Starting phenix.real_space_refine on Fri Sep 27 01:23:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/09_2024/8ari_15603.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/09_2024/8ari_15603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/09_2024/8ari_15603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/09_2024/8ari_15603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/09_2024/8ari_15603.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/09_2024/8ari_15603.cif" } resolution = 3.0 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= -0.000 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 297 5.16 5 C 39655 2.51 5 N 11628 2.21 5 O 12128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63756 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2542 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2546 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Chain: "D" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "E" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "F" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "H" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "I" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "J" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "K" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "L" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "M" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "N" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "O" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "P" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "Q" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "R" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "S" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "T" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "U" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "V" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2546 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Chain: "W" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2546 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Chain: "X" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "a" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "c" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "f" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "g" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "h" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "j" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.90, per 1000 atoms: 0.45 Number of scatterers: 63756 At special positions: 0 Unit cell: (126.15, 333.21, 119.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 297 16.00 P 48 15.00 O 12128 8.00 N 11628 7.00 C 39655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.09 Conformation dependent library (CDL) restraints added in 6.2 seconds 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15148 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 48 sheets defined 40.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE A 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 143 through 152 Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU A 269 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 270 " --> pdb=" O GLY A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE B 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 124 through 141 Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.617A pdb=" N ALA B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU B 269 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 270 " --> pdb=" O GLY B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.996A pdb=" N ILE C 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 124 through 141 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU C 269 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 270 " --> pdb=" O GLY C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE D 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 124 through 141 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 215 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU D 269 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 270 " --> pdb=" O GLY D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 270' Processing helix chain 'D' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE E 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 124 through 141 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 210 through 216 removed outlier: 3.615A pdb=" N ALA E 214 " --> pdb=" O GLY E 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 215 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU E 269 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 270 " --> pdb=" O GLY E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 270' Processing helix chain 'E' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.998A pdb=" N ILE F 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 69 Processing helix chain 'F' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 Processing helix chain 'F' and resid 124 through 141 Processing helix chain 'F' and resid 143 through 152 Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA F 214 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 229 removed outlier: 3.665A pdb=" N HIS F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU F 269 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 270 " --> pdb=" O GLY F 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 266 through 270' Processing helix chain 'F' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN F 277 " --> pdb=" O LYS F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE G 62 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 82 through 88 removed outlier: 3.693A pdb=" N LYS G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'G' and resid 124 through 141 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 183 through 194 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 215 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS G 253 " --> pdb=" O ASP G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU G 269 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL G 270 " --> pdb=" O GLY G 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 270' Processing helix chain 'G' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 69 Processing helix chain 'H' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 114 Processing helix chain 'H' and resid 124 through 141 Processing helix chain 'H' and resid 143 through 152 Processing helix chain 'H' and resid 158 through 166 Processing helix chain 'H' and resid 183 through 194 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 210 through 216 removed outlier: 3.615A pdb=" N ALA H 214 " --> pdb=" O GLY H 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU H 215 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS H 229 " --> pdb=" O ASP H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS H 253 " --> pdb=" O ASP H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU H 269 " --> pdb=" O ARG H 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 270 " --> pdb=" O GLY H 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 266 through 270' Processing helix chain 'H' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.998A pdb=" N ILE I 62 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 69 Processing helix chain 'I' and resid 82 through 88 removed outlier: 3.691A pdb=" N LYS I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 124 through 141 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 158 through 166 Processing helix chain 'I' and resid 183 through 194 Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA I 214 " --> pdb=" O GLY I 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 215 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS I 229 " --> pdb=" O ASP I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS I 253 " --> pdb=" O ASP I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU I 269 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL I 270 " --> pdb=" O GLY I 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 266 through 270' Processing helix chain 'I' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN I 277 " --> pdb=" O LYS I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE J 62 " --> pdb=" O THR J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 69 Processing helix chain 'J' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 114 Processing helix chain 'J' and resid 124 through 141 Processing helix chain 'J' and resid 143 through 152 Processing helix chain 'J' and resid 158 through 166 Processing helix chain 'J' and resid 183 through 194 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA