Starting phenix.real_space_refine on Fri Feb 23 12:29:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezm_4160/02_2024/6ezm_4160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezm_4160/02_2024/6ezm_4160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezm_4160/02_2024/6ezm_4160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezm_4160/02_2024/6ezm_4160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezm_4160/02_2024/6ezm_4160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezm_4160/02_2024/6ezm_4160_updated.pdb" } resolution = 3.2 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= 0.005 sd= 0.048 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: 6 Type Number sf(0) Gaussians Mn 48 7.51 5 P 24 5.49 5 S 144 5.16 5 C 24000 2.51 5 N 6960 2.21 5 O 7224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38400 Number of models: 1 Model: "" Number of chains: 38 Chain: "U" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "T" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "V" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "W" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "U" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' MN': 4, '5LD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb="MN MN U 302 " occ=0.50 residue: pdb=" C3 5LD U 303 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD U 303 " occ=0.30 residue: pdb="MN MN U 305 " occ=0.50 residue: pdb=" C3 5LD U 306 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD U 306 " occ=0.30 residue: pdb="MN MN A 401 " occ=0.50 residue: pdb=" C3 5LD A 402 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD A 402 " occ=0.30 residue: pdb="MN MN A 405 " occ=0.50 residue: pdb=" C3 5LD A 406 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD A 406 " occ=0.30 residue: pdb="MN MN B 302 " occ=0.50 residue: pdb=" C3 5LD B 303 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD B 303 " occ=0.30 residue: pdb="MN MN B 304 " occ=0.50 residue: pdb=" C3 5LD B 305 " occ=0.30 ... (11 atoms not shown) pdb=" P9 5LD B 305 " occ=0.30 ... (remaining 36 not shown) Time building chain proxies: 20.65, per 1000 atoms: 0.54 Number of scatterers: 38400 At special positions: 0 Unit cell: (145.905, 145.905, 145.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 48 24.99 S 144 16.00 P 24 15.00 O 7224 8.00 N 6960 7.00 C 24000 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: 15.65 Conformation dependent library (CDL) restraints added in 7.6 seconds 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 48 sheets defined 28.8% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.00 Creating SS restraints... Processing helix chain 'U' and resid 60 through 71 Processing helix chain 'U' and resid 91 through 107 removed outlier: 3.660A pdb=" N ASP U 95 " --> pdb=" O HIS U 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS U 96 " --> pdb=" O THR U 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU U 100 " --> pdb=" O CYS U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU U 164 " --> pdb=" O ILE U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA U 192 " --> pdb=" O ARG U 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 203 removed outlier: 3.655A pdb=" N ALA A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.675A pdb=" N LEU B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP C 95 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA C 192 " --> pdb=" O ARG C 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP D 95 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 71 Processing helix chain 'E' and resid 91 through 107 removed outlier: 3.660A pdb=" N ASP E 95 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 203 removed outlier: 3.655A pdb=" N ALA E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP F 95 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 100 " --> pdb=" O CYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU F 164 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 71 Processing helix chain 'G' and resid 91 through 107 removed outlier: 3.660A pdb=" N ASP G 95 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU G 100 " --> pdb=" O CYS G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 203 removed outlier: 3.655A pdb=" N ALA G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP H 95 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 100 " --> pdb=" O CYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA H 192 " --> pdb=" O ARG H 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 71 Processing helix chain 'I' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU I 100 " --> pdb=" O CYS I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU I 164 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA I 192 " --> pdb=" O ARG I 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 71 Processing helix chain 'J' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP J 95 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU J 100 " --> pdb=" O CYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA J 192 " --> pdb=" O ARG J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 71 Processing helix chain 'K' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP K 95 " --> pdb=" O HIS K 91 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU K 100 " --> pdb=" O CYS K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU K 164 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA K 192 " --> pdb=" O ARG K 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 71 Processing helix chain 'L' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP L 95 " --> pdb=" O HIS L 91 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS L 96 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 100 " --> pdb=" O CYS L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU L 164 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 203 removed outlier: 3.655A pdb=" N ALA L 192 " --> pdb=" O ARG L 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 71 Processing helix chain 'M' and resid 91 through 107 removed outlier: 3.645A pdb=" N ASP M 95 " --> pdb=" O HIS M 91 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS M 96 " --> pdb=" O THR M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA M 192 " --> pdb=" O ARG M 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 91 through 107 removed outlier: 3.644A pdb=" N ASP N 95 " --> pdb=" O HIS N 91 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU N 164 " --> pdb=" O ILE N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA N 192 " --> pdb=" O ARG N 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 71 Processing helix chain 'O' and resid 91 through 107 removed outlier: 3.649A pdb=" N ASP O 95 " --> pdb=" O HIS O 91 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA O 192 " --> pdb=" O ARG O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 71 Processing helix chain 'P' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP P 95 " --> pdb=" O HIS P 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS P 96 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU P 100 " --> pdb=" O CYS P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA P 192 " --> pdb=" O ARG P 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 71 Processing helix chain 'Q' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP Q 95 " --> pdb=" O HIS Q 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS Q 96 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU Q 100 " --> pdb=" O CYS Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA Q 192 " --> pdb=" O ARG Q 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 71 Processing helix chain 'R' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP R 95 " --> pdb=" O HIS R 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA R 192 " --> pdb=" O ARG R 188 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 71 Processing helix chain 'S' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP S 95 " --> pdb=" O HIS S 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU S 100 " --> pdb=" O CYS S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 