Starting phenix.real_space_refine on Fri Feb 23 10:58:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlo_11270/02_2024/6zlo_11270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlo_11270/02_2024/6zlo_11270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlo_11270/02_2024/6zlo_11270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlo_11270/02_2024/6zlo_11270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlo_11270/02_2024/6zlo_11270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlo_11270/02_2024/6zlo_11270.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 66600 2.51 5 N 18120 2.21 5 O 20100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZA TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 105060 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "B" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "C" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "F" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "G" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "H" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "I" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "J" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "K" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "L" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "M" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "N" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "O" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "P" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "Q" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "R" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "T" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "V" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "W" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "X" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "Y" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "Z" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "AA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "BA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "CA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "DA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "EA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "FA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "GA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "HA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "IA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "JA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "KA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "LA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "MA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "NA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "OA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "PA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "QA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "RA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "SA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "TA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "UA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "VA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "WA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "XA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "YA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "ZA" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "AB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "BB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "CB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "DB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "EB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "FB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "GB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "HB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "IB" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Time building chain proxies: 40.03, per 1000 atoms: 0.38 Number of scatterers: 105060 At special positions: 0 Unit cell: (249.76, 249.76, 249.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 20100 8.00 N 18120 7.00 C 66600 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: 31.37 Conformation dependent library (CDL) restraints added in 15.5 seconds 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25800 Finding SS restraints... Secondary structure from input PDB file: 420 helices and 180 sheets defined 41.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.92 Creating SS restraints... Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 452 Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU A 457 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU B 457 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.640A pdb=" N LYS C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 452 Processing helix chain 'C' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU C 457 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 452 Processing helix chain 'D' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU D 457 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 358 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 452 Processing helix chain 'E' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU E 457 " --> pdb=" O LEU E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 358 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR F 365 " --> pdb=" O LYS F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 452 Processing helix chain 'F' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU F 457 " --> pdb=" O LEU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR G 238 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS G 266 " --> pdb=" O SER G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE G 286 " --> pdb=" O SER G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 358 Processing helix chain 'G' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR G 365 " --> pdb=" O LYS G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 452 Processing helix chain 'G' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU G 457 " --> pdb=" O LEU G 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR H 238 " --> pdb=" O GLY H 