J 214 " --> pdb=" O GLY J 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU J 215 " --> pdb=" O VAL J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS J 229 " --> pdb=" O ASP J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS J 253 " --> pdb=" O ASP J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU J 269 " --> pdb=" O ARG J 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL J 270 " --> pdb=" O GLY J 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 266 through 270' Processing helix chain 'J' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE K 62 " --> pdb=" O THR K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 82 through 88 removed outlier: 3.693A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 124 through 141 Processing helix chain 'K' and resid 143 through 152 Processing helix chain 'K' and resid 158 through 166 Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 195 through 197 No H-bonds generated for 'chain 'K' and resid 195 through 197' Processing helix chain 'K' and resid 210 through 216 removed outlier: 3.617A pdb=" N ALA K 214 " --> pdb=" O GLY K 210 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU K 215 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS K 229 " --> pdb=" O ASP K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS K 253 " --> pdb=" O ASP K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU K 269 " --> pdb=" O ARG K 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL K 270 " --> pdb=" O GLY K 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 266 through 270' Processing helix chain 'K' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE K 325 " --> pdb=" O GLU K 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE L 62 " --> pdb=" O THR L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 114 Processing helix chain 'L' and resid 124 through 141 Processing helix chain 'L' and resid 143 through 152 Processing helix chain 'L' and resid 158 through 166 Processing helix chain 'L' and resid 183 through 194 Processing helix chain 'L' and resid 195 through 197 No H-bonds generated for 'chain 'L' and resid 195 through 197' Processing helix chain 'L' and resid 210 through 216 removed outlier: 3.615A pdb=" N ALA L 214 " --> pdb=" O GLY L 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU L 215 " --> pdb=" O VAL L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 229 removed outlier: 3.665A pdb=" N HIS L 229 " --> pdb=" O ASP L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS L 253 " --> pdb=" O ASP L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU L 269 " --> pdb=" O ARG L 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL L 270 " --> pdb=" O GLY L 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 266 through 270' Processing helix chain 'L' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN L 277 " --> pdb=" O LYS L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE L 325 " --> pdb=" O GLU L 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE M 62 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 69 Processing helix chain 'M' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS M 88 " --> pdb=" O GLU M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 114 Processing helix chain 'M' and resid 124 through 141 Processing helix chain 'M' and resid 143 through 152 Processing helix chain 'M' and resid 158 through 166 Processing helix chain 'M' and resid 183 through 194 Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA M 214 " --> pdb=" O GLY M 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU M 215 " --> pdb=" O VAL M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS M 253 " --> pdb=" O ASP M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU M 269 " --> pdb=" O ARG M 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL M 270 " --> pdb=" O GLY M 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 266 through 270' Processing helix chain 'M' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN M 277 " --> pdb=" O LYS M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE M 325 " --> pdb=" O GLU M 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE N 62 " --> pdb=" O THR N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 69 Processing helix chain 'N' and resid 82 through 88 removed outlier: 3.693A pdb=" N LYS N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 114 Processing helix chain 'N' and resid 124 through 141 Processing helix chain 'N' and resid 143 through 152 Processing helix chain 'N' and resid 158 through 166 Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 195 through 197 No H-bonds generated for 'chain 'N' and resid 195 through 197' Processing helix chain 'N' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA N 214 " --> pdb=" O GLY N 210 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU N 215 " --> pdb=" O VAL N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS N 229 " --> pdb=" O ASP N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS N 253 " --> pdb=" O ASP N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU N 269 " --> pdb=" O ARG N 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL N 270 " --> pdb=" O GLY N 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 266 through 270' Processing helix chain 'N' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN N 277 " --> pdb=" O LYS N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE N 325 " --> pdb=" O GLU N 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.996A pdb=" N ILE O 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 69 Processing helix chain 'O' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS O 88 " --> pdb=" O GLU O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 114 Processing helix chain 'O' and resid 124 through 141 Processing helix chain 'O' and resid 143 through 152 Processing helix chain 'O' and resid 158 through 166 Processing helix chain 'O' and resid 183 through 194 Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA O 214 " --> pdb=" O GLY O 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU O 215 " --> pdb=" O VAL O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 229 removed outlier: 3.665A pdb=" N HIS O 229 " --> pdb=" O ASP O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS O 253 " --> pdb=" O ASP O 249 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU O 269 " --> pdb=" O ARG O 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL O 270 " --> pdb=" O GLY O 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 266 through 270' Processing helix chain 'O' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN O 277 " --> pdb=" O LYS O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE O 325 " --> pdb=" O GLU O 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE P 62 " --> pdb=" O THR P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 69 Processing helix chain 'P' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 114 Processing helix chain 'P' and resid 124 through 141 Processing helix chain 'P' and resid 143 through 152 Processing helix chain 'P' and resid 158 through 166 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 195 through 197 No H-bonds generated for 'chain 'P' and resid 195 through 197' Processing helix chain 'P' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA P 214 " --> pdb=" O GLY P 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU P 215 " --> pdb=" O VAL P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS P 229 " --> pdb=" O ASP P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS P 253 " --> pdb=" O ASP P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU P 269 " --> pdb=" O ARG P 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL P 270 " --> pdb=" O GLY P 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 266 through 270' Processing helix chain 'P' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN P 277 " --> pdb=" O LYS P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 62 removed outlier: 3.998A pdb=" N ILE Q 62 " --> pdb=" O THR Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 69 Processing helix chain 'Q' and resid 82 through 88 removed outlier: 3.693A pdb=" N LYS Q 88 " --> pdb=" O GLU Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 114 Processing helix chain 'Q' and resid 124 through 141 Processing helix chain 'Q' and resid 143 through 152 Processing helix chain 'Q' and resid 158 through 166 Processing helix chain 'Q' and resid 183 through 194 Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 210 through 216 removed outlier: 3.615A pdb=" N ALA Q 214 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU Q 215 " --> pdb=" O VAL Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 