229 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 282 through 283 removed outlier: 4.571A pdb=" N VAL V 270 " --> pdb=" O GLY V 289 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI6, first strand: chain 'V' and resid 237 through 238 Processing sheet with id=AI7, first strand: chain 'V' and resid 267 through 268 Processing sheet with id=AI8, first strand: chain 'V' and resid 387 through 391 Processing sheet with id=AI9, first strand: chain 'W' and resid 25 through 26 removed outlier: 6.397A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 44 through 49 removed outlier: 6.653A pdb=" N VAL W 44 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLN W 111 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL W 46 " --> pdb=" O GLN W 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG W 113 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR W 48 " --> pdb=" O ARG W 113 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.603A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ4, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.786A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Y' and resid 221 through 222 Processing sheet with id=AJ6, first strand: chain 'Y' and resid 237 through 238 Processing sheet with id=AJ7, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 25 through 26 removed outlier: 6.588A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE Z 125 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N MET Z 57 " --> pdb=" O PHE Z 125 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.495A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 202 through 204 removed outlier: 4.671A 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 195 through 196 removed outlier: 6.912A pdb=" N SER b 195 " --> pdb=" O ASP e 382 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 198 through 199 removed outlier: 3.539A pdb=" N VAL e 282 " --> pdb=" O GLY b 198 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL e 270 " --> pdb=" O GLY e 289 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS e 252 " --> pdb=" O ILE e 275 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE e 275 " --> pdb=" O LYS e 252 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL e 254 " --> pdb=" O SER e 273 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 282 through 283 removed outlier: 4.636A pdb=" N VAL b 270 " --> pdb=" O GLY b 289 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY b 227 " --> pdb=" O TYR b 257 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY b 255 " --> pdb=" O THR b 229 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS b 252 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE b 275 " --> pdb=" O LYS b 252 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL b 254 " --> pdb=" O SER b 273 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AK7, first strand: chain 'b' and resid 237 through 238 removed outlier: 6.827A pdb=" N VAL b 237 " --> pdb=" O LEU b 246 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AK9, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.674A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'c' and resid 44 through 48 removed outlier: 6.848A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 64 through 66 removed outlier: 3.511A pdb=" N THR c 66 " --> pdb=" O VAL c 100 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'c' and resid 202 through 204 removed outlier: 4.520A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'c' and resid 172 through 175 Processing sheet with id=AL5, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.711A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'e' and resid 198 through 199 removed outlier: 4.572A pdb=" N VAL h 270 " --> pdb=" O GLY h 289 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY h 255 " --> pdb=" O THR h 229 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS h 252 " --> pdb=" O ILE h 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE h 275 " --> pdb=" O LYS h 252 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL h 254 " --> pdb=" O SER h 273 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AL8, first strand: chain 'e' and resid 237 through 238 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: 6.755A pdb=" N ARG f 34 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ARG f 126 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL f 36 " --> pdb=" O ARG f 126 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.410A 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 49 removed outlier: 