Starting phenix.real_space_refine on Mon Mar 18 07:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7brm_30160/03_2024/7brm_30160.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7brm_30160/03_2024/7brm_30160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7brm_30160/03_2024/7brm_30160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7brm_30160/03_2024/7brm_30160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7brm_30160/03_2024/7brm_30160.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7brm_30160/03_2024/7brm_30160.pdb" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 12780 2.51 5 N 3537 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 170": "OD1" <-> "OD2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 170": "OD1" <-> "OD2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "C" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "D" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "G" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "I" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1995 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 244} Chain: "a" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "d" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "h" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 10.67, per 1000 atoms: 0.53 Number of scatterers: 20277 At special positions: 0 Unit cell: (130, 131, 116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3879 8.00 N 3537 7.00 C 12780 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 - 3.50 Amino acid : False - 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: 7.10 Conformation dependent library (CDL) restraints added in 3.3 seconds 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4842 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 19 sheets defined 30.6% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.542A pdb=" N LYS A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 100 through 116 Processing helix chain 'B' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN B 261 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.541A pdb=" N LYS B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 100 through 116 Processing helix chain 'C' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 100 through 116 Processing helix chain 'D' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN D 261 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.820A pdb=" N LYS E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 100 through 116 Processing helix chain 'E' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG E 249 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN E 261 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.822A pdb=" N LYS F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 100 through 116 Processing helix chain 'F' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG F 249 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 250 " --> pdb=" O GLY F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN F 261 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG F 269 " --> pdb=" O LEU F 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 100 through 116 Processing helix chain 'G' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG G 249 " --> pdb=" O ASP G 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN G 261 " --> pdb=" O ALA G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 271 removed outlier: 3.542A pdb=" N LYS G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 269 " --> pdb=" O LEU G 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS H 37 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 100 through 116 Processing helix chain 'H' and resid 226 through 250 removed outlier: 3.898A pdb=" N ARG H 249 " --> pdb=" O ASP H 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY H 250 " --> pdb=" O GLY H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 261 removed outlier: 3.832A pdb=" N GLN H 261 " --> pdb=" O ALA H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 271 removed outlier: 3.543A pdb=" N LYS H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 40 removed outlier: 3.821A pdb=" N LYS I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 100 through 116 Processing helix chain 'I' and resid 226 through 250 removed outlier: 3.897A pdb=" N ARG I 249 " --> pdb=" O ASP I 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 250 " --> pdb=" O GLY I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 261 removed outlier: 3.833A pdb=" N GLN I 261 " --> pdb=" O ALA I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 271 removed outlier: 3.542A pdb=" N LYS I 267 " --> pdb=" O ASP I 263 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG I 269 " --> pdb=" O LEU I 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 37 No H-bonds generated for 'chain 'a' and resid 35 through 37' Processing helix chain 'a' and resid 38 through 48 removed outlier: 3.516A pdb=" N LEU a 43 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 37 No H-bonds generated for 'chain 'c' and resid 35 through 37' Processing helix chain 'c' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU c 43 " --> pdb=" O GLY c 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 37 No H-bonds generated for 'chain 'd' and resid 35 through 37' Processing helix chain 'd' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU d 43 " --> pdb=" O GLY d 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 37 No H-bonds generated for 'chain 'e' and resid 35 through 37' Processing helix chain 'e' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU e 43 " --> pdb=" O GLY e 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 37 No H-bonds generated for 'chain 'f' and resid 35 through 37' Processing helix chain 'f' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU f 43 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 37 No H-bonds generated for 'chain 'g' and resid 35 through 37' Processing helix chain 'g' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU g 43 " --> pdb=" O GLY g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 37 No H-bonds generated for 'chain 'h' and resid 35 through 37' Processing helix chain 'h' and resid 38 through 48 removed outlier: 