171 removed outlier: 3.673A pdb=" N LEU S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 203 removed outlier: 3.655A pdb=" N ALA S 192 " --> pdb=" O ARG S 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 71 Processing helix chain 'T' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP T 95 " --> pdb=" O HIS T 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS T 96 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU T 100 " --> pdb=" O CYS T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU T 164 " --> pdb=" O ILE T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA T 192 " --> pdb=" O ARG T 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 71 Processing helix chain 'V' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP V 95 " --> pdb=" O HIS V 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS V 96 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU V 100 " --> pdb=" O CYS V 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU V 164 " --> pdb=" O ILE V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA V 192 " --> pdb=" O ARG V 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 71 Processing helix chain 'W' and resid 91 through 107 removed outlier: 3.661A pdb=" N ASP W 95 " --> pdb=" O HIS W 91 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS W 96 " --> pdb=" O THR W 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU W 100 " --> pdb=" O CYS W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU W 164 " --> pdb=" O ILE W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA W 192 " --> pdb=" O ARG W 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 71 Processing helix chain 'X' and resid 91 through 107 removed outlier: 3.660A pdb=" N ASP X 95 " --> pdb=" O HIS X 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU X 100 " --> pdb=" O CYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 171 removed outlier: 3.674A pdb=" N LEU X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 185 through 203 removed outlier: 3.656A pdb=" N ALA X 192 " --> pdb=" O ARG X 188 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'U' and resid 5 through 8 Processing sheet with id= B, first strand: chain 'U' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG U 181 " --> pdb=" O LEU U 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG U 130 " --> pdb=" O CYS U 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS U 179 " --> pdb=" O ARG U 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL U 132 " --> pdb=" O VAL U 177 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL U 177 " --> pdb=" O VAL U 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR U 140 " --> pdb=" O LEU U 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL U 177 " --> pdb=" O TYR U 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL U 142 " --> pdb=" O VAL U 177 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N CYS U 179 " --> pdb=" O VAL U 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU U 144 " --> pdb=" O CYS U 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG U 181 " --> pdb=" O GLU U 144 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 5 through 8 Processing sheet with id= D, first strand: chain 'A' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG A 181 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG A 130 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS A 179 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL A 177 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 140 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 177 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 142 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS A 179 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 144 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG A 181 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 5 through 8 Processing sheet with id= F, first strand: chain 'B' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG B 181 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG B 130 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS B 179 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL B 177 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR B 140 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL B 177 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 142 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS B 179 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU B 144 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG B 181 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= H, first strand: chain 'C' and resid 118 through 124 removed outlier: 3.514A pdb=" N ARG C 181 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG C 130 " --> pdb=" O CYS C 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS C 179 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL C 177 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR C 140 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL C 177 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 142 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS C 179 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU C 144 " --> pdb=" O CYS C 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG C 181 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 5 through 8 Processing sheet with id= J, first strand: chain 'D' and resid 118 through 124 removed outlier: 3.512A pdb=" N ARG D 181 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG D 130 " --> pdb=" O CYS D 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS D 179 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL D 177 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 140 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL D 177 " --> pdb=" O TYR D 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 142 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS D 179 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU D 144 " --> pdb=" O CYS D 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG D 181 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= L, first strand: chain 'E' and resid 118 through 124 removed outlier: 3.512A pdb=" N ARG E 181 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG E 130 " --> pdb=" O CYS E 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS E 179 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL E 132 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL E 177 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR E 140 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL E 177 " --> pdb=" O TYR E 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 142 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS E 179 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU E 144 " --> pdb=" O CYS E 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG E 181 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 5 through 8 Processing sheet with id= N, first strand: chain 'F' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG F 181 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG F 130 " --> pdb=" O CYS F 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS F 179 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL F 132 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL F 177 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR F 140 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL F 177 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL F 142 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS F 179 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU F 144 " --> pdb=" O CYS F 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG F 181 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 5 through 8 Processing sheet with id= P, first strand: chain 'G' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG G 181 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG G 130 " --> pdb=" O CYS G 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS G 179 " --> pdb=" O ARG G 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL G 132 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL G 177 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR G 140 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL G 177 " --> pdb=" O TYR G 140 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL G 142 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS G 179 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU G 144 " --> pdb=" O CYS G 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG G 181 " --> pdb=" O GLU G 144 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 5 through 8 Processing sheet with id= R, first strand: chain 'H' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG H 181 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG H 130 " --> pdb=" O CYS H 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS H 179 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL H 132 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL H 177 " --> pdb=" O VAL H 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR H 140 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL H 177 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL H 142 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS H 179 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU H 144 " --> pdb=" O CYS H 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG H 181 " --> pdb=" O GLU H 144 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 5 through 8 Processing sheet with id= T, first strand: chain 'I' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG I 181 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG I 130 " --> pdb=" O CYS I 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS I 179 " --> pdb=" O ARG I 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL I 132 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL I 177 " --> pdb=" O VAL I 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR I 140 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL I 177 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL I 142 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS I 179 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU I 144 " --> pdb=" O CYS I 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG I 181 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 5 through 8 Processing sheet with id= V, first strand: chain 'J' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG J 181 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG J 130 " --> pdb=" O CYS J 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS J 179 " --> pdb=" O ARG J 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL J 132 " --> pdb=" O VAL J 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL J 177 " --> pdb=" O VAL J 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR J 140 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL J 177 " --> pdb=" O TYR J 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL J 142 " --> pdb=" O VAL J 177 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N CYS J 179 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU J 144 " --> pdb=" O CYS J 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG J 181 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 5 through 8 Processing sheet with id= X, first strand: chain 'K' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG K 181 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG K 130 " --> pdb=" O CYS K 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS K 179 " --> pdb=" O ARG K 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL K 132 " --> pdb=" O VAL K 177 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL K 177 " --> pdb=" O VAL K 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR K 140 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL K 177 " --> pdb=" O TYR K 140 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL K 142 " --> pdb=" O VAL K 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS K 179 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU K 144 " --> pdb=" O CYS K 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG K 181 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'L' and resid 118 through 124 removed outlier: 3.512A pdb=" N ARG L 181 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG L 130 " --> pdb=" O CYS L 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS L 179 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL L 132 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL L 177 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR L 140 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL L 177 " --> pdb=" O TYR L 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL L 142 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS L 179 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU L 144 " --> pdb=" O CYS L 179 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG L 181 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AB, first strand: chain 'M' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG M 181 " --> pdb=" O LEU M 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG M 130 " --> pdb=" O CYS M 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS M 179 " --> pdb=" O ARG M 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL M 132 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL M 177 " --> pdb=" O VAL M 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR M 140 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL M 177 " --> pdb=" O TYR M 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL M 142 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS M 179 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU M 144 " --> pdb=" O CYS M 179 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG M 181 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AD, first strand: chain 'N' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG N 181 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG N 130 " --> pdb=" O CYS N 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS N 179 " --> pdb=" O ARG N 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL N 132 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL N 177 " --> pdb=" O VAL N 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR N 140 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL N 177 " --> pdb=" O TYR N 140 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL N 142 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS N 179 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU N 144 " --> pdb=" O CYS N 179 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG N 181 " --> pdb=" O GLU N 144 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 5 through 8 Processing sheet with id= AF, first strand: chain 'O' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG O 181 " --> pdb=" O LEU O 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG O 130 " --> pdb=" O CYS O 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS O 179 " --> pdb=" O ARG O 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL O 132 " --> pdb=" O VAL O 177 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL O 177 " --> pdb=" O VAL O 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR O 140 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL O 177 " --> pdb=" O TYR O 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL O 142 " --> pdb=" O VAL O 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS O 179 " --> pdb=" O VAL O 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU O 144 " --> pdb=" O CYS O 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG O 181 " --> pdb=" O GLU O 144 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 5 through 8 Processing sheet with id= AH, first strand: chain 'P' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG P 181 " --> pdb=" O LEU P 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG P 130 " --> pdb=" O CYS P 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS P 179 " --> pdb=" O ARG P 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL P 132 " --> pdb=" O VAL P 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL P 177 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR P 140 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL P 177 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL P 142 " --> pdb=" O VAL P 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS P 179 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU P 144 " --> pdb=" O CYS P 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG P 181 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Q' and resid 5 through 8 Processing sheet with id= AJ, first strand: chain 'Q' and resid 118 through 124 removed outlier: 3.514A pdb=" N ARG Q 181 " --> pdb=" O LEU Q 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG Q 130 " --> pdb=" O CYS Q 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS Q 179 " --> pdb=" O ARG Q 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL Q 132 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL Q 177 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR Q 140 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL Q 177 " --> pdb=" O TYR Q 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL Q 142 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS Q 179 " --> pdb=" O VAL Q 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU Q 144 " --> pdb=" O CYS Q 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG Q 181 " --> pdb=" O GLU Q 144 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'R' and resid 5 through 8 Processing sheet with id= AL, first strand: chain 'R' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG R 181 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG R 130 " --> pdb=" O CYS R 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS R 179 " --> pdb=" O ARG R 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL R 132 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL R 177 " --> pdb=" O VAL R 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR R 140 " --> pdb=" O LEU R 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL R 177 " --> pdb=" O TYR R 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL R 142 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N CYS R 179 " --> pdb=" O VAL R 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU R 144 " --> pdb=" O CYS R 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG R 181 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'S' and resid 5 through 8 Processing sheet with id= AN, first strand: chain 'S' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG S 181 " --> pdb=" O LEU S 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG S 130 " --> pdb=" O CYS S 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS S 179 " --> pdb=" O ARG S 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL S 132 " --> pdb=" O VAL S 177 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL S 177 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR S 140 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL S 177 " --> pdb=" O TYR S 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL S 142 " --> pdb=" O VAL S 177 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N CYS S 179 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU S 144 " --> pdb=" O CYS S 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG S 181 " --> pdb=" O GLU S 144 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'T' and resid 5 through 8 Processing sheet with id= AP, first strand: chain 'T' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG T 181 " --> pdb=" O LEU T 128 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG T 130 " --> pdb=" O CYS T 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS T 179 " --> pdb=" O ARG T 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL T 132 " --> pdb=" O VAL T 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL T 177 " --> pdb=" O VAL T 132 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR T 140 " --> pdb=" O LEU T 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL T 177 " --> pdb=" O TYR T 140 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL T 142 " --> pdb=" O VAL T 177 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N CYS T 179 " --> pdb=" O VAL T 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU T 144 " --> pdb=" O CYS T 179 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG T 181 " --> pdb=" O GLU T 144 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'V' and resid 5 through 8 Processing sheet with id= AR, first strand: chain 'V' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG V 181 " --> pdb=" O LEU V 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG V 130 " --> pdb=" O CYS V 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS V 179 " --> pdb=" O ARG V 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL V 132 " --> pdb=" O VAL V 177 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL V 177 " --> pdb=" O VAL V 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR V 140 " --> pdb=" O LEU V 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL V 177 " --> pdb=" O TYR V 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL V 142 " --> pdb=" O VAL V 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS V 179 " --> pdb=" O VAL V 142 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU V 144 " --> pdb=" O CYS V 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG V 181 " --> pdb=" O GLU V 144 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'W' and resid 5 through 8 Processing sheet with id= AT, first strand: chain 'W' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG W 181 " --> pdb=" O LEU W 128 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG W 130 " --> pdb=" O CYS W 179 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS W 179 " --> pdb=" O ARG W 130 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL W 132 " --> pdb=" O VAL W 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL W 177 " --> pdb=" O VAL W 132 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR W 140 " --> pdb=" O LEU W 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL W 177 " --> pdb=" O TYR W 140 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL W 142 " --> pdb=" O VAL W 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS W 179 " --> pdb=" O VAL W 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU W 144 " --> pdb=" O CYS W 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG W 181 " --> pdb=" O GLU W 144 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'X' and resid 5 through 8 Processing sheet with id= AV, first strand: chain 'X' and resid 118 through 124 removed outlier: 3.513A pdb=" N ARG X 181 " --> pdb=" O LEU X 128 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG X 130 " --> pdb=" O CYS X 179 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS X 179 " --> pdb=" O ARG X 130 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL X 132 " --> pdb=" O VAL X 177 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL X 177 " --> pdb=" O VAL X 132 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR X 140 " --> pdb=" O LEU X 175 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL X 177 " --> pdb=" O TYR X 140 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL X 142 " --> pdb=" O VAL X 177 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS X 179 " --> pdb=" O VAL X 142 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU X 144 " --> pdb=" O CYS X 179 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG X 181 " --> pdb=" O GLU X 144 " (cutoff:3.500A) 1635 hydrogen bonds defined for protein. 4689 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: 13.62 Time building geometry restraints manager: 16.