7.034A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG f 113 " --> pdb=" O VAL f 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR f 48 " --> pdb=" O ARG f 113 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 202 through 204 removed outlier: 3.516A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.513A 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: 6.955A 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: 4.621A pdb=" N VAL k 270 " --> pdb=" O GLY k 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM8, first strand: chain 'h' and resid 237 through 238 Processing sheet with id=AM9, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AN1, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN2, first strand: chain 'i' and resid 25 through 26 removed outlier: 3.839A pdb=" N ARG i 34 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA i 124 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE i 86 " --> pdb=" O THR i 54 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'i' and resid 44 through 48 removed outlier: 3.713A pdb=" N VAL i 46 " --> pdb=" O ARG i 109 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 202 through 204 removed outlier: 3.556A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN6, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.908A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'k' and resid 198 through 199 removed outlier: 4.675A pdb=" N VAL n 270 " --> pdb=" O GLY n 289 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY n 227 " --> pdb=" O TYR n 257 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AN9, first strand: chain 'k' and resid 237 through 238 Processing sheet with id=AO1, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AO2, first strand: chain 'k' and resid 387 through 391 Processing sheet with id=AO3, first strand: chain 'l' and resid 25 through 26 removed outlier: 6.726A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'l' and resid 44 through 48 removed outlier: 6.770A pdb=" N VAL l 44 " --> pdb=" O ARG l 109 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN l 111 " --> pdb=" O VAL l 44 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL l 46 " --> pdb=" O GLN l 111 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 202 through 204 removed outlier: 4.562A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AO7, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AO8, first strand: chain 'n' and resid 237 through 238 Processing sheet with id=AO9, first strand: chain 'n' and resid 267 through 268 Processing sheet with id=AP1, first strand: chain 'o' and resid 25 through 26 removed outlier: 3.593A pdb=" N ARG o 34 " --> pdb=" O GLU o 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA o 124 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS o 55 " --> pdb=" O LEU o 123 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE o 125 " --> pdb=" O HIS o 55 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N MET o 57 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 44 through 49 removed outlier: 3.509A pdb=" N VAL o 46 " --> pdb=" O ARG o 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU o 97 " --> pdb=" O PHE o 108 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'o' and resid 202 through 203 removed outlier: 4.585A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'o' and resid 172 through 175 Processing sheet with id=AP5, first strand: chain 'v' and resid 25 through 26 removed outlier: 6.422A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'v' and resid 44 through 48 removed outlier: 6.921A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN v 111 " --> pdb=" O VAL v 44 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL v 46 " --> pdb=" O GLN v 111 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'z' and resid 25 through 26 removed outlier: 6.293A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'z' and resid 45 through 48 removed outlier: 6.394A pdb=" N VAL z 46 " --> pdb=" O GLN z 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP8 Processing sheet with id=AP9, first strand: chain 'z' and resid 64 through 66 2125 hydrogen bonds defined for protein. 5529 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: 24.67 Time building geometry restraints manager: 11.