229 removed outlier: 3.663A pdb=" N HIS Q 229 " --> pdb=" O ASP Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS Q 253 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU Q 269 " --> pdb=" O ARG Q 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL Q 270 " --> pdb=" O GLY Q 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 266 through 270' Processing helix chain 'Q' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN Q 277 " --> pdb=" O LYS Q 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE Q 325 " --> pdb=" O GLU Q 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 69 Processing helix chain 'R' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS R 88 " --> pdb=" O GLU R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 114 Processing helix chain 'R' and resid 124 through 141 Processing helix chain 'R' and resid 143 through 152 Processing helix chain 'R' and resid 158 through 166 Processing helix chain 'R' and resid 183 through 194 Processing helix chain 'R' and resid 195 through 197 No H-bonds generated for 'chain 'R' and resid 195 through 197' Processing helix chain 'R' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA R 214 " --> pdb=" O GLY R 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS R 229 " --> pdb=" O ASP R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 253 removed outlier: 3.843A pdb=" N LYS R 253 " --> pdb=" O ASP R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU R 269 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL R 270 " --> pdb=" O GLY R 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 266 through 270' Processing helix chain 'R' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE R 325 " --> pdb=" O GLU R 321 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 62 removed outlier: 3.998A pdb=" N ILE S 62 " --> pdb=" O THR S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 69 Processing helix chain 'S' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS S 88 " --> pdb=" O GLU S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 114 Processing helix chain 'S' and resid 124 through 141 Processing helix chain 'S' and resid 143 through 152 Processing helix chain 'S' and resid 158 through 166 Processing helix chain 'S' and resid 183 through 194 Processing helix chain 'S' and resid 195 through 197 No H-bonds generated for 'chain 'S' and resid 195 through 197' Processing helix chain 'S' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA S 214 " --> pdb=" O GLY S 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU S 215 " --> pdb=" O VAL S 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS S 229 " --> pdb=" O ASP S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS S 253 " --> pdb=" O ASP S 249 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU S 269 " --> pdb=" O ARG S 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL S 270 " --> pdb=" O GLY S 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 266 through 270' Processing helix chain 'S' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN S 277 " --> pdb=" O LYS S 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE S 325 " --> pdb=" O GLU S 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE T 62 " --> pdb=" O THR T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 69 Processing helix chain 'T' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS T 88 " --> pdb=" O GLU T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 114 Processing helix chain 'T' and resid 124 through 141 Processing helix chain 'T' and resid 143 through 152 Processing helix chain 'T' and resid 158 through 166 Processing helix chain 'T' and resid 183 through 194 Processing helix chain 'T' and resid 195 through 197 No H-bonds generated for 'chain 'T' and resid 195 through 197' Processing helix chain 'T' and resid 210 through 216 removed outlier: 3.615A pdb=" N ALA T 214 " --> pdb=" O GLY T 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) Processing helix chain 'T' and resid 222 through 229 removed outlier: 3.663A pdb=" N HIS T 229 " --> pdb=" O ASP T 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 248 through 253 removed outlier: 3.841A pdb=" N LYS T 253 " --> pdb=" O ASP T 249 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU T 269 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL T 270 " --> pdb=" O GLY T 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 266 through 270' Processing helix chain 'T' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN T 277 " --> pdb=" O LYS T 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE T 325 " --> pdb=" O GLU T 321 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 62 removed outlier: 3.998A pdb=" N ILE U 62 " --> pdb=" O THR U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 69 Processing helix chain 'U' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS U 88 " --> pdb=" O GLU U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 114 Processing helix chain 'U' and resid 124 through 141 Processing helix chain 'U' and resid 143 through 152 Processing helix chain 'U' and resid 158 through 166 Processing helix chain 'U' and resid 183 through 194 Processing helix chain 'U' and resid 195 through 197 No H-bonds generated for 'chain 'U' and resid 195 through 197' Processing helix chain 'U' and resid 210 through 216 removed outlier: 3.615A pdb=" N ALA U 214 " --> pdb=" O GLY U 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU U 215 " --> pdb=" O VAL U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 229 removed outlier: 3.665A pdb=" N HIS U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS U 253 " --> pdb=" O ASP U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 270 removed outlier: 3.963A pdb=" N LEU U 269 " --> pdb=" O ARG U 266 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL U 270 " --> pdb=" O GLY U 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 266 through 270' Processing helix chain 'U' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN U 277 " --> pdb=" O LYS U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE U 325 " --> pdb=" O GLU U 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE V 62 " --> pdb=" O THR V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 69 Processing helix chain 'V' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 114 Processing helix chain 'V' and resid 124 through 141 Processing helix chain 'V' and resid 143 through 152 Processing helix chain 'V' and resid 158 through 166 Processing helix chain 'V' and resid 183 through 194 Processing helix chain 'V' and resid 195 through 197 No H-bonds generated for 'chain 'V' and resid 195 through 197' Processing helix chain 'V' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA V 214 " --> pdb=" O GLY V 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU V 215 " --> pdb=" O VAL V 211 " (cutoff:3.500A) Processing helix chain 'V' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) Processing helix chain 'V' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS V 253 " --> pdb=" O ASP V 249 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU V 269 " --> pdb=" O ARG V 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL V 270 " --> pdb=" O GLY V 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 266 through 270' Processing helix chain 'V' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN V 277 " --> pdb=" O LYS V 273 " (cutoff:3.500A) Processing helix chain 'V' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE V 325 " --> pdb=" O GLU V 321 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 62 removed outlier: 3.998A pdb=" N ILE W 62 " --> pdb=" O THR W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 69 Processing helix chain 'W' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS W 88 " --> pdb=" O GLU W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 114 Processing helix chain 'W' and resid 124 through 141 Processing helix chain 'W' and resid 143 through 152 Processing helix chain 'W' and resid 158 through 166 Processing helix chain 'W' and resid 183 through 194 Processing helix chain 'W' and resid 195 through 197 No H-bonds generated for 'chain 'W' and resid 195 through 197' Processing helix chain 'W' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA W 214 " --> pdb=" O GLY W 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU W 215 " --> pdb=" O VAL W 211 " (cutoff:3.500A) Processing helix chain 'W' and resid 222 through 229 removed outlier: 3.663A pdb=" N HIS W 229 " --> pdb=" O ASP W 225 " (cutoff:3.500A) Processing helix chain 'W' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS W 253 " --> pdb=" O ASP W 249 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU W 269 " --> pdb=" O ARG W 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL W 270 " --> pdb=" O GLY W 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 266 through 270' Processing helix chain 'W' and resid 271 through 282 removed outlier: 3.811A pdb=" N GLN W 277 " --> pdb=" O LYS W 273 " (cutoff:3.500A) Processing helix chain 'W' and resid 320 through 340 removed outlier: 3.837A pdb=" N ILE W 325 " --> pdb=" O GLU W 321 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 62 removed outlier: 3.997A pdb=" N ILE X 62 " --> pdb=" O THR X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 69 Processing helix chain 'X' and resid 82 through 88 removed outlier: 3.692A pdb=" N LYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 114 Processing helix chain 'X' and resid 124 through 141 Processing helix chain 'X' and resid 143 through 152 Processing helix chain 'X' and resid 158 through 166 Processing helix chain 'X' and resid 183 through 194 Processing helix chain 'X' and resid 195 through 197 No H-bonds generated for 'chain 'X' and resid 195 through 197' Processing helix chain 'X' and resid 210 through 216 removed outlier: 3.616A pdb=" N ALA X 214 " --> pdb=" O GLY X 210 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU X 215 " --> pdb=" O VAL X 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 222 through 229 removed outlier: 3.664A pdb=" N HIS X 229 " --> pdb=" O ASP X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 248 through 253 removed outlier: 3.842A pdb=" N LYS X 253 " --> pdb=" O ASP X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 266 through 270 removed outlier: 3.962A pdb=" N LEU X 269 " --> pdb=" O ARG X 266 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL X 270 " --> pdb=" O GLY X 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 266 through 270' Processing helix chain 'X' and resid 271 through 282 removed outlier: 3.810A pdb=" N GLN X 277 " --> pdb=" O LYS X 273 " (cutoff:3.500A) Processing helix chain 'X' and resid 320 through 340 removed outlier: 3.836A pdb=" N ILE X 325 " --> pdb=" O GLU X 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA A 73 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 72 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN A 218 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 232 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 233 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 259 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA A 288 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 261 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 50 through 53 removed outlier: 3.949A pdb=" N GLY B 72 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA B 73 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN B 218 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 232 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 233 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 259 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA B 288 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 261 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 53 removed outlier: 3.949A pdb=" N GLY C 72 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA C 73 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN C 218 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS C 232 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 233 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 259 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA C 288 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 261 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA D 73 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 72 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN D 218 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS D 232 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 233 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA D 259 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA D 288 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 261 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA E 73 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY E 72 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 51 " --> pdb=" O LEU c 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN E 218 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS E 232 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL E 233 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA E 259 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA E 288 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 261 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA F 73 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY F 72 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL F 51 " --> pdb=" O LEU b 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN F 218 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS F 232 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL F 233 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA F 259 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA F 288 " --> pdb=" O ALA F 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU F 261 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA G 73 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY G 72 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL G 51 " --> pdb=" O LEU a 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN G 218 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS G 232 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL G 233 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA G 259 " --> pdb=" O GLY G 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA G 288 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU G 261 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA H 73 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY H 72 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU d 343 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE H 53 " --> pdb=" O LEU d 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN H 218 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS H 232 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL H 233 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA H 259 " --> pdb=" O GLY H 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA H 288 " --> pdb=" O ALA H 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU H 261 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 116 through 119 removed outlier: 6.362A pdb=" N ALA I 73 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY I 72 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN I 218 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS I 232 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL I 233 " --> pdb=" O VAL I 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA I 259 " --> pdb=" O GLY I 286 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ALA I 288 " --> pdb=" O ALA I 259 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU I 261 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 116 through 119 removed outlier: 6.362A pdb=" N ALA J 73 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY J 72 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN J 218 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS J 232 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL J 233 " --> pdb=" O VAL J 262 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA J 259 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA J 288 " --> pdb=" O ALA J 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU J 261 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA K 73 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY K 72 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN K 218 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS K 232 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL K 233 " --> pdb=" O VAL K 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA K 259 " --> pdb=" O GLY K 286 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA K 288 " --> pdb=" O ALA K 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU K 261 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 116 through 119 removed outlier: 6.362A pdb=" N ALA L 73 " --> pdb=" O VAL L 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY L 72 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU f 317 " --> pdb=" O VAL L 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN L 218 " --> pdb=" O VAL L 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS L 232 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL L 233 " --> pdb=" O VAL L 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA L 259 " --> pdb=" O GLY L 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA L 288 " --> pdb=" O ALA L 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU L 261 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA M 73 " --> pdb=" O VAL M 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY M 72 " --> pdb=" O LEU M 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN M 218 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS M 232 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL M 233 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA M 259 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA M 288 " --> pdb=" O ALA M 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU M 261 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA N 73 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY N 72 " --> pdb=" O LEU N 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN N 218 " --> pdb=" O VAL N 200 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS N 232 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL N 233 " --> pdb=" O VAL N 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA N 259 " --> pdb=" O GLY N 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA N 288 " --> pdb=" O ALA N 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU N 261 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA O 73 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY O 72 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN O 218 " --> pdb=" O VAL O 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS O 232 " --> pdb=" O THR O 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL O 233 " --> pdb=" O VAL O 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA O 259 " --> pdb=" O GLY O 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA O 288 " --> pdb=" O ALA O 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU O 261 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA P 73 " --> pdb=" O VAL P 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY P 72 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN P 218 " --> pdb=" O VAL P 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS P 232 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL P 233 " --> pdb=" O VAL P 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA P 259 " --> pdb=" O GLY P 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA P 288 " --> pdb=" O ALA P 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU P 261 " --> pdb=" O ALA P 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA Q 73 " --> pdb=" O VAL Q 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY Q 72 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL Q 51 " --> pdb=" O LEU h 343 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN Q 218 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS Q 232 " --> pdb=" O THR Q 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL Q 233 " --> pdb=" O VAL Q 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA Q 259 " --> pdb=" O GLY Q 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA Q 288 " --> pdb=" O ALA Q 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU Q 261 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA R 73 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY R 72 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL R 51 " --> pdb=" O LEU i 343 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN R 218 " --> pdb=" O VAL R 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS R 232 " --> pdb=" O THR R 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL R 233 " --> pdb=" O VAL R 262 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA R 259 " --> pdb=" O GLY R 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA R 288 " --> pdb=" O ALA R 259 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU R 261 " --> pdb=" O ALA R 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA S 73 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY S 72 " --> pdb=" O LEU S 29 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL S 51 " --> pdb=" O LEU j 343 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN S 218 " --> pdb=" O VAL S 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS S 232 " --> pdb=" O THR S 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL S 233 " --> pdb=" O VAL S 262 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA S 259 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA S 288 " --> pdb=" O ALA S 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU S 261 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA T 73 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY T 72 " --> pdb=" O LEU T 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 218 through 219 removed outlier: 3.799A pdb=" N GLN T 218 " --> pdb=" O VAL T 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS T 232 " --> pdb=" O THR T 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL T 233 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA T 259 " --> pdb=" O GLY T 286 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA T 288 " --> pdb=" O ALA T 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU T 261 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 116 through 119 removed outlier: 6.363A pdb=" N ALA U 73 " --> pdb=" O VAL U 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY U 72 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN U 218 " --> pdb=" O VAL U 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS U 232 " --> pdb=" O THR U 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL U 233 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA U 259 " --> pdb=" O GLY U 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA U 288 " --> pdb=" O ALA U 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU U 261 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 50 through 53 removed outlier: 3.947A pdb=" N GLY V 72 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA V 73 " --> pdb=" O VAL V 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN V 218 " --> pdb=" O VAL V 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS V 232 " --> pdb=" O THR V 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL V 233 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA V 259 " --> pdb=" O GLY V 286 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA V 288 " --> pdb=" O ALA V 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU V 261 " --> pdb=" O ALA V 288 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 50 through 53 removed outlier: 3.949A pdb=" N GLY W 72 " --> pdb=" O LEU W 29 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA W 73 " --> pdb=" O VAL W 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN W 218 " --> pdb=" O VAL W 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS W 232 " --> pdb=" O THR W 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL W 233 " --> pdb=" O VAL W 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA W 259 " --> pdb=" O GLY W 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA W 288 " --> pdb=" O ALA W 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU W 261 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 116 through 119 removed outlier: 6.362A pdb=" N ALA X 73 " --> pdb=" O VAL X 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY X 72 " --> pdb=" O LEU X 29 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 218 through 219 removed outlier: 3.800A pdb=" N GLN X 218 " --> pdb=" O VAL X 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS X 232 " --> pdb=" O THR X 176 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL X 233 " --> pdb=" O VAL X 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA X 259 " --> pdb=" O GLY X 286 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA X 288 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU X 261 " --> pdb=" O ALA X 288 " (cutoff:3.500A) 2185 hydrogen bonds defined for protein. 6447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.82 Time building geometry restraints manager: 13.