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9370 1.33 - 1.45: 7371 1.45 - 1.57: 22043 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 39000 Sorted by residual: bond pdb=" O12 5LD U 306 " pdb=" P9 5LD U 306 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O12 5LD E 402 " pdb=" P9 5LD E 402 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O12 5LD O 305 " pdb=" P9 5LD O 305 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O12 5LD H 302 " pdb=" P9 5LD H 302 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O12 5LD B 305 " pdb=" P9 5LD B 305 " ideal model delta sigma weight residual 1.561 1.488 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 38995 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.46: 1195 106.46 - 113.56: 22543 113.56 - 120.66: 15907 120.66 - 127.76: 12699 127.76 - 134.86: 456 Bond angle restraints: 52800 Sorted by residual: angle pdb=" CG ARG X 138 " pdb=" CD ARG X 138 " pdb=" NE ARG X 138 " ideal model delta sigma weight residual 112.00 100.92 11.08 2.20e+00 2.07e-01 2.54e+01 angle pdb=" CG ARG T 138 " pdb=" CD ARG T 138 " pdb=" NE ARG T 138 " ideal model delta sigma weight residual 112.00 100.93 11.07 2.20e+00 2.07e-01 2.53e+01 angle pdb=" CG ARG G 138 " pdb=" CD ARG G 138 " pdb=" NE ARG G 138 " ideal model delta sigma weight residual 112.00 100.94 11.06 2.20e+00 2.07e-01 2.53e+01 angle pdb=" CG ARG K 138 " pdb=" CD ARG K 138 " pdb=" NE ARG K 138 " ideal model delta sigma weight residual 112.00 100.94 11.06 2.20e+00 2.07e-01 2.53e+01 angle pdb=" CG ARG L 138 " pdb=" CD ARG L 138 " pdb=" NE ARG L 138 " ideal model delta sigma weight residual 112.00 100.94 11.06 2.20e+00 2.07e-01 2.53e+01 ... (remaining 52795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.30: 20935 12.30 - 24.60: 1926 24.60 - 36.90: 315 36.90 - 49.20: 100 49.20 - 61.50: 52 Dihedral angle restraints: 23328 sinusoidal: 8904 harmonic: 14424 Sorted by residual: dihedral pdb=" CA THR F 48 " pdb=" C THR F 48 " pdb=" N GLN F 49 " pdb=" CA GLN F 49 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR V 48 " pdb=" C THR V 48 " pdb=" N GLN V 49 " pdb=" CA GLN V 49 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR T 48 " pdb=" C THR T 48 " pdb=" N GLN T 49 " pdb=" CA GLN T 49 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 23325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4446 0.061 - 0.123: 1462 0.123 - 0.184: 214 0.184 - 0.246: 40 0.246 - 0.307: 6 Chirality restraints: 6168 Sorted by residual: chirality pdb=" CA ILE B 82 " pdb=" N ILE B 82 " pdb=" C ILE B 82 " pdb=" CB ILE B 82 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ILE K 82 " pdb=" N ILE K 82 " pdb=" C ILE K 82 " pdb=" CB ILE K 82 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ILE J 82 " pdb=" N ILE J 82 " pdb=" C ILE J 82 " pdb=" CB ILE J 82 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 6165 not shown) Planarity restraints: 6840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 94 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C GLU N 94 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU N 94 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP N 95 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 94 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C GLU M 94 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU M 94 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP M 95 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 116 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ARG P 116 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG P 116 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE P 117 " 0.015 2.00e-02 2.50e+03 ... (remaining 6837 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 435 2.51 - 3.11: 25981 3.11 - 3.71: 59666 3.71 - 4.30: 89390 4.30 - 4.90: 153619 Nonbonded interactions: 329091 Sorted by model distance: nonbonded pdb="MN MN M 405 " pdb=" O13 5LD M 406 " model vdw 1.913 2.320 nonbonded pdb="MN MN K 304 " pdb=" O13 5LD K 305 " model vdw 1.927 2.320 nonbonded pdb="MN MN U 305 " pdb=" O13 5LD U 306 " model vdw 1.928 2.320 nonbonded pdb="MN MN O 304 " pdb=" O13 5LD O 305 " model vdw 1.928 2.320 nonbonded pdb="MN MN C 304 " pdb=" O13 5LD C 305 " model vdw 1.929 2.320 ... (remaining 329086 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' and resid 3 through 219) selection = (chain 'B' and resid 3 through 219) selection = (chain 'C' and resid 3 through 219) selection = (chain 'D' and resid 3 through 219) selection = (chain 'E' and resid 3 through 219) selection = (chain 'F' and resid 3 through 219) selection = (chain 'G' and resid 3 through 219) selection = (chain 'H' and resid 3 through 219) selection = (chain 'I' and resid 3 through 219) selection = (chain 'J' and resid 3 through 219) selection = (chain 'K' and resid 3 through 219) selection = chain 'L' selection = (chain 'M' and resid 3 through 219) selection = chain 'N' selection = (chain 'O' and resid 3 through 219) selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = (chain 'U' and resid 3 through 219) selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.900 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 103.080 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.360 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: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.010 0.073 39000 Z= 0.650 Angle : 1.278 14.218 52800 Z= 0.643 Chirality : 0.062 0.307 6168 Planarity : 0.008 0.051 6840 Dihedral : 10.323 61.498 13968 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.08), residues: 4992 helix: -3.98 (0.07), residues: 1584 sheet: -1.94 (0.12), residues: 1392 loop : -3.55 (0.09), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP L 75 HIS 0.019 0.006 HIS T 90 PHE 0.019 0.004 PHE C 117 TYR 0.024 0.007 TYR X 140 ARG 0.012 0.002 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1371 time to evaluate : 4.650 Fit side-chains REVERT: U 94 GLU cc_start: 0.7943 (tt0) cc_final: 0.7725 (tt0) REVERT: U 188 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8410 (mtp180) REVERT: A 94 GLU cc_start: 0.7985 (tt0) cc_final: 0.7734 (tt0) REVERT: A 185 ASP cc_start: 0.8164 (m-30) cc_final: 0.7923 (m-30) REVERT: A 188 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8434 (mtp180) REVERT: B 94 GLU cc_start: 0.7973 (tt0) cc_final: 0.7729 (tt0) REVERT: B 188 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8379 (mtp180) REVERT: D 63 ASP cc_start: 0.7652 (m-30) cc_final: 0.7444 (m-30) REVERT: E 63 ASP cc_start: 0.7624 (m-30) cc_final: 0.7385 (m-30) REVERT: E 185 ASP cc_start: 0.8176 (m-30) cc_final: 0.7945 (m-30) REVERT: E 188 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8423 (mtp180) REVERT: F 188 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8404 (mtp180) REVERT: G 55 VAL cc_start: 0.9000 (m) cc_final: 0.8761 (t) REVERT: G 80 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7836 (mt-10) REVERT: H 61 PHE cc_start: 0.8785 (t80) cc_final: 0.8302 (t80) REVERT: H 63 ASP cc_start: 0.7600 (m-30) cc_final: 0.7395 (m-30) REVERT: I 181 ARG cc_start: 0.8598 (ptp-170) cc_final: 0.8071 (ptp90) REVERT: J 80 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7703 (mt-10) REVERT: K 94 GLU cc_start: 0.7994 (tt0) cc_final: 0.7726 (tt0) REVERT: K 185 ASP cc_start: 0.8168 (m-30) cc_final: 0.7937 (m-30) REVERT: K 188 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8483 (mtp180) REVERT: L 188 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8419 (mtp180) REVERT: M 94 GLU cc_start: 0.7950 (tt0) cc_final: 0.7706 (tt0) REVERT: M 181 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8082 (ptp90) REVERT: M 188 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8437 (mtp180) REVERT: N 94 GLU cc_start: 0.7992 (tt0) cc_final: 0.7755 (tt0) REVERT: N 169 GLU cc_start: 0.6853 (tt0) cc_final: 0.6583 (tt0) REVERT: N 188 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8429 (mtp180) REVERT: O 94 GLU cc_start: 0.8022 (tt0) cc_final: 0.7759 (tt0) REVERT: O 185 ASP cc_start: 0.8168 (m-30) cc_final: 0.7936 (m-30) REVERT: O 188 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8480 (mtp180) REVERT: P 61 PHE cc_start: 0.8791 (t80) cc_final: 0.8282 (t80) REVERT: P 169 GLU cc_start: 0.6867 (tt0) cc_final: 0.6642 (tt0) REVERT: P 181 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8091 (ptp90) REVERT: Q 181 ARG cc_start: 0.8606 (ptp-170) cc_final: 0.8138 (ptp90) REVERT: Q 188 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8465 (mtp180) REVERT: R 63 ASP cc_start: 0.7604 (m-30) cc_final: 0.7401 (m-30) REVERT: R 94 GLU cc_start: 0.7914 (tt0) cc_final: 0.7614 (tt0) REVERT: R 188 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8447 (mtp180) REVERT: S 94 GLU cc_start: 0.7909 (tt0) cc_final: 0.7675 (tt0) REVERT: S 181 ARG cc_start: 0.8608 (ptp-170) cc_final: 0.8075 (ptp90) REVERT: T 63 ASP cc_start: 0.7615 (m-30) cc_final: 0.7406 (m-30) REVERT: T 94 GLU cc_start: 0.7902 (tt0) cc_final: 0.7640 (tt0) REVERT: T 181 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8014 (ptp90) REVERT: V 63 ASP cc_start: 0.7669 (m-30) cc_final: 0.7464 (m-30) REVERT: V 188 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8448 (mtp180) REVERT: W 188 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8421 (mtp180) REVERT: X 181 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8371 (ptp90) REVERT: X 188 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8434 (mtp180) outliers start: 4 outliers final: 4 residues processed: 1375 average time/residue: 0.6383 time to fit residues: 1309.5221 Evaluate side-chains 937 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 933 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.9980 chunk 382 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 257 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 395 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 457 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 13 ASN U 54 ASN U 67 HIS U 176 HIS U 207 ASN A 13 ASN A 54 ASN A 67 HIS A 148 GLN A 176 HIS A 207 ASN A 210 ASN B 13 ASN B 54 ASN B 67 HIS B 176 HIS B 207 ASN B 210 ASN C 13 ASN C 18 GLN C 67 HIS C 207 ASN C 210 ASN D 13 ASN D 54 ASN D 67 HIS D 207 ASN D 210 ASN E 13 ASN E 54 ASN E 67 HIS E 148 GLN E 207 ASN E 210 ASN F 13 ASN F 18 GLN F 54 ASN F 67 HIS F 176 HIS F 207 ASN F 210 ASN G 13 ASN G 54 ASN G 67 HIS G 207 ASN H 13 ASN H 54 ASN H 67 HIS H 207 ASN H 210 ASN I 13 ASN I 18 GLN I 54 ASN I 67 HIS I 207 ASN I 210 ASN J 13 ASN J 67 HIS J 176 HIS J 207 ASN J 210 ASN K 13 ASN K 67 HIS K 148 GLN K 176 HIS K 207 ASN K 210 ASN L 13 ASN L 54 ASN L 67 HIS L 176 HIS L 207 ASN L 210 ASN M 13 ASN M 67 HIS M 207 ASN M 210 ASN N 13 ASN N 54 ASN N 67 HIS N 176 HIS N 207 ASN N 210 ASN O 13 ASN O 67 HIS O 148 GLN O 176 HIS O 207 ASN O 210 ASN P 13 ASN P 54 ASN P 67 HIS P 176 HIS P 207 ASN P 210 ASN Q 13 ASN Q 67 HIS Q 176 HIS Q 207 ASN R 13 ASN R 54 ASN R 67 HIS R 176 HIS R 207 ASN R 210 ASN S 13 ASN S 54 ASN S 67 HIS S 176 HIS S 207 ASN S 210 ASN T 13 ASN T 18 GLN T 54 ASN T 67 HIS T 176 HIS T 207 ASN T 210 ASN V 13 ASN V 54 ASN V 67 HIS V 176 HIS V 207 ASN V 210 ASN W 13 ASN W 18 GLN W 67 HIS W 176 HIS W 207 ASN W 210 ASN X 13 ASN X 18 GLN X 54 ASN X 67 HIS X 176 HIS X 207 ASN X 210 ASN Total number of N/Q/H flips: 137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 39000 Z= 0.241 Angle : 0.661 8.503 52800 Z= 0.338 Chirality : 0.045 0.164 6168 Planarity : 0.008 0.091 6840 Dihedral : 7.863 55.240 5452 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.85 % Allowed : 7.42 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.10), residues: 4992 helix: -1.57 (0.11), residues: 1608 sheet: -1.35 (0.13), residues: 1224 loop : -3.30 (0.10), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 75 HIS 0.007 0.002 HIS C 90 PHE 0.013 0.002 PHE L 35 TYR 0.012 0.002 TYR H 140 ARG 0.008 0.001 ARG G 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1035 time to evaluate : 4.754 Fit side-chains revert: symmetry clash REVERT: U 183 LYS cc_start: 0.7921 (pttp) cc_final: 0.7716 (pttp) REVERT: B 80 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 183 LYS cc_start: 0.8025 (pttp) cc_final: 0.7809 (pttp) REVERT: G 55 VAL cc_start: 0.8987 (m) cc_final: 0.8710 (t) REVERT: M 80 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7737 (mt-10) REVERT: O 80 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7820 (mt-10) REVERT: R 183 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7695 (pttp) outliers start: 192 outliers final: 144 residues processed: 1116 average time/residue: 0.6103 time to fit residues: 1028.0607 Evaluate side-chains 1050 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 905 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 148 GLN Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 183 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 148 GLN Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 96 CYS Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 183 LYS Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 96 CYS Chi-restraints excluded: chain X residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 380 optimal weight: 8.9990 chunk 311 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 458 optimal weight: 8.9990 chunk 495 optimal weight: 10.0000 chunk 408 optimal weight: 9.9990 chunk 454 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 13 ASN U 54 ASN ** U 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 54 ASN B 13 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN C 54 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS D 13 ASN D 54 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS E 13 ASN E 54 ASN E 176 HIS E 210 ASN F 13 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN G 54 ASN G 176 HIS H 13 ASN H 54 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 HIS H 210 ASN I 13 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 HIS I 210 ASN J 13 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN K 210 ASN L 13 ASN L 54 ASN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 HIS M 210 ASN N 13 ASN N 54 ASN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 ASN O 13 ASN O 210 ASN P 13 ASN ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 ASN Q 13 ASN R 13 ASN R 54 ASN S 13 ASN ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 ASN T 54 ASN T 210 ASN V 13 ASN V 54 ASN V 210 ASN W 13 ASN ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 210 ASN X 13 ASN ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 39000 Z= 0.553 Angle : 0.790 9.659 52800 Z= 0.403 Chirality : 0.051 0.160 6168 Planarity : 0.007 0.083 6840 Dihedral : 8.309 59.996 5448 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 6.82 % Allowed : 9.39 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 4992 helix: -0.45 (0.11), residues: 1656 sheet: -1.30 (0.14), residues: 1272 loop : -3.26 (0.10), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 75 HIS 0.010 0.003 HIS T 64 PHE 0.014 0.003 PHE Q 117 TYR 0.016 0.004 TYR B 140 ARG 0.006 0.001 ARG T 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 856 time to evaluate : 4.443 Fit side-chains REVERT: A 150 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: C 10 ARG cc_start: 0.8665 (ttt-90) cc_final: 0.8460 (ttt-90) REVERT: E 150 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: G 149 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8329 (ttt90) REVERT: H 10 ARG cc_start: 0.8591 (ttt-90) cc_final: 0.8231 (ttt-90) REVERT: J 10 ARG cc_start: 0.8545 (ttt-90) cc_final: 0.8284 (ttt-90) REVERT: K 150 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: O 150 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: R 183 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7822 (pttp) REVERT: T 10 ARG cc_start: 0.8579 (ttt-90) cc_final: 0.8129 (ttt-90) REVERT: V 149 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8141 (mtp180) REVERT: V 183 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7802 (pttp) REVERT: W 10 ARG cc_start: 0.8525 (ttt-90) cc_final: 0.8096 (ttt-90) outliers start: 270 outliers final: 206 residues processed: 1000 average time/residue: 0.5976 time to fit residues: 911.9138 Evaluate side-chains 1021 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 808 time to evaluate : 4.