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS H 266 " --> pdb=" O SER H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE H 286 " --> pdb=" O SER H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 358 Processing helix chain 'H' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR H 365 " --> pdb=" O LYS H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 452 Processing helix chain 'H' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU H 457 " --> pdb=" O LEU H 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR I 238 " --> pdb=" O GLY I 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS I 266 " --> pdb=" O SER I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE I 286 " --> pdb=" O SER I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 358 Processing helix chain 'I' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR I 365 " --> pdb=" O LYS I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 452 Processing helix chain 'I' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU I 457 " --> pdb=" O LEU I 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR J 238 " --> pdb=" O GLY J 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE J 239 " --> pdb=" O MET J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS J 266 " --> pdb=" O SER J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE J 286 " --> pdb=" O SER J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 358 Processing helix chain 'J' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR J 365 " --> pdb=" O LYS J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 452 Processing helix chain 'J' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU J 457 " --> pdb=" O LEU J 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR K 238 " --> pdb=" O GLY K 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE K 239 " --> pdb=" O MET K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS K 266 " --> pdb=" O SER K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE K 286 " --> pdb=" O SER K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 358 Processing helix chain 'K' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR K 365 " --> pdb=" O LYS K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 452 Processing helix chain 'K' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU K 457 " --> pdb=" O LEU K 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR L 238 " --> pdb=" O GLY L 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE L 239 " --> pdb=" O MET L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE L 286 " --> pdb=" O SER L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 358 Processing helix chain 'L' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR L 365 " --> pdb=" O LYS L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 452 Processing helix chain 'L' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU L 457 " --> pdb=" O LEU L 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR M 238 " --> pdb=" O GLY M 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE M 239 " --> pdb=" O MET M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS M 266 " --> pdb=" O SER M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE M 286 " --> pdb=" O SER M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 358 Processing helix chain 'M' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR M 365 " --> pdb=" O LYS M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 452 Processing helix chain 'M' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU M 457 " --> pdb=" O LEU M 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR N 238 " --> pdb=" O GLY N 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE N 239 " --> pdb=" O MET N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE N 286 " --> pdb=" O SER N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 358 Processing helix chain 'N' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR N 365 " --> pdb=" O LYS N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 452 Processing helix chain 'N' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU N 457 " --> pdb=" O LEU N 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR O 238 " --> pdb=" O GLY O 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE O 239 " --> pdb=" O MET O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS O 266 " --> pdb=" O SER O 262 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE O 286 " --> pdb=" O SER O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 358 Processing helix chain 'O' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR O 365 " --> pdb=" O LYS O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 452 Processing helix chain 'O' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU O 457 " --> pdb=" O LEU O 454 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR P 238 " --> pdb=" O GLY P 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE P 239 " --> pdb=" O MET P 235 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE P 286 " --> pdb=" O SER P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 358 Processing helix chain 'P' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR P 365 " --> pdb=" O LYS P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 435 through 452 Processing helix chain 'P' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU P 457 " --> pdb=" O LEU P 454 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR Q 238 " --> pdb=" O GLY Q 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE Q 239 " --> pdb=" O MET Q 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS Q 266 " --> pdb=" O SER Q 262 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE Q 286 " --> pdb=" O SER Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 358 Processing helix chain 'Q' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR Q 365 " --> pdb=" O LYS Q 361 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 452 Processing helix chain 'Q' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU Q 457 " --> pdb=" O LEU Q 454 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE R 239 " --> pdb=" O MET R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS R 266 " --> pdb=" O SER R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 