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21998 1.34 - 1.46: 10022 1.46 - 1.57: 32283 1.57 - 1.69: 96 1.69 - 1.81: 403 Bond restraints: 64802 Sorted by residual: bond pdb=" O3 NAD A 501 " pdb=" PA NAD A 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" O3 NAD P 501 " pdb=" PA NAD P 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" O3 NAD L 501 " pdb=" PA NAD L 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" O3 NAD B 501 " pdb=" PA NAD B 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" O3 NAD I 501 " pdb=" PA NAD I 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 64797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 86617 1.66 - 3.31: 953 3.31 - 4.97: 255 4.97 - 6.62: 24 6.62 - 8.28: 34 Bond angle restraints: 87883 Sorted by residual: angle pdb=" N PRO b 325 " pdb=" CA PRO b 325 " pdb=" CB PRO b 325 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.17e+01 angle pdb=" N PRO e 325 " pdb=" CA PRO e 325 " pdb=" CB PRO e 325 " ideal model delta sigma weight residual 103.25 110.79 -7.54 1.05e+00 9.07e-01 5.16e+01 angle pdb=" N PRO d 325 " pdb=" CA PRO d 325 " pdb=" CB PRO d 325 " ideal model delta sigma weight residual 103.25 110.78 -7.53 1.05e+00 9.07e-01 5.15e+01 angle pdb=" N PRO g 325 " pdb=" CA PRO g 325 " pdb=" CB PRO g 325 " ideal model delta sigma weight residual 103.25 110.78 -7.53 1.05e+00 9.07e-01 5.15e+01 angle pdb=" N PRO c 325 " pdb=" CA PRO c 325 " pdb=" CB PRO c 325 " ideal model delta sigma weight residual 103.25 110.78 -7.53 1.05e+00 9.07e-01 5.14e+01 ... (remaining 87878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.26: 36384 11.26 - 22.52: 2454 22.52 - 33.78: 771 33.78 - 45.05: 145 45.05 - 56.31: 123 Dihedral angle restraints: 39877 sinusoidal: 16483 harmonic: 23394 Sorted by residual: dihedral pdb=" N PRO g 325 " pdb=" C PRO g 325 " pdb=" CA PRO g 325 " pdb=" CB PRO g 325 " ideal model delta harmonic sigma weight residual 115.10 123.34 -8.24 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" N PRO b 325 " pdb=" C PRO b 325 " pdb=" CA PRO b 325 " pdb=" CB PRO b 325 " ideal model delta harmonic sigma weight residual 115.10 123.33 -8.23 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" N PRO e 325 " pdb=" C PRO e 325 " pdb=" CA PRO e 325 " pdb=" CB PRO e 325 " ideal model delta harmonic sigma weight residual 115.10 123.33 -8.23 0 2.50e+00 1.60e-01 1.08e+01 ... (remaining 39874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 8292 0.048 - 0.097: 1391 0.097 - 0.145: 497 0.145 - 0.194: 1 0.194 - 0.242: 34 Chirality restraints: 10215 Sorted by residual: chirality pdb=" C1D NAD J 501 " pdb=" C2D NAD J 501 " pdb=" N1N NAD J 501 " pdb=" O4D NAD J 501 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1D NAD E 501 " pdb=" C2D NAD E 501 " pdb=" N1N NAD E 501 " pdb=" O4D NAD E 501 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1D NAD U 501 " pdb=" C2D NAD U 501 " pdb=" N1N NAD U 501 " pdb=" O4D NAD U 501 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 10212 not shown) Planarity restraints: 11364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Q 343 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO Q 344 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO Q 344 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 343 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO K 344 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO K 344 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE S 343 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO S 344 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO S 344 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 344 " -0.021 5.00e-02 4.00e+02 ... (remaining 11361 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 12605 2.78 - 3.31: 53067 3.31 - 3.84: 92153 3.84 - 4.37: 113135 4.37 - 4.90: 205248 Nonbonded interactions: 476208 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 290 " pdb=" OG1 THR Q 313 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP U 290 " pdb=" OG1 THR U 313 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP A 290 " pdb=" OG1 THR A 313 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP J 290 " pdb=" OG1 THR J 313 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP V 290 " pdb=" OG1 THR V 313 " model vdw 2.255 3.040 ... (remaining 476203 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' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'D' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'E' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'F' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'G' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'H' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'I' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'J' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'K' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'L' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'M' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'N' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'O' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'P' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'Q' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'R' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'S' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'T' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'U' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'V' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'W' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'X' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 67.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.910 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 116.110 Find NCS groups from input model: 4.190 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.003 0.049 64802 Z= 0.206 Angle : 0.499 8.280 87883 Z= 0.259 Chirality : 0.043 0.242 10215 Planarity : 0.003 0.041 11364 Dihedral : 9.097 56.307 24729 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.70 % Rotamer: Outliers : 0.38 % Allowed : 2.95 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: -0.94 (0.09), residues: 8092 helix: -0.02 (0.09), residues: 2640 sheet: 0.97 (0.21), residues: 908 loop : -1.36 (0.08), residues: 4544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 318 HIS 0.002 0.000 HIS K 236 PHE 0.009 0.001 PHE D 198 TYR 0.005 0.001 TYR O 319 ARG 0.003 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 295 time to evaluate : 5.579 Fit side-chains REVERT: B 43 PRO cc_start: 0.9354 (Cg_endo) cc_final: 0.9008 (Cg_exo) REVERT: B 75 MET cc_start: 0.8814 (ptm) cc_final: 0.8592 (ptm) REVERT: B 319 TYR cc_start: 0.9297 (t80) cc_final: 0.8425 (t80) REVERT: C 43 PRO cc_start: 0.9356 (Cg_endo) cc_final: 0.9008 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9287 (t80) cc_final: 0.8364 (t80) REVERT: V 43 PRO cc_start: 0.9361 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: V 319 TYR cc_start: 0.9294 (t80) cc_final: 0.8384 (t80) REVERT: W 43 PRO cc_start: 0.9359 (Cg_endo) cc_final: 0.9026 (Cg_exo) REVERT: W 319 TYR cc_start: 0.9301 (t80) cc_final: 0.8425 (t80) outliers start: 25 outliers final: 4 residues processed: 316 average time/residue: 1.6026 time to fit residues: 641.7340 Evaluate side-chains 216 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 5.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain V residue 354 ASP Chi-restraints excluded: chain W residue 354 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 685 optimal weight: 0.0050 chunk 615 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 415 optimal weight: 0.6980 chunk 328 optimal weight: 4.9990 chunk 636 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 386 optimal weight: 0.8980 chunk 473 optimal weight: 4.9990 chunk 737 optimal weight: 10.0000 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 64802 Z= 0.159 Angle : 0.442 7.653 87883 Z= 0.246 Chirality : 0.042 0.147 10215 Planarity : 0.004 0.045 11364 Dihedral : 7.454 106.548 10170 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.18 % Allowed : 5.39 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: -0.08 (0.09), residues: 8092 helix: 1.33 (0.10), residues: 2756 sheet: 1.05 (0.19), residues: 1028 loop : -1.32 (0.09), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 318 HIS 0.003 0.000 HIS B 63 PHE 0.007 0.001 PHE Q 198 TYR 0.008 0.001 TYR A 140 ARG 0.009 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 5.617 Fit side-chains REVERT: B 43 PRO cc_start: 0.9291 (Cg_endo) cc_final: 0.9050 (Cg_exo) REVERT: B 75 MET cc_start: 0.8687 (ptm) cc_final: 0.8444 (ptm) REVERT: B 319 TYR cc_start: 0.9111 (t80) cc_final: 0.8600 (t80) REVERT: C 43 PRO cc_start: 0.9284 (Cg_endo) cc_final: 0.9056 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9105 (t80) cc_final: 0.8559 (t80) REVERT: V 43 PRO cc_start: 0.9323 (Cg_endo) cc_final: 0.9079 (Cg_exo) REVERT: V 319 TYR cc_start: 0.9133 (t80) cc_final: 0.8674 (t80) REVERT: W 43 PRO cc_start: 0.9321 (Cg_endo) cc_final: 0.9073 (Cg_exo) REVERT: W 319 TYR cc_start: 0.9133 (t80) cc_final: 0.8679 (t80) REVERT: i 321 MET cc_start: 0.7629 (ttp) cc_final: 0.7226 (ttp) REVERT: i 344 ASP cc_start: 0.9026 (t0) cc_final: 0.8784 (t0) outliers start: 12 outliers final: 5 residues processed: 229 average time/residue: 1.5007 time to fit residues: 444.7026 Evaluate side-chains 198 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain f residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 613 optimal weight: 5.9990 chunk 502 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 738 optimal weight: 3.9990 chunk 798 optimal weight: 9.9990 chunk 657 optimal weight: 0.9990 chunk 732 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 592 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN J 57 GLN K 57 GLN N 57 GLN O 57 GLN R 199 ASN S 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 64802 Z= 0.130 Angle : 0.393 7.026 87883 Z= 0.215 Chirality : 0.041 0.143 10215 Planarity : 0.003 0.038 11364 Dihedral : 7.016 47.357 10162 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.70 % Allowed : 4.99 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: 0.26 (0.10), residues: 8092 helix: 1.89 (0.10), residues: 2756 sheet: 0.91 (0.18), residues: 1036 loop : -1.23 (0.09), residues: 4300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 318 HIS 0.002 0.000 HIS R 63 PHE 0.008 0.001 PHE L 53 TYR 0.005 0.001 TYR K 140 ARG 0.009 0.000 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 222 time to evaluate : 5.756 Fit side-chains REVERT: A 321 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7182 (tp30) REVERT: B 75 MET cc_start: 0.8637 (ptm) cc_final: 0.8398 (ptm) REVERT: B 319 TYR cc_start: 0.9040 (t80) cc_final: 0.8634 (t80) REVERT: C 43 PRO cc_start: 0.9243 (Cg_endo) cc_final: 0.9023 (Cg_exo) REVERT: C 319 TYR cc_start: 0.8994 (t80) cc_final: 0.8566 (t80) REVERT: D 321 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7178 (tp30) REVERT: U 321 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7242 (tp30) REVERT: V 319 TYR cc_start: 0.9035 (t80) cc_final: 0.8686 (t80) REVERT: W 319 TYR cc_start: 0.9054 (t80) cc_final: 0.8714 (t80) REVERT: X 321 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7205 (tp30) REVERT: i 321 MET cc_start: 0.7775 (ttp) cc_final: 0.7267 (ttp) outliers start: 46 outliers final: 26 residues processed: 263 average time/residue: 1.3408 time to fit residues: 470.6046 Evaluate side-chains 217 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain f residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 5.9990 chunk 555 optimal weight: 5.9990 chunk 383 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 352 optimal weight: 2.9990 chunk 496 optimal weight: 0.0030 chunk 741 optimal weight: 10.0000 chunk 784 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 702 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 64802 Z= 0.336 Angle : 0.499 8.014 87883 Z= 0.272 Chirality : 0.044 0.159 10215 Planarity : 0.004 0.042 11364 Dihedral : 7.476 52.763 10162 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.73 % Allowed : 5.28 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.10), residues: 8092 helix: 1.99 (0.11), residues: 2736 sheet: 0.72 (0.18), residues: 1036 loop : -1.38 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 318 HIS 0.004 0.001 HIS K 229 PHE 0.013 0.001 PHE O 260 TYR 0.009 0.001 TYR O 319 ARG 0.010 0.000 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 196 time to evaluate : 5.783 Fit side-chains REVERT: A 321 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7523 (tp30) REVERT: B 75 MET cc_start: 0.8774 (ptm) cc_final: 0.8509 (ptm) REVERT: B 319 TYR cc_start: 0.9097 (t80) cc_final: 0.8681 (t80) REVERT: C 43 PRO cc_start: 0.9222 (Cg_endo) cc_final: 0.8980 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9044 (t80) cc_final: 0.8603 (t80) REVERT: D 321 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7565 (tp30) REVERT: U 321 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7586 (tp30) REVERT: V 319 TYR cc_start: 0.9101 (t80) cc_final: 0.8668 (t80) REVERT: W 319 TYR cc_start: 0.9101 (t80) cc_final: 0.8674 (t80) REVERT: X 321 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7541 (tp30) REVERT: i 321 MET cc_start: 0.7877 (ttp) cc_final: 0.7401 (ttp) outliers start: 48 outliers final: 28 residues processed: 239 average time/residue: 1.3903 time to fit residues: 439.3302 Evaluate side-chains 214 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain f residue 343 LEU Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 653 optimal weight: 3.9990 chunk 445 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 584 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 669 optimal weight: 8.9990 chunk 542 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 400 optimal weight: 3.9990 chunk 704 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 64802 Z= 0.398 Angle : 0.526 8.033 87883 Z= 0.286 Chirality : 0.045 0.163 10215 Planarity : 0.004 0.045 11364 Dihedral : 7.623 53.192 10162 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.95 % Allowed : 6.07 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: 0.04 (0.10), residues: 8092 helix: 1.96 (0.11), residues: 2736 sheet: 0.65 (0.16), residues: 1228 loop : -1.61 (0.09), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 318 HIS 0.004 0.001 HIS K 229 PHE 0.014 0.002 PHE O 260 TYR 0.011 0.002 TYR J 319 ARG 0.012 0.000 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 208 time to evaluate : 5.761 Fit side-chains REVERT: A 321 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7570 (tp30) REVERT: B 75 MET cc_start: 0.8834 (ptm) cc_final: 0.8572 (ptm) REVERT: B 319 TYR cc_start: 0.9134 (t80) cc_final: 0.8664 (t80) REVERT: C 319 TYR cc_start: 0.9086 (t80) cc_final: 0.8607 (t80) REVERT: D 321 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7524 (tp30) REVERT: U 321 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7570 (tp30) REVERT: V 319 TYR cc_start: 0.9145 (t80) cc_final: 0.8682 (t80) REVERT: W 319 TYR cc_start: 0.9144 (t80) cc_final: 0.8685 (t80) REVERT: X 321 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7586 (tp30) REVERT: i 321 MET cc_start: 0.7972 (ttp) cc_final: 0.7441 (ttp) outliers start: 63 outliers final: 38 residues processed: 249 average time/residue: 1.3564 time to fit residues: 451.6460 Evaluate side-chains 238 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain a residue 345 LEU Chi-restraints excluded: chain a residue 347 VAL Chi-restraints excluded: chain b residue 345 LEU Chi-restraints excluded: chain b residue 347 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain f residue 343 LEU Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain j residue 347 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 264 optimal weight: 6.9990 chunk 706 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 460 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 785 optimal weight: 6.9990 chunk 652 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 259 optimal weight: 2.9990 chunk 412 optimal weight: 0.8980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 64802 Z= 0.168 Angle : 0.415 8.292 87883 Z= 0.228 Chirality : 0.041 0.168 10215 Planarity : 0.003 0.050 11364 Dihedral : 7.230 49.289 10162 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.64 % Allowed : 6.83 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 8092 helix: 2.20 (0.11), residues: 2756 sheet: 0.51 (0.17), residues: 1136 loop : -1.41 (0.09), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 318 HIS 0.004 0.000 HIS B 355 PHE 0.011 0.001 PHE L 53 TYR 0.007 0.001 TYR O 140 ARG 0.012 0.000 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 6.010 Fit side-chains REVERT: A 321 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7317 (tp30) REVERT: B 75 MET cc_start: 0.8711 (ptm) cc_final: 0.8445 (ptm) REVERT: B 319 TYR cc_start: 0.9062 (t80) cc_final: 0.8640 (t80) REVERT: C 319 TYR cc_start: 0.9029 (t80) cc_final: 0.8600 (t80) REVERT: D 321 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7306 (tp30) REVERT: U 321 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7335 (tp30) REVERT: V 319 TYR cc_start: 0.9070 (t80) cc_final: 0.8651 (t80) REVERT: W 319 TYR cc_start: 0.9073 (t80) cc_final: 0.8657 (t80) REVERT: X 321 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7332 (tp30) REVERT: i 321 MET cc_start: 0.7965 (ttp) cc_final: 0.7516 (ttp) outliers start: 42 outliers final: 31 residues processed: 237 average time/residue: 1.3512 time to fit residues: 424.5686 Evaluate side-chains 233 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 5.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 757 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 chunk 447 optimal weight: 2.9990 chunk 573 optimal weight: 4.9990 chunk 444 optimal weight: 5.9990 chunk 661 optimal weight: 0.0670 chunk 438 optimal weight: 6.9990 chunk 782 optimal weight: 10.0000 chunk 489 optimal weight: 3.9990 chunk 477 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 overall best weight: 1.