3.514A pdb=" N LEU h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 37 No H-bonds generated for 'chain 'i' and resid 35 through 37' Processing helix chain 'i' and resid 38 through 48 removed outlier: 3.515A pdb=" N LEU i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE A 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 96 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 51 " --> pdb=" O LEU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 150 through 157 removed outlier: 3.939A pdb=" N LYS C 150 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 167 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 171 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 145 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 173 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 173 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR D 145 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 171 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 162 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA D 203 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP D 164 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 201 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN D 166 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR D 199 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 168 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU D 197 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP D 170 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR D 195 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 172 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER D 193 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 174 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN D 191 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 176 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER D 189 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 215 " --> pdb=" O ARG D 207 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 214 through 224 current: chain 'E' and resid 186 through 208 removed outlier: 6.755A pdb=" N VAL E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER E 189 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU E 176 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN E 191 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 174 " --> pdb=" O ASN E 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER E 193 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 172 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR E 195 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP E 170 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU E 197 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN E 168 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR E 199 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN E 166 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 201 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP E 164 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 203 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY E 162 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 171 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 145 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA E 173 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.900A pdb=" N THR E 222 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 171 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B 145 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 173 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 173 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 145 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN A 171 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 162 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 203 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP A 164 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 201 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 166 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 199 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A 168 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 197 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP A 170 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 195 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 172 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 193 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 174 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 191 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 176 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 189 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 215 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 222 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS I 150 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR I 167 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY I 162 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA I 203 " --> pdb=" O GLY I 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP I 164 " --> pdb=" O VAL I 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL I 201 " --> pdb=" O ASP I 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN I 166 " --> pdb=" O TYR I 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR I 199 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN I 168 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU I 197 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP I 170 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR I 195 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE I 172 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER I 193 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL I 174 " --> pdb=" O ASN I 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN I 191 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU I 176 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER I 189 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 178 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 207 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 215 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR I 222 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS G 150 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR G 167 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN G 171 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR G 145 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA G 173 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 173 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B 145 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 171 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 162 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 203 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 164 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL B 201 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 166 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 199 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN B 168 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 197 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP B 170 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 195 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 172 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 193 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL B 174 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 191 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 176 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 189 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 178 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 207 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 215 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 222 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 150 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 167 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN A 171 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 145 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 173 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 173 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 145 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 171 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 162 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 203 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP C 164 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL C 201 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN C 166 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR C 199 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 168 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 197 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP C 170 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR C 195 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 172 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER C 193 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 174 " --> pdb=" O ASN C 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 191 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 176 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER C 189 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 207 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 215 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 222 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS D 150 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D 167 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 162 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA D 203 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP D 164 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 201 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN D 166 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR D 199 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 168 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU D 197 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP D 170 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR D 195 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 172 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER D 193 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL D 174 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN D 191 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 176 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER D 189 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 215 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 153 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 222 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS F 150 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 167 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN F 171 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR F 145 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA F 173 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA F 173 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR F 145 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN F 171 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY F 162 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA F 203 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP F 164 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL F 201 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN F 166 " --> pdb=" O TYR F 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR F 199 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN F 168 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU F 197 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP F 170 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR F 195 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE F 172 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER F 193 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL F 174 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN F 191 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU F 176 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER F 189 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 178 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 207 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 215 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 222 " --> pdb=" O SER H 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS H 150 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR H 167 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 171 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR H 145 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA H 173 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA I 173 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR I 145 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN I 171 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR I 167 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS I 150 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 222 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 215 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 189 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 176 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 191 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 174 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 193 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 172 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 195 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP A 170 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 197 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A 168 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 199 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 166 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 201 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP A 164 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 203 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 162 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN A 171 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 145 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 173 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.545A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA H 173 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR H 145 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 171 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY H 162 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA H 203 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP H 164 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL H 201 " --> pdb=" O ASP H 164 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN H 166 " --> pdb=" O TYR H 199 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR H 199 " --> pdb=" O GLN H 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN H 168 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU H 197 " --> pdb=" O GLN H 168 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP H 170 " --> pdb=" O THR H 195 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR H 195 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 172 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER H 193 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL H 174 " --> pdb=" O ASN H 191 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN H 191 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU H 176 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER H 189 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG H 207 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 215 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY E 153 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR H 222 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS E 150 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 167 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 171 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 145 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA E 173 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.544A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 173 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 145 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 171 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 167 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 150 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR G 222 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 215 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 207 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL G 178 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER G 189 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU G 176 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN G 191 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL G 174 " --> pdb=" O ASN G 191 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER G 193 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE G 172 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR G 195 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP G 170 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU G 197 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN G 168 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR G 199 " --> pdb=" O GLN G 166 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN G 166 " --> pdb=" O TYR G 199 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL G 201 " --> pdb=" O ASP G 164 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP G 164 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA G 203 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY G 162 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN G 171 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR G 145 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA G 173 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE D 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU D 96 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 51 " --> pdb=" O LEU D 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE E 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU E 96 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 51 " --> pdb=" O LEU E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.277A pdb=" N ILE F 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU F 96 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL F 51 " --> pdb=" O LEU F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 49 through 52 removed outlier: 6.276A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.275A pdb=" N ILE H 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU H 96 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 51 " --> pdb=" O LEU H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 49 through 52 removed outlier: 6.275A pdb=" N ILE I 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU I 96 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL I 51 " --> pdb=" O LEU I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 813 hydrogen bonds defined for protein. 