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18747 1.33 - 1.45: 9203 1.45 - 1.57: 28575 1.57 - 1.69: 3 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" C GLU M 276 " pdb=" N THR M 277 " ideal model delta sigma weight residual 1.330 1.276 0.054 1.47e-02 4.63e+03 1.33e+01 bond pdb=" C GLU S 276 " pdb=" N THR S 277 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.37e-02 5.33e+03 1.17e+01 bond pdb=" C LYS d 24 " pdb=" N GLN d 25 " ideal model delta sigma weight residual 1.333 1.279 0.054 1.61e-02 3.86e+03 1.13e+01 bond pdb=" C GLU J 276 " pdb=" N THR J 277 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.47e-02 4.63e+03 1.12e+01 bond pdb=" C GLU e 276 " pdb=" N THR e 277 " ideal model delta sigma weight residual 1.330 1.285 0.046 1.37e-02 5.33e+03 1.11e+01 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 76949 5.34 - 10.68: 78 10.68 - 16.02: 4 16.02 - 21.36: 0 21.36 - 26.70: 5 Bond angle restraints: 77036 Sorted by residual: angle pdb=" O GLN a 43 " pdb=" C GLN a 43 " pdb=" N ARG a 44 " ideal model delta sigma weight residual 122.91 96.21 26.70 1.19e+00 7.06e-01 5.04e+02 angle pdb=" O GLN U 43 " pdb=" C GLN U 43 " pdb=" N ARG U 44 " ideal model delta sigma weight residual 122.67 97.73 24.94 1.13e+00 7.83e-01 4.87e+02 angle pdb=" O GLN I 43 " pdb=" C GLN I 43 " pdb=" N ARG I 44 " ideal model delta sigma weight residual 122.58 98.45 24.13 1.20e+00 6.94e-01 4.04e+02 angle pdb=" O GLN j 43 " pdb=" C GLN j 43 " pdb=" N ARG j 44 " ideal model delta sigma weight residual 122.41 96.63 25.78 1.34e+00 5.57e-01 3.70e+02 angle pdb=" O GLN C 43 " pdb=" C GLN C 43 " pdb=" N ARG C 44 " ideal model delta sigma weight residual 122.91 101.39 21.52 1.19e+00 7.06e-01 3.27e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31031 17.97 - 35.94: 2578 35.94 - 53.90: 490 53.90 - 71.87: 74 71.87 - 89.84: 17 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA MET W 57 " pdb=" C MET W 57 " pdb=" N LEU W 58 " pdb=" CA LEU W 58 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA VAL B 152 " pdb=" C VAL B 152 " pdb=" N GLY B 153 " pdb=" CA GLY B 153 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PHE B 69 " pdb=" C PHE B 69 " pdb=" N GLY B 70 " pdb=" CA GLY B 70 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5935 0.053 - 0.105: 1980 0.105 - 0.158: 446 0.158 - 0.210: 5 0.210 - 0.263: 4 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB ILE N 98 " pdb=" CA ILE N 98 " pdb=" CG1 ILE N 98 " pdb=" CG2 ILE N 98 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE K 98 " pdb=" CA ILE K 98 " pdb=" CG1 ILE K 98 " pdb=" CG2 ILE K 98 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR E 66 " pdb=" CA THR E 66 " pdb=" OG1 THR E 66 " pdb=" CG2 THR E 66 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN j 43 " -0.106 2.00e-02 2.50e+03 1.82e-01 3.33e+02 pdb=" C GLN j 43 " 0.316 2.00e-02 2.50e+03 pdb=" O GLN j 43 " -0.114 2.00e-02 2.50e+03 pdb=" N ARG j 44 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 43 " 0.106 2.00e-02 2.50e+03 1.82e-01 3.31e+02 pdb=" C GLN a 43 " -0.315 2.00e-02 2.50e+03 pdb=" O GLN a 43 " 0.114 2.00e-02 2.50e+03 pdb=" N ARG a 44 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN U 43 " 0.101 2.00e-02 2.50e+03 1.76e-01 3.08e+02 pdb=" C GLN U 43 " -0.304 2.00e-02 2.50e+03 pdb=" O GLN U 43 " 0.110 2.00e-02 2.50e+03 pdb=" N ARG U 44 " 0.092 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 733 2.63 - 3.20: 47966 3.20 - 3.77: 83619 3.77 - 4.33: 123507 4.33 - 4.90: 211846 Nonbonded interactions: 467671 Sorted by model distance: nonbonded pdb=" OH TYR H 106 " pdb=" OH TYR H 127 " model vdw 2.066 3.040 nonbonded pdb=" OG SER D 148 " pdb=" OD1 ASP E 71 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR E 253 " pdb=" O VAL E 258 " model vdw 2.131 3.040 nonbonded pdb=" OE1 GLN T 45 " pdb=" NH2 ARG T 109 " model vdw 2.132 3.120 nonbonded pdb=" OE2 GLU c 62 " pdb=" OG1 THR c 101 " model vdw 2.137 3.040 ... (remaining 467666 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.570 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 101.970 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.650 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.145 56894 Z= 0.693 Angle : 0.803 26.704 77036 Z= 0.477 Chirality : 0.052 0.263 8370 Planarity : 0.008 0.182 10228 Dihedral : 13.559 89.841 21096 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.49 % 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: -0.79 (0.09), residues: 7036 helix: 1.12 (0.15), residues: 1125 sheet: -0.62 (0.12), residues: 1936 loop : -0.93 (0.09), residues: 3975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP h 325 HIS 0.007 0.002 HIS D 305 PHE 0.029 0.002 PHE T 148 TYR 0.037 0.002 TYR K 64 ARG 0.016 0.001 ARG Z 104 *********************** 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 854 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 850 time to evaluate : 4.