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 64802 Z= 0.215 Angle : 0.438 8.934 87883 Z= 0.237 Chirality : 0.042 0.172 10215 Planarity : 0.003 0.054 11364 Dihedral : 7.223 50.132 10162 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.59 % Allowed : 7.51 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 8092 helix: 2.23 (0.11), residues: 2756 sheet: 0.51 (0.18), residues: 1036 loop : -1.40 (0.09), residues: 4300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 318 HIS 0.003 0.000 HIS F 355 PHE 0.011 0.001 PHE L 53 TYR 0.008 0.001 TYR J 319 ARG 0.012 0.000 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 5.599 Fit side-chains REVERT: A 321 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7353 (tp30) REVERT: B 75 MET cc_start: 0.8686 (ptm) cc_final: 0.8413 (ptm) REVERT: B 319 TYR cc_start: 0.9059 (t80) cc_final: 0.8629 (t80) REVERT: C 319 TYR cc_start: 0.9015 (t80) cc_final: 0.8573 (t80) REVERT: D 321 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7316 (tp30) REVERT: U 321 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7279 (tp30) REVERT: V 319 TYR cc_start: 0.9055 (t80) cc_final: 0.8626 (t80) REVERT: W 319 TYR cc_start: 0.9067 (t80) cc_final: 0.8647 (t80) REVERT: X 321 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7367 (tp30) REVERT: i 321 MET cc_start: 0.8032 (ttp) cc_final: 0.7695 (ttp) outliers start: 39 outliers final: 29 residues processed: 226 average time/residue: 1.3292 time to fit residues: 399.8069 Evaluate side-chains 223 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 484 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 467 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 497 optimal weight: 3.9990 chunk 533 optimal weight: 6.9990 chunk 386 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 615 optimal weight: 7.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 64802 Z= 0.365 Angle : 0.510 9.511 87883 Z= 0.275 Chirality : 0.044 0.180 10215 Planarity : 0.004 0.062 11364 Dihedral : 7.509 52.489 10162 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.67 % Allowed : 7.60 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: 8092 helix: 2.10 (0.11), residues: 2756 sheet: 0.59 (0.16), residues: 1236 loop : -1.59 (0.09), residues: 4100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 318 HIS 0.004 0.001 HIS F 355 PHE 0.012 0.001 PHE L 53 TYR 0.011 0.002 TYR N 319 ARG 0.014 0.000 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 5.671 Fit side-chains REVERT: A 321 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7583 (tp30) REVERT: B 75 MET cc_start: 0.8763 (ptm) cc_final: 0.8469 (ptm) REVERT: B 319 TYR cc_start: 0.9118 (t80) cc_final: 0.8652 (t80) REVERT: C 319 TYR cc_start: 0.9081 (t80) cc_final: 0.8601 (t80) REVERT: D 321 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7473 (tp30) REVERT: U 321 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7509 (tp30) REVERT: V 319 TYR cc_start: 0.9114 (t80) cc_final: 0.8646 (t80) REVERT: W 319 TYR cc_start: 0.9114 (t80) cc_final: 0.8649 (t80) REVERT: X 321 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7598 (tp30) REVERT: i 321 MET cc_start: 0.8033 (ttp) cc_final: 0.7728 (ttp) REVERT: j 344 ASP cc_start: 0.9219 (t0) cc_final: 0.8997 (t0) REVERT: j 346 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8981 (p) outliers start: 44 outliers final: 31 residues processed: 233 average time/residue: 1.3388 time to fit residues: 414.7240 Evaluate side-chains 228 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain a residue 319 LEU Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 319 LEU Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 711 optimal weight: 0.8980 chunk 749 optimal weight: 9.9990 chunk 684 optimal weight: 10.0000 chunk 729 optimal weight: 9.9990 chunk 438 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 572 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 659 optimal weight: 0.9980 chunk 689 optimal weight: 5.9990 chunk 726 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 64802 Z= 0.203 Angle : 0.443 10.161 87883 Z= 0.239 Chirality : 0.042 0.182 10215 Planarity : 0.004 0.061 11364 Dihedral : 7.272 51.034 10162 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.47 % Allowed : 7.88 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: 0.26 (0.10), residues: 8092 helix: 2.25 (0.11), residues: 2756 sheet: 0.65 (0.16), residues: 1236 loop : -1.55 (0.09), residues: 4100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 318 HIS 0.004 0.000 HIS F 355 PHE 0.011 0.001 PHE L 53 TYR 0.009 0.001 TYR N 319 ARG 0.014 0.000 ARG N 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 5.596 Fit side-chains REVERT: A 321 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7386 (tp30) REVERT: B 75 MET cc_start: 0.8715 (ptm) cc_final: 0.8433 (ptm) REVERT: B 319 TYR cc_start: 0.9081 (t80) cc_final: 0.8638 (t80) REVERT: C 319 TYR cc_start: 0.9042 (t80) cc_final: 0.8587 (t80) REVERT: D 321 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7311 (tp30) REVERT: U 321 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7345 (tp30) REVERT: V 319 TYR cc_start: 0.9077 (t80) cc_final: 0.8632 (t80) REVERT: W 319 TYR cc_start: 0.9076 (t80) cc_final: 0.8635 (t80) REVERT: X 321 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7402 (tp30) REVERT: i 321 MET cc_start: 0.8007 (ttp) cc_final: 0.7731 (ptp) REVERT: j 346 SER cc_start: 0.9129 (p) cc_final: 0.8888 (p) outliers start: 31 outliers final: 30 residues processed: 214 average time/residue: 1.4046 time to fit residues: 394.2493 Evaluate side-chains 215 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain a residue 319 LEU Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 478 optimal weight: 0.6980 chunk 771 optimal weight: 7.9990 chunk 470 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 536 optimal weight: 6.9990 chunk 808 optimal weight: 7.9990 chunk 744 optimal weight: 6.9990 chunk 644 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 497 optimal weight: 0.2980 chunk 394 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 64802 Z= 0.291 Angle : 0.486 11.546 87883 Z= 0.259 Chirality : 0.043 0.200 10215 Planarity : 0.004 0.067 11364 Dihedral : 7.386 51.374 10162 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.54 % Allowed : 7.87 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 8092 helix: 2.19 (0.11), residues: 2756 sheet: 0.59 (0.16), residues: 1236 loop : -1.57 (0.09), residues: 4100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 318 HIS 0.004 0.001 HIS F 355 PHE 0.011 0.001 PHE L 53 TYR 0.011 0.001 TYR D 76 ARG 0.015 0.000 ARG O 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 5.620 Fit side-chains REVERT: A 321 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7490 (tp30) REVERT: B 75 MET cc_start: 0.8730 (ptm) cc_final: 0.8409 (ptm) REVERT: B 319 TYR cc_start: 0.9094 (t80) cc_final: 0.8635 (t80) REVERT: C 319 TYR cc_start: 0.9044 (t80) cc_final: 0.8630 (t80) REVERT: D 321 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7383 (tp30) REVERT: U 321 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7414 (tp30) REVERT: V 319 TYR cc_start: 0.9090 (t80) cc_final: 0.8631 (t80) REVERT: W 319 TYR cc_start: 0.9091 (t80) cc_final: 0.8634 (t80) REVERT: X 321 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7506 (tp30) REVERT: i 321 MET cc_start: 0.8014 (ttp) cc_final: 0.7597 (ptp) REVERT: j 346 SER cc_start: 0.9091 (p) cc_final: 0.8879 (p) outliers start: 36 outliers final: 33 residues processed: 217 average time/residue: 1.3950 time to fit residues: 399.6589 Evaluate side-chains 218 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 511 optimal weight: 0.9980 chunk 686 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 593 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 645 optimal weight: 0.7980 chunk 270 optimal weight: 0.0770 chunk 662 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.071050 restraints weight = 131153.753| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.69 r_work: 0.2586 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 64802 Z= 0.191 Angle : 0.442 11.687 87883 Z= 0.235 Chirality : 0.041 0.198 10215 Planarity : 0.004 0.064 11364 Dihedral : 7.188 52.303 10162 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.56 % Allowed : 7.87 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % 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: 0.31 (0.10), residues: 8092 helix: 2.31 (0.11), residues: 2756 sheet: 0.66 (0.16), residues: 1236 loop : -1.52 (0.09), residues: 4100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 318 HIS 0.004 0.000 HIS F 355 PHE 0.011 0.001 PHE L 53 TYR 0.009 0.001 TYR D 76 ARG 0.015 0.000 ARG O 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12404.21 seconds wall clock time: 216 minutes 48.53 seconds (13008.53 seconds total)