2382 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: 5.69 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6834 1.34 - 1.45: 3405 1.45 - 1.57: 10263 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 20646 Sorted by residual: bond pdb=" C ARG C 91 " pdb=" N TRP C 92 " ideal model delta sigma weight residual 1.332 1.305 0.028 1.40e-02 5.10e+03 3.94e+00 bond pdb=" C ARG H 91 " pdb=" N TRP H 92 " ideal model delta sigma weight residual 1.332 1.305 0.028 1.40e-02 5.10e+03 3.86e+00 bond pdb=" C ARG E 91 " pdb=" N TRP E 92 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.78e+00 bond pdb=" C ARG A 91 " pdb=" N TRP A 92 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.78e+00 bond pdb=" C ARG B 91 " pdb=" N TRP B 92 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.73e+00 ... (remaining 20641 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.57: 442 105.57 - 112.70: 11034 112.70 - 119.83: 6712 119.83 - 126.96: 9624 126.96 - 134.09: 205 Bond angle restraints: 28017 Sorted by residual: angle pdb=" N VAL C 266 " pdb=" CA VAL C 266 " pdb=" C VAL C 266 " ideal model delta sigma weight residual 113.42 107.44 5.98 1.17e+00 7.31e-01 2.61e+01 angle pdb=" N VAL A 266 " pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 113.42 107.46 5.96 1.17e+00 7.31e-01 2.59e+01 angle pdb=" N VAL D 266 " pdb=" CA VAL D 266 " pdb=" C VAL D 266 " ideal model delta sigma weight residual 113.42 107.47 5.95 1.17e+00 7.31e-01 2.58e+01 angle pdb=" N VAL I 266 " pdb=" CA VAL I 266 " pdb=" C VAL I 266 " ideal model delta sigma weight residual 113.42 107.48 5.94 1.17e+00 7.31e-01 2.58e+01 angle pdb=" N VAL B 266 " pdb=" CA VAL B 266 " pdb=" C VAL B 266 " ideal model delta sigma weight residual 113.42 107.50 5.92 1.17e+00 7.31e-01 2.56e+01 ... (remaining 28012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.16: 10487 13.16 - 26.33: 1402 26.33 - 39.49: 468 39.49 - 52.65: 72 52.65 - 65.81: 36 Dihedral angle restraints: 12465 sinusoidal: 4923 harmonic: 7542 Sorted by residual: dihedral pdb=" CA GLN A 99 " pdb=" C GLN A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLN B 99 " pdb=" C GLN B 99 " pdb=" N GLY B 100 " pdb=" CA GLY B 100 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLN D 99 " pdb=" C GLN D 99 " pdb=" N GLY D 100 " pdb=" CA GLY D 100 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 12462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1451 0.029 - 0.058: 1027 0.058 - 0.087: 410 0.087 - 0.115: 224 0.115 - 0.144: 56 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA PHE b 32 " pdb=" N PHE b 32 " pdb=" C PHE b 32 " pdb=" CB PHE b 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA PHE c 32 " pdb=" N PHE c 32 " pdb=" C PHE c 32 " pdb=" CB PHE c 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE i 32 " pdb=" N PHE i 32 " pdb=" C PHE i 32 " pdb=" CB PHE i 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 3165 not shown) Planarity restraints: 3699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 94 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO I 95 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 94 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 95 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 94 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO F 95 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 95 " -0.025 5.00e-02 4.00e+02 ... (remaining 3696 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 732 2.68 - 3.24: 21043 3.24 - 3.79: 32333 3.79 - 4.35: 42853 4.35 - 4.90: 75035 Nonbonded interactions: 171996 Sorted by model distance: nonbonded pdb=" OG1 THR A 132 " pdb=" OG1 THR I 183 " model vdw 2.128 2.440 nonbonded pdb=" OG1 THR E 183 " pdb=" OG1 THR H 132 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR C 132 " pdb=" OG1 THR D 183 " model vdw 2.175 2.440 nonbonded pdb=" OG1 THR A 183 " pdb=" OG1 THR B 132 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR D 132 " pdb=" OG1 THR F 183 " model vdw 2.204 2.440 ... (remaining 171991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: 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' } 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.120 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 51.430 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.069 20646 Z= 0.692 Angle : 0.831 5.980 28017 Z= 0.484 Chirality : 0.048 0.144 3168 Planarity : 0.004 0.045 3699 Dihedral : 13.834 65.814 7623 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.24 (0.16), residues: 2583 helix: -2.35 (0.15), residues: 819 sheet: -1.49 (0.21), residues: 648 loop : -2.25 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 252 HIS 0.002 0.001 HIS F 41 PHE 0.023 0.003 PHE h 32 TYR 0.007 0.002 TYR I 211 ARG 0.003 0.001 ARG G 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 PHE cc_start: 0.8298 (t80) cc_final: 0.7409 (t80) REVERT: C 213 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7536 (mmt180) REVERT: D 88 LYS cc_start: 0.8875 (tptp) cc_final: 0.8530 (tptt) REVERT: D 221 TYR cc_start: 0.8867 (t80) cc_final: 0.8580 (t80) REVERT: E 109 LYS cc_start: 0.8732 (mttt) cc_final: 0.8457 (mtmm) REVERT: F 164 ASP cc_start: 0.8277 (p0) cc_final: 0.8025 (p0) REVERT: G 221 TYR cc_start: 0.8788 (t80) cc_final: 0.8515 (t80) REVERT: H 88 LYS cc_start: 0.8865 (tptp) cc_final: 0.8487 (tptt) REVERT: I 164 ASP cc_start: 0.8043 (p0) cc_final: 0.7803 (p0) REVERT: b 32 PHE cc_start: 0.7439 (p90) cc_final: 0.6370 (p90) REVERT: b 52 TYR cc_start: 0.8097 (m-80) cc_final: 0.7716 (m-10) REVERT: c 44 ASN cc_start: 0.8653 (m-40) cc_final: 0.8421 (m-40) REVERT: d 44 ASN cc_start: 0.8602 (m-40) cc_final: 0.8274 (m110) REVERT: h 49 GLN cc_start: 0.7436 (mm110) cc_final: 0.6819 (mm-40) REVERT: i 44 ASN cc_start: 0.8673 (m-40) cc_final: 0.8432 (m110) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.3848 time to fit residues: 231.5559 Evaluate side-chains 330 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 270 HIS ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 270 HIS D 77 GLN D 148 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 270 HIS ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 270 HIS ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 GLN F 270 HIS G 148 ASN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN G 270 HIS ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 270 HIS I 77 GLN ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 GLN I 270 HIS a 31 ASN b 44 ASN b 49 GLN c 31 ASN e 31 ASN e 44 ASN g 31 ASN i 31 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20646 Z= 0.192 Angle : 0.582 6.675 28017 Z= 0.316 Chirality : 0.043 0.166 3168 Planarity : 0.003 0.030 3699 Dihedral : 5.050 26.230 2835 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.50 % Allowed : 13.71 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.10 (0.17), residues: 2583 helix: -1.14 (0.17), residues: 801 sheet: -0.70 (0.24), residues: 585 loop : -1.86 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 252 HIS 0.003 0.001 HIS C 270 PHE 0.021 0.002 PHE d 32 TYR 0.019 0.001 TYR E 158 ARG 0.005 0.000 ARG a 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 372 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8341 (mmmt) REVERT: B 88 LYS cc_start: 0.8710 (tptp) cc_final: 0.8449 (tptt) REVERT: C 88 LYS cc_start: 0.8694 (tptp) cc_final: 0.8469 (tptt) REVERT: C 212 GLN cc_start: 0.7767 (mt0) cc_final: 0.7516 (mt0) REVERT: C 213 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7558 (mmt180) REVERT: D 38 ASP cc_start: 0.7869 (t0) cc_final: 0.7610 (t0) REVERT: D 88 LYS cc_start: 0.8734 (tptp) cc_final: 0.8457 (tptt) REVERT: D 97 GLU cc_start: 0.7527 (tt0) cc_final: 0.7045 (tt0) REVERT: D 221 TYR cc_start: 0.8816 (t80) cc_final: 0.8508 (t80) REVERT: E 109 LYS cc_start: 0.8645 (mttt) cc_final: 0.8421 (mtmm) REVERT: E 159 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7695 (t80) REVERT: E 211 TYR cc_start: 0.7968 (t80) cc_final: 0.7686 (t80) REVERT: E 212 GLN cc_start: 0.7838 (mt0) cc_final: 0.7508 (mt0) REVERT: G 97 GLU cc_start: 0.7441 (tt0) cc_final: 0.7163 (tt0) REVERT: G 216 GLU cc_start: 0.7692 (tt0) cc_final: 0.7150 (tt0) REVERT: H 38 ASP cc_start: 0.7735 (t0) cc_final: 0.7528 (t0) REVERT: H 88 LYS cc_start: 0.8700 (tptp) cc_final: 0.8282 (tptt) REVERT: H 109 LYS cc_start: 0.8671 (mttt) cc_final: 0.8379 (mtmm) REVERT: a 28 ARG cc_start: 0.6411 (mmt180) cc_final: 0.5695 (mmt180) REVERT: b 52 TYR cc_start: 0.7984 (m-80) cc_final: 0.7611 (m-10) REVERT: d 29 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7275 (m110) REVERT: h 49 GLN cc_start: 0.7386 (mm110) cc_final: 0.6844 (mm-40) outliers start: 55 outliers final: 24 residues processed: 401 average time/residue: 0.3492 time to fit residues: 207.8641 Evaluate side-chains 350 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 324 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 159 PHE Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain d residue 29 ASN Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain g residue 45 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS B 62 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 HIS c 31 ASN e 31 ASN ** g 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 20646 Z= 0.543 Angle : 0.708 7.213 28017 Z= 0.379 Chirality : 0.048 0.175 3168 Planarity : 0.004 0.028 3699 Dihedral : 5.391 27.075 2835 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 3.78 % Allowed : 15.85 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.80 (0.17), residues: 2583 helix: -0.91 (0.18), residues: 810 sheet: -0.52 (0.25), residues: 504 loop : -1.62 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 252 HIS 0.003 0.001 HIS F 41 PHE 0.028 0.003 PHE f 32 TYR 0.027 0.002 TYR I 158 ARG 0.007 0.000 ARG e 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 354 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8839 (tptp) cc_final: 0.8571 (tptt) REVERT: D 88 LYS cc_start: 0.8939 (tptp) cc_final: 0.8720 (tptt) REVERT: E 159 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7711 (t80) REVERT: F 109 LYS cc_start: 0.8650 (mttt) cc_final: 0.8266 (ttmm) REVERT: G 119 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (m) REVERT: H 88 LYS cc_start: 0.8931 (tptp) cc_final: 0.8533 (tptt) REVERT: H 109 LYS cc_start: 0.8679 (mttt) cc_final: 0.8414 (mtmm) REVERT: H 212 GLN cc_start: 0.7914 (mt0) cc_final: 0.7628 (mt0) REVERT: I 119 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8604 (m) REVERT: a 28 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6601 (mmt180) REVERT: a 44 ASN cc_start: 0.8611 (m-40) cc_final: 0.8335 (m-40) REVERT: b 52 TYR cc_start: 0.7964 (m-80) cc_final: 0.7568 (m-10) REVERT: h 49 GLN cc_start: 0.7494 (mm110) cc_final: 0.7102 (mm-40) outliers start: 83 outliers final: 53 residues processed: 408 average time/residue: 0.3319 time to fit residues: 203.5030 Evaluate side-chains 382 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 326 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 PHE Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 29 ASN Chi-restraints excluded: chain b residue 35 ASN Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain e residue 29 ASN Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain g residue 45 SER Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 243 optimal weight: 0.0470 chunk 120 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS B 77 GLN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 270 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS E 77 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 270 HIS F 77 GLN F 148 ASN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS G 77 GLN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS H 77 GLN ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 HIS g 49 GLN i 31 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20646 Z= 0.167 Angle : 0.560 7.308 28017 Z= 0.302 Chirality : 0.043 0.150 3168 Planarity : 0.003 0.026 3699 Dihedral : 4.882 25.647 2835 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.32 % Allowed : 16.44 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.27 (0.17), residues: 2583 helix: -0.17 (0.18), residues: 810 sheet: -0.56 (0.23), residues: 585 loop : -1.39 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 252 HIS 0.002 0.000 HIS A 270 PHE 0.019 0.002 PHE B 159 TYR 0.016 0.001 TYR C 158 ARG 0.005 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 338 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 MET cc_start: 0.8672 (ttp) cc_final: 0.8451 (ttp) REVERT: D 88 LYS cc_start: 0.8709 (tptp) cc_final: 0.8347 (tptt) REVERT: E 159 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7770 (t80) REVERT: H 88 LYS cc_start: 0.8739 (tptp) cc_final: 0.8318 (tptt) REVERT: H 159 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7409 (t80) REVERT: H 212 GLN cc_start: 0.7726 (mt0) cc_final: 0.7508 (mt0) REVERT: a 28 ARG cc_start: 0.6377 (mmt180) cc_final: 0.6049 (mmt180) REVERT: b 52 TYR cc_start: 0.7951 (m-80) cc_final: 0.7736 (m-10) REVERT: f 52 TYR cc_start: 0.7415 (m-80) cc_final: 0.7171 (m-80) outliers start: 73 outliers final: 41 residues processed: 385 average time/residue: 0.3435 time to fit residues: 198.0133 Evaluate side-chains 355 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 312 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 159 PHE Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 159 PHE Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain c residue 29 ASN Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain g residue 45 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 0.2980 chunk 100 optimal weight: 0.3980 chunk 207 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS ** F 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20646 Z= 0.149 Angle : 0.545 8.838 28017 Z= 0.294 Chirality : 0.042 0.160 3168 Planarity : 0.003 0.025 3699 Dihedral : 4.664 24.535 2835 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.14 % Allowed : 17.44 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.90 (0.18), residues: 2583 helix: 0.20 (0.19), residues: 819 sheet: -0.23 (0.24), residues: 585 loop : -1.32 (0.20), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 252 HIS 0.002 0.000 HIS D 270 PHE 0.023 0.001 PHE i 32 TYR 0.014 0.001 TYR F 54 ARG 0.003 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 347 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8527 (t0) cc_final: 0.8279 (t0) REVERT: B 54 TYR cc_start: 0.8541 (m-80) cc_final: 0.8247 (m-80) REVERT: D 88 LYS cc_start: 0.8672 (tptp) cc_final: 0.8258 (tptt) REVERT: G 158 TYR cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: H 88 LYS cc_start: 0.8654 (tptp) cc_final: 0.8240 (tptt) REVERT: H 159 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7546 (t80) REVERT: H 221 TYR cc_start: 0.8623 (t80) cc_final: 0.8356 (t80) REVERT: a 28 ARG cc_start: 0.6268 (mmt180) cc_final: 0.5894 (mmt180) REVERT: g 28 ARG cc_start: 0.6193 (mmt180) cc_final: 0.5919 (mtt180) REVERT: g 52 TYR cc_start: 0.7485 (m-80) cc_final: 0.7110 (m-10) REVERT: h 44 ASN cc_start: 0.8550 (m-40) cc_final: 0.8221 (m-40) outliers start: 47 outliers final: 33 residues processed: 376 average time/residue: 0.3501 time to fit residues: 196.3895 Evaluate side-chains 353 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 319 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 210 ASP Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain g residue 45 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 143 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20646 Z= 0.327 Angle : 0.597 7.246 28017 Z= 0.322 Chirality : 0.044 0.183 3168 Planarity : 0.003 0.022 3699 Dihedral : 4.840 25.769 2835 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 2.64 % Allowed : 18.21 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.73 (0.18), residues: 2583 helix: 0.25 (0.19), residues: 810 sheet: 0.08 (0.27), residues: 459 loop : -1.14 (0.19), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 252 HIS 0.006 0.001 HIS D 270 PHE 0.031 0.002 PHE i 32 TYR 0.016 0.001 TYR C 158 ARG 0.004 0.000 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 324 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7798 (t0) cc_final: 0.7573 (t0) REVERT: B 221 TYR cc_start: 0.8756 (t80) cc_final: 0.8524 (t80) REVERT: D 88 LYS cc_start: 0.8802 (tptp) cc_final: 0.8422 (tptt) REVERT: H 88 LYS cc_start: 0.8753 (tptp) cc_final: 0.8333 (tptt) REVERT: H 159 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7719 (t80) REVERT: a 23 MET cc_start: 0.7942 (mtp) cc_final: 0.7644 (mtt) REVERT: a 28 ARG cc_start: 0.6628 (mmt180) cc_final: 0.5979 (mmt180) REVERT: g 28 ARG cc_start: 0.6533 (mmt180) cc_final: 0.6186 (mmt180) outliers start: 58 outliers final: 41 residues processed: 364 average time/residue: 0.3756 time to fit residues: 206.6189 Evaluate side-chains 353 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 22 THR Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 45 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 0.2980 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20646 Z= 0.286 Angle : 0.584 6.980 28017 Z= 0.316 Chirality : 0.044 0.195 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.814 25.421 2835 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.60 % Allowed : 17.99 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.59 (0.18), residues: 2583 helix: 0.42 (0.19), residues: 810 sheet: -0.14 (0.25), residues: 558 loop : -1.03 (0.20), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 252 HIS 0.002 0.001 HIS A 270 PHE 0.034 0.002 PHE i 32 TYR 0.018 0.001 TYR I 54 ARG 0.003 0.000 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7842 (t0) cc_final: 0.7623 (t0) REVERT: B 221 TYR cc_start: 0.8782 (t80) cc_final: 0.8527 (t80) REVERT: D 88 LYS cc_start: 0.8796 (tptp) cc_final: 0.8430 (tptt) REVERT: D 216 GLU cc_start: 0.7139 (tt0) cc_final: 0.6873 (tt0) REVERT: F 158 TYR cc_start: 0.8127 (t80) cc_final: 0.7830 (t80) REVERT: G 158 TYR cc_start: 0.7743 (t80) cc_final: 0.7125 (t80) REVERT: H 88 LYS cc_start: 0.8756 (tptp) cc_final: 0.8336 (tptt) REVERT: H 159 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7830 (t80) REVERT: a 28 ARG cc_start: 0.6639 (mmt180) cc_final: 0.6031 (mmt180) REVERT: g 28 ARG cc_start: 0.6648 (mmt180) cc_final: 0.6222 (mmt180) outliers start: 57 outliers final: 47 residues processed: 359 average time/residue: 0.3461 time to fit residues: 183.8370 Evaluate side-chains 361 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 313 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 22 THR Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 145 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20646 Z= 0.225 Angle : 0.567 7.216 28017 Z= 0.307 Chirality : 0.043 0.186 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.749 25.287 2835 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 2.50 % Allowed : 18.67 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.56 (0.18), residues: 2583 helix: 0.65 (0.20), residues: 810 sheet: -0.32 (0.23), residues: 648 loop : -1.10 (0.21), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 252 HIS 0.004 0.001 HIS G 270 PHE 0.029 0.002 PHE i 32 TYR 0.019 0.001 TYR I 54 ARG 0.003 0.000 ARG I 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 318 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7817 (t0) cc_final: 0.7610 (t0) REVERT: A 180 ASN cc_start: 0.8505 (t0) cc_final: 0.8279 (t0) REVERT: D 88 LYS cc_start: 0.8755 (tptp) cc_final: 0.8405 (tptt) REVERT: D 216 GLU cc_start: 0.7132 (tt0) cc_final: 0.6790 (tt0) REVERT: E 97 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: F 158 TYR cc_start: 0.8128 (t80) cc_final: 0.7777 (t80) REVERT: G 158 TYR cc_start: 0.7761 (t80) cc_final: 0.7200 (t80) REVERT: H 88 LYS cc_start: 0.8728 (tptp) cc_final: 0.8321 (tptt) REVERT: I 213 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7262 (mmp-170) REVERT: g 28 ARG cc_start: 0.6560 (mmt180) cc_final: 0.6121 (mmt180) REVERT: g 52 TYR cc_start: 0.7572 (m-80) cc_final: 0.7186 (m-10) outliers start: 55 outliers final: 45 residues processed: 353 average time/residue: 0.3474 time to fit residues: 182.8174 Evaluate side-chains 352 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 306 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 22 THR Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 177 optimal weight: 0.0870 chunk 69 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20646 Z= 0.233 Angle : 0.565 7.101 28017 Z= 0.306 Chirality : 0.043 0.179 3168 Planarity : 0.003 0.063 3699 Dihedral : 4.721 25.188 2835 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.55 % Allowed : 19.08 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.49 (0.18), residues: 2583 helix: 0.73 (0.20), residues: 810 sheet: -0.26 (0.23), residues: 648 loop : -1.08 (0.21), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 252 HIS 0.005 0.001 HIS G 270 PHE 0.027 0.002 PHE i 32 TYR 0.019 0.001 TYR I 54 ARG 0.026 0.000 ARG i 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 310 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8006 (tp40) cc_final: 0.7800 (pm20) REVERT: A 180 ASN cc_start: 0.8502 (t0) cc_final: 0.8280 (t0) REVERT: D 88 LYS cc_start: 0.8763 (tptp) cc_final: 0.8420 (tptt) REVERT: E 97 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: G 158 TYR cc_start: 0.7848 (t80) cc_final: 0.7296 (t80) REVERT: H 88 LYS cc_start: 0.8728 (tptp) cc_final: 0.8323 (tptt) REVERT: I 213 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7297 (mmp-170) REVERT: g 52 TYR cc_start: 0.7632 (m-80) cc_final: 0.7229 (m-10) outliers start: 56 outliers final: 48 residues processed: 348 average time/residue: 0.3435 time to fit residues: 179.1058 Evaluate side-chains 353 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 304 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.0970 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 166 optimal weight: 0.5980 chunk 251 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20646 Z= 0.204 Angle : 0.560 7.390 28017 Z= 0.303 Chirality : 0.043 0.177 3168 Planarity : 0.003 0.049 3699 Dihedral : 4.687 24.851 2835 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.32 % Allowed : 19.58 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.43 (0.18), residues: 2583 helix: 1.02 (0.21), residues: 756 sheet: -0.22 (0.23), residues: 648 loop : -1.16 (0.20), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 252 HIS 0.005 0.001 HIS A 270 PHE 0.029 0.002 PHE i 32 TYR 0.019 0.001 TYR I 54 ARG 0.002 0.000 ARG f 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8023 (tp40) cc_final: 0.7816 (pm20) REVERT: A 180 ASN cc_start: 0.8530 (t0) cc_final: 0.8273 (t0) REVERT: B 164 ASP cc_start: 0.8463 (p0) cc_final: 0.8255 (p0) REVERT: D 88 LYS cc_start: 0.8739 (tptp) cc_final: 0.8395 (tptt) REVERT: D 216 GLU cc_start: 0.7192 (tt0) cc_final: 0.6531 (tt0) REVERT: E 97 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: G 158 TYR cc_start: 0.7810 (t80) cc_final: 0.7206 (t80) REVERT: H 88 LYS cc_start: 0.8701 (tptp) cc_final: 0.8303 (tptt) REVERT: I 213 ARG cc_start: 0.8178 (mmt-90) cc_final: 0.7280 (mmp-170) REVERT: d 52 TYR cc_start: 0.7518 (m-80) cc_final: 0.7203 (m-10) REVERT: g 52 TYR cc_start: 0.7622 (m-80) cc_final: 0.7193 (m-10) outliers start: 51 outliers final: 45 residues processed: 351 average time/residue: 0.3567 time to fit residues: 185.1719 Evaluate side-chains 357 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 311 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 256 ASN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain h residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117797 restraints weight = 28467.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120772 restraints weight = 15307.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122610 restraints weight = 9875.337| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20646 Z= 0.189 Angle : 0.556 7.506 28017 Z= 0.301 Chirality : 0.043 0.172 3168 Planarity : 0.003 0.023 3699 Dihedral : 4.636 24.462 2835 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.14 % Allowed : 19.95 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2583 helix: 1.12 (0.21), residues: 756 sheet: -0.16 (0.23), residues: 648 loop : -1.14 (0.20), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 252 HIS 0.008 0.001 HIS A 270 PHE 0.029 0.002 PHE i 32 TYR 0.022 0.001 TYR C 211 ARG 0.004 0.000 ARG i 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.69 seconds wall clock time: 76 minutes 48.00 seconds (4608.00 seconds total)