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 140 LEU cc_start: 0.8724 (mt) cc_final: 0.8502 (mt) REVERT: V 140 LEU cc_start: 0.8447 (mt) cc_final: 0.8237 (mt) outliers start: 4 outliers final: 0 residues processed: 854 average time/residue: 0.5829 time to fit residues: 805.7618 Evaluate side-chains 499 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 4.812 ------------------------------------------------------------------------------- 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: 6.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 543 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 630 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 360 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN G 271 GLN J 271 GLN J 305 HIS K 31 HIS K 201 ASN M 209 GLN M 271 GLN P 271 GLN Q 63 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 271 GLN S 357 ASN T 89 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 201 ASN V 209 GLN W 45 GLN W 201 ASN Y 271 GLN Y 305 HIS b 209 GLN e 271 GLN e 284 ASN f 45 GLN ** f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 209 GLN h 212 GLN h 263 GLN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 374 ASN o 31 HIS z 55 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2097 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= 0.307 Angle : 0.650 9.855 77036 Z= 0.341 Chirality : 0.045 0.189 8370 Planarity : 0.005 0.082 10228 Dihedral : 4.658 28.939 7996 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 0.89 % Allowed : 7.94 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7036 helix: 1.93 (0.16), residues: 1124 sheet: -0.37 (0.12), residues: 1878 loop : -0.52 (0.09), residues: 4034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 325 HIS 0.005 0.001 HIS K 83 PHE 0.030 0.002 PHE l 195 TYR 0.024 0.002 TYR V 138 ARG 0.009 0.001 ARG c 28 *********************** 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 636 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 584 time to evaluate : 4.927 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: D 139 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6922 (tm-30) REVERT: D 146 LEU cc_start: 0.8665 (mt) cc_final: 0.8334 (mt) REVERT: J 140 LEU cc_start: 0.8597 (mt) cc_final: 0.8105 (mm) REVERT: J 145 MET cc_start: 0.7993 (mtt) cc_final: 0.7766 (mmt) REVERT: k 143 GLU cc_start: 0.6817 (pt0) cc_final: 0.6592 (pt0) REVERT: v 112 MET cc_start: 0.7299 (tpp) cc_final: 0.7085 (tpt) outliers start: 52 outliers final: 20 residues processed: 614 average time/residue: 0.5575 time to fit residues: 570.5946 Evaluate side-chains 469 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 449 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain h residue 263 GLN Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 30 ASP Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 107 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 350 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 524 optimal weight: 7.9990 chunk 429 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 631 optimal weight: 1.9990 chunk 682 optimal weight: 50.0000 chunk 562 optimal weight: 5.9990 chunk 626 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 506 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN J 232 HIS ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN Q 220 HIS T 134 GLN V 271 GLN W 150 GLN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 360 ASN c 131 GLN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** f 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 232 HIS h 271 GLN h 357 ASN ** i 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 220 HIS ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 56894 Z= 0.362 Angle : 0.630 10.517 77036 Z= 0.327 Chirality : 0.044 0.180 8370 Planarity : 0.005 0.061 10228 Dihedral : 4.414 29.455 7996 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.85 % Favored : 98.14 % Rotamer: Outliers : 1.43 % Allowed : 9.32 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 7036 helix: 2.15 (0.16), residues: 1132 sheet: -0.24 (0.12), residues: 1882 loop : -0.29 (0.09), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.007 0.001 HIS K 31 PHE 0.025 0.001 PHE l 195 TYR 0.024 0.001 TYR b 138 ARG 0.005 0.000 ARG K 79 *********************** 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 564 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 480 time to evaluate : 4.892 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: D 146 LEU cc_start: 0.8681 (mt) cc_final: 0.8332 (mt) REVERT: E 112 MET cc_start: 0.7822 (tpp) cc_final: 0.7444 (tpp) REVERT: N 162 MET cc_start: 0.6872 (ppp) cc_final: 0.5906 (ptt) REVERT: k 139 GLU cc_start: 0.7090 (pp20) cc_final: 0.5893 (pp20) REVERT: k 143 GLU cc_start: 0.6809 (pt0) cc_final: 0.6287 (pt0) REVERT: l 162 MET cc_start: 0.6934 (ppp) cc_final: 0.6541 (ptt) REVERT: u 140 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7659 (mm) REVERT: v 111 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7199 (mm-40) REVERT: v 112 MET cc_start: 0.7413 (tpp) cc_final: 0.7168 (tpt) outliers start: 84 outliers final: 34 residues processed: 537 average time/residue: 0.5484 time to fit residues: 494.3981 Evaluate side-chains 454 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 418 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain Z residue 263 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain z residue 30 ASP Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 623 optimal weight: 0.8980 chunk 474 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 423 optimal weight: 0.9980 chunk 633 optimal weight: 7.9990 chunk 670 optimal weight: 10.0000 chunk 331 optimal weight: 7.9990 chunk 600 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN D 209 GLN D 271 GLN J 360 ASN M 284 ASN N 134 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 111 GLN ** i 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 56894 Z= 0.187 Angle : 0.577 13.803 77036 Z= 0.296 Chirality : 0.044 0.357 8370 Planarity : 0.004 0.062 10228 Dihedral : 4.185 28.397 7996 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.82 % Favored : 98.17 % Rotamer: Outliers : 1.26 % Allowed : 10.93 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.10), residues: 7036 helix: 2.22 (0.16), residues: 1132 sheet: -0.07 (0.12), residues: 1866 loop : -0.23 (0.09), residues: 4038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 307 HIS 0.005 0.001 HIS K 31 PHE 0.026 0.001 PHE N 195 TYR 0.016 0.001 TYR V 138 ARG 0.008 0.000 ARG y 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 477 time to evaluate : 4.931 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: D 146 LEU cc_start: 0.8579 (mt) cc_final: 0.8306 (mt) REVERT: N 162 MET cc_start: 0.6688 (ppp) cc_final: 0.6017 (ptt) REVERT: V 139 GLU cc_start: 0.7351 (pp20) cc_final: 0.7020 (pp20) REVERT: W 120 MET cc_start: 0.7346 (tpp) cc_final: 0.7139 (tpp) REVERT: o 112 MET cc_start: 0.6980 (tpp) cc_final: 0.6419 (tpp) REVERT: v 112 MET cc_start: 0.7439 (tpp) cc_final: 0.7236 (tpt) REVERT: z 47 ASP cc_start: 0.7710 (t0) cc_final: 0.7400 (t0) outliers start: 74 outliers final: 32 residues processed: 535 average time/residue: 0.5442 time to fit residues: 489.4864 Evaluate side-chains 447 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 415 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain S residue 282 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 263 LYS Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 100 VAL Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 3.9990 chunk 380 optimal weight: 20.0000 chunk 9 optimal weight: 0.4980 chunk 499 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 572 optimal weight: 9.9990 chunk 463 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 342 optimal weight: 5.9990 chunk 602 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN K 45 GLN Q 63 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN g 25 GLN h 188 GLN ** i 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 56894 Z= 0.272 Angle : 0.590 11.450 77036 Z= 0.302 Chirality : 0.044 0.194 8370 Planarity : 0.004 0.051 10228 Dihedral : 4.105 29.636 7996 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.92 % Favored : 98.07 % Rotamer: Outliers : 1.55 % Allowed : 11.66 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7036 helix: 2.30 (0.16), residues: 1132 sheet: -0.14 (0.12), residues: 1864 loop : -0.12 (0.10), residues: 4040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 307 HIS 0.005 0.001 HIS K 67 PHE 0.024 0.001 PHE N 195 TYR 0.022 0.001 TYR u 138 ARG 0.013 0.000 ARG K 34 *********************** 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 541 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 450 time to evaluate : 4.905 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: D 146 LEU cc_start: 0.8691 (mt) cc_final: 0.8343 (mt) REVERT: N 162 MET cc_start: 0.6661 (ppp) cc_final: 0.6015 (ptt) REVERT: W 120 MET cc_start: 0.7422 (tpp) cc_final: 0.7196 (tpp) REVERT: c 120 MET cc_start: 0.6783 (ttp) cc_final: 0.6521 (mtm) outliers start: 91 outliers final: 56 