358 Processing helix chain 'R' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR R 365 " --> pdb=" O LYS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 452 Processing helix chain 'R' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU R 457 " --> pdb=" O LEU R 454 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR S 238 " --> pdb=" O GLY S 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE S 239 " --> pdb=" O MET S 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS S 266 " --> pdb=" O SER S 262 " (cutoff:3.500A) Processing helix chain 'S' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE S 286 " --> pdb=" O SER S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 340 through 358 Processing helix chain 'S' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR S 365 " --> pdb=" O LYS S 361 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 452 Processing helix chain 'S' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU S 457 " --> pdb=" O LEU S 454 " (cutoff:3.500A) Processing helix chain 'T' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR T 238 " --> pdb=" O GLY T 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE T 239 " --> pdb=" O MET T 235 " (cutoff:3.500A) Processing helix chain 'T' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS T 266 " --> pdb=" O SER T 262 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE T 286 " --> pdb=" O SER T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 358 Processing helix chain 'T' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR T 365 " --> pdb=" O LYS T 361 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 452 Processing helix chain 'T' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU T 457 " --> pdb=" O LEU T 454 " (cutoff:3.500A) Processing helix chain 'V' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR V 238 " --> pdb=" O GLY V 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE V 239 " --> pdb=" O MET V 235 " (cutoff:3.500A) Processing helix chain 'V' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS V 266 " --> pdb=" O SER V 262 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE V 286 " --> pdb=" O SER V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 340 through 358 Processing helix chain 'V' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 452 Processing helix chain 'V' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU V 457 " --> pdb=" O LEU V 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR W 238 " --> pdb=" O GLY W 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE W 239 " --> pdb=" O MET W 235 " (cutoff:3.500A) Processing helix chain 'W' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS W 266 " --> pdb=" O SER W 262 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE W 286 " --> pdb=" O SER W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 358 Processing helix chain 'W' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR W 365 " --> pdb=" O LYS W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 452 Processing helix chain 'W' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU W 457 " --> pdb=" O LEU W 454 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR X 238 " --> pdb=" O GLY X 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE X 239 " --> pdb=" O MET X 235 " (cutoff:3.500A) Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS X 266 " --> pdb=" O SER X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHE X 286 " --> pdb=" O SER X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 340 through 358 Processing helix chain 'X' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR X 365 " --> pdb=" O LYS X 361 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 452 Processing helix chain 'X' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU X 457 " --> pdb=" O LEU X 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 250 removed outlier: 3.840A pdb=" N THR Y 238 " --> pdb=" O GLY Y 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE Y 239 " --> pdb=" O MET Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS Y 266 " --> pdb=" O SER Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE Y 286 " --> pdb=" O SER Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 358 Processing helix chain 'Y' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYR Y 365 " --> pdb=" O LYS Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 435 through 452 Processing helix chain 'Y' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEU Y 457 " --> pdb=" O LEU Y 454 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 250 removed outlier: 3.841A pdb=" N THR Z 238 " --> pdb=" O GLY Z 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE Z 239 " --> pdb=" O MET Z 235 " (cutoff:3.500A) Processing helix chain 'Z' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYS Z 266 " --> pdb=" O SER Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHE Z 286 " --> pdb=" O SER Z 282 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 358 Processing helix chain 'Z' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYR Z 365 " --> pdb=" O LYS Z 361 " (cutoff:3.500A) Processing helix chain 'Z' and resid 435 through 452 Processing helix chain 'Z' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEU Z 457 " --> pdb=" O LEU Z 454 " (cutoff:3.500A) Processing helix chain 'AA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRAA 238 " --> pdb=" O GLYAA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEAA 239 " --> pdb=" O METAA 235 " (cutoff:3.500A) Processing helix chain 'AA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSAA 266 " --> pdb=" O SERAA 262 " (cutoff:3.500A) Processing helix chain 'AA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEAA 286 " --> pdb=" O SERAA 282 " (cutoff:3.500A) Processing helix chain 'AA' and resid 340 through 358 Processing helix chain 'AA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRAA 365 " --> pdb=" O LYSAA 361 " (cutoff:3.500A) Processing helix chain 'AA' and resid 435 through 452 Processing helix chain 'AA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUAA 457 " --> pdb=" O LEUAA 454 " (cutoff:3.500A) Processing helix chain 'BA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRBA 238 " --> pdb=" O