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 96 CYS Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 96 CYS Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 96 CYS Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 460 optimal weight: 9.9990 chunk 487 optimal weight: 10.0000 chunk 240 optimal weight: 0.9990 chunk 436 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 ASN N 54 ASN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 ASN P 54 ASN ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 ASN S 54 ASN ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 39000 Z= 0.336 Angle : 0.656 9.446 52800 Z= 0.335 Chirality : 0.047 0.157 6168 Planarity : 0.006 0.050 6840 Dihedral : 8.149 59.891 5448 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.71 % Allowed : 10.88 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.11), residues: 4992 helix: 0.36 (0.12), residues: 1680 sheet: -1.19 (0.14), residues: 1272 loop : -3.28 (0.10), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP W 75 HIS 0.007 0.002 HIS U 162 PHE 0.009 0.002 PHE Q 117 TYR 0.011 0.003 TYR Q 140 ARG 0.004 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 823 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 149 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7936 (mtm180) REVERT: A 150 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: C 10 ARG cc_start: 0.8505 (ttt-90) cc_final: 0.8272 (ttt-90) REVERT: D 10 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.7931 (ttt-90) REVERT: E 150 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: F 10 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.8352 (ttt-90) REVERT: H 10 ARG cc_start: 0.8520 (ttt-90) cc_final: 0.8299 (ttt-90) REVERT: J 10 ARG cc_start: 0.8591 (ttt-90) cc_final: 0.8323 (ttt-90) REVERT: K 150 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: O 150 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: R 183 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7727 (pttp) REVERT: T 10 ARG cc_start: 0.8599 (ttt-90) cc_final: 0.8343 (ttt-90) REVERT: W 10 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.8285 (ttt-90) outliers start: 226 outliers final: 158 residues processed: 959 average time/residue: 0.5984 time to fit residues: 879.9285 Evaluate side-chains 957 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 794 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 362 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 415 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 54 ASN G 54 ASN J 54 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN M 54 ASN N 13 ASN O 54 ASN Q 54 ASN S 54 ASN W 54 ASN X 54 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 39000 Z= 0.421 Angle : 0.704 8.801 52800 Z= 0.360 Chirality : 0.048 0.159 6168 Planarity : 0.006 0.056 6840 Dihedral : 8.198 58.503 5448 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.68 % Allowed : 11.26 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.11), residues: 4992 helix: 0.58 (0.12), residues: 1680 sheet: -0.95 (0.14), residues: 1248 loop : -3.26 (0.10), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 75 HIS 0.008 0.002 HIS O 162 PHE 0.011 0.002 PHE W 117 TYR 0.011 0.003 TYR L 140 ARG 0.004 0.001 ARG X 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 795 time to evaluate : 4.740 Fit side-chains REVERT: U 149 ARG cc_start: 0.8243 (mtp180) cc_final: 0.8032 (mtm180) REVERT: A 150 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: C 10 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.8034 (ttt-90) REVERT: E 10 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.8193 (ttt-90) REVERT: E 150 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: F 10 ARG cc_start: 0.8474 (ttt-90) cc_final: 0.8063 (ttt-90) REVERT: H 10 ARG cc_start: 0.8395 (ttt-90) cc_final: 0.8141 (ttt-90) REVERT: J 10 ARG cc_start: 0.8410 (ttt-90) cc_final: 0.8189 (ttt-90) REVERT: K 150 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: O 150 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: R 183 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7782 (pttp) REVERT: T 10 ARG cc_start: 0.8456 (ttt-90) cc_final: 0.8179 (ttt-90) REVERT: W 10 ARG cc_start: 0.8313 (ttt-90) cc_final: 0.8062 (ttt-90) outliers start: 225 outliers final: 177 residues processed: 927 average time/residue: 0.5920 time to fit residues: 842.5048 Evaluate side-chains 956 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 774 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 5.9990 chunk 438 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 487 optimal weight: 10.0000 chunk 404 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN J 54 ASN M 54 ASN N 13 ASN O 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 39000 Z= 0.240 Angle : 0.611 8.771 52800 Z= 0.313 Chirality : 0.045 0.149 6168 Planarity : 0.005 0.043 6840 Dihedral : 7.982 59.290 5448 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.09 % Allowed : 13.16 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 4992 helix: 1.24 (0.12), residues: 1680 sheet: -0.75 (0.14), residues: 1248 loop : -3.19 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 75 HIS 0.005 0.002 HIS F 162 PHE 0.006 0.001 PHE G 61 TYR 0.009 0.002 TYR K 140 ARG 0.004 0.000 ARG F 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 894 time to evaluate : 4.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 149 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7826 (mtm180) REVERT: A 150 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: C 10 ARG cc_start: 0.8405 (ttt-90) cc_final: 0.8148 (ttt-90) REVERT: C 149 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7768 (mtm180) REVERT: E 150 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: F 10 ARG cc_start: 0.8544 (ttt-90) cc_final: 0.8331 (ttt-90) REVERT: H 10 ARG cc_start: 0.8372 (ttt-90) cc_final: 0.7926 (ttt-90) REVERT: J 10 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8105 (ttt-90) REVERT: K 150 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: O 62 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8894 (tp) REVERT: O 150 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: R 183 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7718 (pttp) REVERT: T 10 ARG cc_start: 0.8450 (ttt-90) cc_final: 0.8168 (ttt-90) REVERT: W 10 ARG cc_start: 0.8335 (ttt-90) cc_final: 0.8126 (ttt-90) outliers start: 162 outliers final: 134 residues processed: 963 average time/residue: 0.5869 time to fit residues: 869.9323 Evaluate side-chains 967 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 827 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 165 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 356 optimal weight: 0.0060 chunk 275 optimal weight: 10.0000 chunk 410 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 485 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 chunk 296 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 86 HIS D 86 HIS L 86 HIS M 86 HIS N 13 ASN N 86 HIS P 86 HIS T 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 39000 Z= 0.341 Angle : 0.657 8.538 52800 Z= 0.339 Chirality : 0.047 0.155 6168 Planarity : 0.005 0.048 6840 Dihedral : 8.008 59.579 5448 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.62 % Allowed : 12.45 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 4992 helix: 1.31 (0.12), residues: 1680 sheet: -0.69 (0.14), residues: 1248 loop : -3.13 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 75 HIS 0.006 0.002 HIS X 162 PHE 0.010 0.002 PHE Q 117 TYR 0.010 0.003 TYR K 140 ARG 0.003 0.001 ARG T 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 801 time to evaluate : 5.043 Fit side-chains REVERT: U 149 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7847 (mtm180) REVERT: A 150 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: C 10 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.8146 (ttt-90) REVERT: D 149 ARG cc_start: 0.8254 (mtp180) cc_final: 0.8039 (mtm180) REVERT: E 150 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: F 10 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8153 (ttt-90) REVERT: H 10 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.7994 (ttt-90) REVERT: J 10 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.8177 (ttt-90) REVERT: K 150 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: O 150 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: T 10 ARG cc_start: 0.8460 (ttt-90) cc_final: 0.8157 (ttt-90) REVERT: V 183 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7709 (pttp) REVERT: W 10 ARG cc_start: 0.8377 (ttt-90) cc_final: 0.8145 (ttt-90) outliers start: 183 outliers final: 163 residues processed: 908 average time/residue: 0.6017 time to fit residues: 834.0656 Evaluate side-chains 969 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 801 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 381 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 86 HIS D 86 HIS L 86 HIS M 86 HIS N 86 HIS P 86 HIS T 86 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 39000 Z= 0.319 Angle : 0.643 8.496 52800 Z= 0.332 Chirality : 0.046 0.155 6168 Planarity : 0.005 0.045 6840 Dihedral : 7.983 59.322 5448 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.90 % Allowed : 12.37 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 4992 helix: 1.43 (0.12), residues: 1680 sheet: -0.63 (0.14), residues: 1248 loop : -3.09 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 75 HIS 0.006 0.002 HIS U 162 PHE 0.008 0.002 PHE I 61 TYR 0.010 0.003 TYR K 140 ARG 0.005 0.001 ARG N 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 810 time to evaluate : 4.976 Fit side-chains REVERT: A 150 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: C 10 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.8150 (ttt-90) REVERT: E 150 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: F 10 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.8163 (ttt-90) REVERT: H 10 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7996 (ttt-90) REVERT: J 10 ARG cc_start: 0.8430 (ttt-90) cc_final: 0.8174 (ttt-90) REVERT: K 150 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: O 150 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: T 10 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.8166 (ttt-90) REVERT: W 10 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.8151 (ttt-90) outliers start: 194 outliers final: 172 residues processed: 928 average time/residue: 0.5905 time to fit residues: 838.3790 Evaluate side-chains 978 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 802 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 20.0000 chunk 465 optimal weight: 40.0000 chunk 424 optimal weight: 7.9990 chunk 452 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 409 optimal weight: 20.0000 chunk 428 optimal weight: 9.9990 chunk 451 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 46 GLN U 86 HIS A 46 GLN D 86 HIS E 46 GLN G 86 HIS H 86 HIS I 46 GLN L 86 HIS M 86 HIS N 46 GLN N 86 HIS P 46 GLN P 86 HIS R 46 GLN T 86 HIS V 46 GLN V 86 HIS W 46 GLN X 46 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 39000 Z= 0.296 Angle : 0.634 8.398 52800 Z= 0.328 Chirality : 0.046 0.156 6168 Planarity : 0.005 0.043 6840 Dihedral : 7.958 58.797 5448 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 4.44 % Allowed : 12.80 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.11), residues: 4992 helix: 1.56 (0.12), residues: 1680 sheet: -0.57 (0.14), residues: 1248 loop : -3.04 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 75 HIS 0.006 0.002 HIS D 162 PHE 0.008 0.002 PHE C 117 TYR 0.010 0.003 TYR K 140 ARG 0.005 0.001 ARG K 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 816 time to evaluate : 4.373 Fit side-chains revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: C 10 ARG cc_start: 0.8431 (ttt-90) cc_final: 0.8155 (ttt-90) REVERT: E 150 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: F 10 ARG cc_start: 0.8411 (ttt-90) cc_final: 0.8181 (ttt-90) REVERT: H 10 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.8002 (ttt-90) REVERT: J 10 ARG cc_start: 0.8439 (ttt-90) cc_final: 0.8181 (ttt-90) REVERT: K 150 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: O 62 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8902 (tp) REVERT: O 150 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: T 10 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8166 (ttt-90) REVERT: W 10 ARG cc_start: 0.8403 (ttt-90) cc_final: 0.8157 (ttt-90) outliers start: 176 outliers final: 163 residues processed: 920 average time/residue: 0.6046 time to fit residues: 852.3428 Evaluate side-chains 979 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 811 time to evaluate : 4.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain V residue 215 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 502 optimal weight: 9.9990 chunk 462 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 86 HIS D 86 HIS E 86 HIS G 46 GLN G 86 HIS H 86 HIS J 46 GLN L 86 HIS M 86 HIS N 86 HIS P 86 HIS Q 86 HIS T 46 GLN T 86 HIS V 86 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 39000 Z= 0.528 Angle : 0.764 8.457 52800 Z= 0.394 Chirality : 0.051 0.164 6168 Planarity : 0.006 0.059 6840 Dihedral : 8.274 56.573 5448 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.67 % Allowed : 12.73 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.11), residues: 4992 helix: 1.09 (0.12), residues: 1656 sheet: -0.60 (0.14), residues: 1248 loop : -3.08 (0.11), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 75 HIS 0.009 0.002 HIS U 162 PHE 0.012 0.002 PHE W 117 TYR 0.010 0.003 TYR X 140 ARG 0.007 0.001 ARG V 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 783 time to evaluate : 4.856 Fit side-chains REVERT: A 150 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: E 150 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: F 10 ARG cc_start: 0.8404 (ttt-90) cc_final: 0.8133 (ttt-90) REVERT: K 150 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: O 150 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: X 181 ARG cc_start: 0.8633 (ptp90) cc_final: 0.8293 (ptp90) outliers start: 185 outliers final: 174 residues processed: 901 average time/residue: 0.6093 time to fit residues: 844.0773 Evaluate side-chains 951 residues out of total 4152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 773 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 165 GLU Chi-restraints excluded: chain U residue 215 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 151 LYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 151 LYS Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 183 LYS Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 183 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 160 ILE Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 12 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 183 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 62 LEU Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 ILE Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 183 LYS Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 62 LEU Chi-restraints excluded: chain W residue 92 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 GLU Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 17 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 92 THR Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 9.9990 chunk 425 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 368 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 400 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 411 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 86 HIS D 46 GLN D 86 HIS E 86 HIS G 86 HIS H 86 HIS L 86 HIS M 46 GLN M 86 HIS N 86 HIS P 86 HIS Q 86 HIS T 86 HIS V 86 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118592 restraints weight = 48927.166| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.61 r_work: 0.3130 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 39000 Z= 0.172 Angle : 0.579 8.524 52800 Z= 0.300 Chirality : 0.044 0.152 6168 Planarity : 0.005 0.043 6840 Dihedral : 8.066 55.735 5448 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.73 % Allowed : 14.77 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4992 helix: 1.87 (0.13), residues: 1680 sheet: -0.44 (0.14), residues: 1248 loop : -2.96 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 75 HIS 0.004 0.001 HIS K 187 PHE 0.007 0.001 PHE E 121 TYR 0.011 0.003 TYR K 140 ARG 0.007 0.000 ARG D 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13515.49 seconds wall clock time: 243 minutes 45.45 seconds (14625.45 seconds total)