residues processed: 520 average time/residue: 0.5248 time to fit residues: 461.1745 Evaluate side-chains 463 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 407 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain S residue 282 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain Z residue 102 ASP Chi-restraints excluded: chain Z residue 263 LYS Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 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 44 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 100 VAL Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 225 optimal weight: 5.9990 chunk 604 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 393 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 671 optimal weight: 6.9990 chunk 557 optimal weight: 20.0000 chunk 310 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 352 optimal weight: 6.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN H 150 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 GLN ** Z 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 134 GLN a 25 GLN ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** i 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 56894 Z= 0.300 Angle : 0.609 13.512 77036 Z= 0.311 Chirality : 0.044 0.220 8370 Planarity : 0.004 0.053 10228 Dihedral : 4.086 29.645 7996 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.96 % Favored : 98.02 % Rotamer: Outliers : 1.66 % Allowed : 12.19 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7036 helix: 2.34 (0.16), residues: 1128 sheet: -0.10 (0.12), residues: 1844 loop : -0.07 (0.10), residues: 4064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 307 HIS 0.005 0.001 HIS K 67 PHE 0.022 0.001 PHE N 195 TYR 0.032 0.001 TYR A 387 ARG 0.007 0.000 ARG y 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 444 time to evaluate : 6.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 LEU cc_start: 0.8709 (mt) cc_final: 0.8346 (mt) REVERT: N 162 MET cc_start: 0.6722 (ppp) cc_final: 0.6049 (ptt) REVERT: c 120 MET cc_start: 0.6790 (ttp) cc_final: 0.6553 (mtm) REVERT: u 146 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7722 (mm) outliers start: 97 outliers final: 70 residues processed: 522 average time/residue: 0.5345 time to fit residues: 471.6961 Evaluate side-chains 481 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 410 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 282 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain V residue 228 MET Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 59 GLU Chi-restraints excluded: chain Z residue 102 ASP Chi-restraints excluded: chain Z residue 263 LYS Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 231 CYS Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 146 LEU 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 44 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 647 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 chunk 490 optimal weight: 2.9990 chunk 379 optimal weight: 3.9990 chunk 565 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 668 optimal weight: 9.9990 chunk 418 optimal weight: 6.9990 chunk 407 optimal weight: 30.0000 chunk 308 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 232 HIS ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** i 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 271 GLN ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 56894 Z= 0.251 Angle : 0.609 14.204 77036 Z= 0.310 Chirality : 0.044 0.245 8370 Planarity : 0.004 0.055 10228 Dihedral : 4.050 28.962 7996 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.43 % Allowed : 12.87 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7036 helix: 2.29 (0.16), residues: 1132 sheet: -0.13 (0.12), residues: 1860 loop : -0.04 (0.10), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 301 HIS 0.004 0.001 HIS N 55 PHE 0.022 0.001 PHE N 195 TYR 0.023 0.001 TYR A 387 ARG 0.007 0.000 ARG u 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 443 time to evaluate : 4.961 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: D 146 LEU cc_start: 0.8697 (mt) cc_final: 0.8312 (mt) REVERT: J 145 MET cc_start: 0.8065 (mtt) cc_final: 0.7823 (mmt) REVERT: N 120 MET cc_start: 0.7225 (tpt) cc_final: 0.6640 (tpp) REVERT: N 162 MET cc_start: 0.6615 (ppp) cc_final: 0.6018 (ptt) REVERT: Q 162 MET cc_start: 0.6756 (ppp) cc_final: 0.6416 (ptt) REVERT: c 120 MET cc_start: 0.6741 (ttp) cc_final: 0.6539 (mtm) outliers start: 84 outliers final: 68 residues processed: 513 average time/residue: 0.5607 time to fit residues: 486.3046 Evaluate side-chains 480 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 412 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 282 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 102 ASP Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 102 ASP Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 263 LYS Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain e residue 390 GLU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 231 CYS Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 315 MET Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 146 LEU Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 413 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 399 optimal weight: 8.9990 chunk 201 optimal weight: 0.0970 chunk 131 optimal weight: 0.0040 chunk 129 optimal weight: 0.9990 chunk 425 optimal weight: 6.9990 chunk 455 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 525 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 134 GLN Q 172 ASN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 HIS ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 201 ASN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 56894 Z= 0.159 Angle : 0.619 16.280 77036 Z= 0.311 Chirality : 0.044 0.297 8370 Planarity : 0.004 0.051 10228 Dihedral : 3.926 28.292 7996 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.33 % Allowed : 13.40 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.10), residues: 7036 helix: 2.22 (0.16), residues: 1124 sheet: -0.05 (0.12), residues: 1920 loop : -0.08 (0.10), residues: 3992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 301 HIS 0.004 0.000 HIS K 67 PHE 0.023 0.001 PHE N 195 TYR 0.022 0.001 TYR A 387 ARG 0.007 0.000 ARG y 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 457 time to evaluate : 4.984 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: D 146 LEU cc_start: 0.8631 (mt) cc_final: 0.8298 (mt) REVERT: M 135 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7561 (mptt) REVERT: N 120 MET cc_start: 0.7030 (tpt) cc_final: 0.6719 (tpp) REVERT: N 162 MET cc_start: 0.6530 (ppp) cc_final: 0.6008 (ptt) REVERT: Q 131 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6760 (tp40) REVERT: Q 162 MET cc_start: 0.6653 (ppp) cc_final: 0.6330 (ptt) REVERT: T 120 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6521 (mmt) REVERT: i 112 MET cc_start: 0.7665 (tpp) cc_final: 0.7263 (tpt) REVERT: v 120 MET cc_start: 0.7905 (tpt) cc_final: 0.7589 (tpp) outliers start: 78 outliers final: 54 residues processed: 520 average time/residue: 0.5347 time to fit residues: 469.9673 Evaluate side-chains 479 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 424 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 231 CYS 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 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 120 MET Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 102 ASP Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 146 LEU Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 608 optimal weight: 0.8980 chunk 640 optimal weight: 10.0000 chunk 584 optimal weight: 0.0060 chunk 623 optimal weight: 0.7980 chunk 375 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 489 optimal weight: 9.9990 chunk 191 optimal weight: 0.0870 chunk 563 optimal weight: 10.0000 chunk 589 optimal weight: 10.0000 chunk 621 optimal weight: 0.4980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN S 374 ASN ** T 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 56894 Z= 0.161 Angle : 0.625 14.822 77036 Z= 0.315 Chirality : 0.044 0.250 8370 Planarity : 0.004 0.072 10228 Dihedral : 3.879 27.981 7996 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.16 % Allowed : 13.72 % Favored : 85.11 % 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: 2.07 (0.16), residues: 1130 sheet: -0.04 (0.12), residues: 1918 loop : -0.08 (0.10), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 301 HIS 0.004 0.000 HIS K 67 PHE 0.021 0.001 PHE N 195 TYR 0.029 0.001 TYR M 387 ARG 0.008 0.000 ARG b 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 459 time to evaluate : 4.865 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: D 146 LEU cc_start: 0.8579 (mt) cc_final: 0.8284 (mt) REVERT: E 57 MET cc_start: 0.8330 (mmm) cc_final: 0.7821 (mmt) REVERT: E 120 MET cc_start: 0.6340 (tpp) cc_final: 0.5985 (tpp) REVERT: N 63 GLN cc_start: 0.6617 (pm20) cc_final: 0.5925 (pm20) REVERT: N 120 MET cc_start: 0.7030 (tpt) cc_final: 0.6731 (tpp) REVERT: P 146 LEU cc_start: 0.8332 (mt) cc_final: 0.7937 (mt) REVERT: Q 162 MET cc_start: 0.6636 (ppp) cc_final: 0.6307 (ptt) REVERT: T 112 MET cc_start: 0.7190 (tpt) cc_final: 0.6780 (mmm) REVERT: T 120 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6522 (mmt) outliers start: 68 outliers final: 60 residues processed: 515 average time/residue: 0.5405 time to fit residues: 471.9233 Evaluate side-chains 482 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 421 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain N residue 134 GLN 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 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 120 MET Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 102 ASP Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain b residue 231 CYS Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 146 LEU Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 409 optimal weight: 20.0000 chunk 659 optimal weight: 2.9990 chunk 402 optimal weight: 0.0980 chunk 312 optimal weight: 0.0060 chunk 458 optimal weight: 10.0000 chunk 691 optimal weight: 0.9990 chunk 636 optimal weight: 5.9990 chunk 550 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 425 optimal weight: 1.9990 chunk 337 optimal weight: 30.0000 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 ASN K 134 GLN N 134 GLN S 271 GLN ** T 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 HIS b 284 ASN ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 HIS ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56894 Z= 0.177 Angle : 0.648 16.191 77036 Z= 0.326 Chirality : 0.044 0.292 8370 Planarity : 0.004 0.050 10228 Dihedral : 3.832 30.464 7996 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.13 % Allowed : 14.15 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 7036 helix: 2.06 (0.16), residues: 1126 sheet: -0.04 (0.12), residues: 1918 loop : -0.06 (0.10), residues: 3992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 301 HIS 0.008 0.000 HIS v 55 PHE 0.020 0.001 PHE N 195 TYR 0.034 0.001 TYR G 387 ARG 0.011 0.000 ARG Y 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 437 time to evaluate : 4.879 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: E 57 MET cc_start: 0.8323 (mmm) cc_final: 0.7813 (mmt) REVERT: E 120 MET cc_start: 0.6507 (tpp) cc_final: 0.6191 (tpp) REVERT: N 120 MET cc_start: 0.6985 (tpt) cc_final: 0.6695 (tpp) REVERT: P 146 LEU cc_start: 0.8330 (mt) cc_final: 0.7952 (mt) REVERT: Q 162 MET cc_start: 0.6640 (ppp) cc_final: 0.6319 (ptt) REVERT: T 120 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6608 (mmt) REVERT: f 120 MET cc_start: 0.6705 (mmp) cc_final: 0.6469 (mmt) REVERT: i 57 MET cc_start: 0.6919 (mmm) cc_final: 0.6679 (mmm) outliers start: 66 outliers final: 62 residues processed: 493 average time/residue: 0.5321 time to fit residues: 445.8215 Evaluate side-chains 475 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 412 time to evaluate : 4.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain J residue 284 ASN Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain N residue 134 GLN 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 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 120 MET Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 102 ASP Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain b residue 231 CYS Chi-restraints excluded: chain b residue 284 ASN Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 146 LEU Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 437 optimal weight: 9.9990 chunk 586 optimal weight: 0.2980 chunk 168 optimal weight: 10.0000 chunk 507 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 551 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 566 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 284 ASN ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.029766 restraints weight = 277618.574| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 3.93 r_work: 0.2353 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 56894 Z= 0.262 Angle : 0.666 16.037 77036 Z= 0.335 Chirality : 0.045 0.313 8370 Planarity : 0.004 0.053 10228 Dihedral : 3.884 30.646 7996 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.25 % Allowed : 14.19 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7036 helix: 2.08 (0.16), residues: 1130 sheet: -0.00 (0.12), residues: 1930 loop : -0.03 (0.10), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 301 HIS 0.004 0.001 HIS c 55 PHE 0.019 0.001 PHE G 269 TYR 0.037 0.001 TYR G 387 ARG 0.016 0.000 ARG J 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9753.78 seconds wall clock time: 173 minutes 12.00 seconds (10392.00 seconds total)