GLYBA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEBA 239 " --> pdb=" O METBA 235 " (cutoff:3.500A) Processing helix chain 'BA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSBA 266 " --> pdb=" O SERBA 262 " (cutoff:3.500A) Processing helix chain 'BA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEBA 286 " --> pdb=" O SERBA 282 " (cutoff:3.500A) Processing helix chain 'BA' and resid 340 through 358 Processing helix chain 'BA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRBA 365 " --> pdb=" O LYSBA 361 " (cutoff:3.500A) Processing helix chain 'BA' and resid 435 through 452 Processing helix chain 'BA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUBA 457 " --> pdb=" O LEUBA 454 " (cutoff:3.500A) Processing helix chain 'CA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRCA 238 " --> pdb=" O GLYCA 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILECA 239 " --> pdb=" O METCA 235 " (cutoff:3.500A) Processing helix chain 'CA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSCA 266 " --> pdb=" O SERCA 262 " (cutoff:3.500A) Processing helix chain 'CA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHECA 286 " --> pdb=" O SERCA 282 " (cutoff:3.500A) Processing helix chain 'CA' and resid 340 through 358 Processing helix chain 'CA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRCA 365 " --> pdb=" O LYSCA 361 " (cutoff:3.500A) Processing helix chain 'CA' and resid 435 through 452 Processing helix chain 'CA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUCA 457 " --> pdb=" O LEUCA 454 " (cutoff:3.500A) Processing helix chain 'DA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRDA 238 " --> pdb=" O GLYDA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEDA 239 " --> pdb=" O METDA 235 " (cutoff:3.500A) Processing helix chain 'DA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSDA 266 " --> pdb=" O SERDA 262 " (cutoff:3.500A) Processing helix chain 'DA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEDA 286 " --> pdb=" O SERDA 282 " (cutoff:3.500A) Processing helix chain 'DA' and resid 340 through 358 Processing helix chain 'DA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRDA 365 " --> pdb=" O LYSDA 361 " (cutoff:3.500A) Processing helix chain 'DA' and resid 435 through 452 Processing helix chain 'DA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUDA 457 " --> pdb=" O LEUDA 454 " (cutoff:3.500A) Processing helix chain 'EA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THREA 238 " --> pdb=" O GLYEA 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILEEA 239 " --> pdb=" O METEA 235 " (cutoff:3.500A) Processing helix chain 'EA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSEA 266 " --> pdb=" O SEREA 262 " (cutoff:3.500A) Processing helix chain 'EA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEEA 286 " --> pdb=" O SEREA 282 " (cutoff:3.500A) Processing helix chain 'EA' and resid 340 through 358 Processing helix chain 'EA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYREA 365 " --> pdb=" O LYSEA 361 " (cutoff:3.500A) Processing helix chain 'EA' and resid 435 through 452 Processing helix chain 'EA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUEA 457 " --> pdb=" O LEUEA 454 " (cutoff:3.500A) Processing helix chain 'FA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRFA 238 " --> pdb=" O GLYFA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEFA 239 " --> pdb=" O METFA 235 " (cutoff:3.500A) Processing helix chain 'FA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSFA 266 " --> pdb=" O SERFA 262 " (cutoff:3.500A) Processing helix chain 'FA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEFA 286 " --> pdb=" O SERFA 282 " (cutoff:3.500A) Processing helix chain 'FA' and resid 340 through 358 Processing helix chain 'FA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRFA 365 " --> pdb=" O LYSFA 361 " (cutoff:3.500A) Processing helix chain 'FA' and resid 435 through 452 Processing helix chain 'FA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUFA 457 " --> pdb=" O LEUFA 454 " (cutoff:3.500A) Processing helix chain 'GA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRGA 238 " --> pdb=" O GLYGA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEGA 239 " --> pdb=" O METGA 235 " (cutoff:3.500A) Processing helix chain 'GA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSGA 266 " --> pdb=" O SERGA 262 " (cutoff:3.500A) Processing helix chain 'GA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEGA 286 " --> pdb=" O SERGA 282 " (cutoff:3.500A) Processing helix chain 'GA' and resid 340 through 358 Processing helix chain 'GA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRGA 365 " --> pdb=" O LYSGA 361 " (cutoff:3.500A) Processing helix chain 'GA' and resid 435 through 452 Processing helix chain 'GA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUGA 457 " --> pdb=" O LEUGA 454 " (cutoff:3.500A) Processing helix chain 'HA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRHA 238 " --> pdb=" O GLYHA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEHA 239 " --> pdb=" O METHA 235 " (cutoff:3.500A) Processing helix chain 'HA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSHA 266 " --> pdb=" O SERHA 262 " (cutoff:3.500A) Processing helix chain 'HA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEHA 286 " --> pdb=" O SERHA 282 " (cutoff:3.500A) Processing helix chain 'HA' and resid 340 through 358 Processing helix chain 'HA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRHA 365 " --> pdb=" O LYSHA 361 " (cutoff:3.500A) Processing helix chain 'HA' and resid 435 through 452 Processing helix chain 'HA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUHA 457 " --> pdb=" O LEUHA 454 " (cutoff:3.500A) Processing helix chain 'IA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRIA 238 " --> pdb=" O GLYIA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEIA 239 " --> pdb=" O METIA 235 " (cutoff:3.500A) Processing helix chain 'IA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSIA 266 " --> pdb=" O SERIA 262 " (cutoff:3.500A) Processing helix chain 'IA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEIA 286 " --> pdb=" O SERIA 282 " (cutoff:3.500A) Processing helix chain 'IA' and resid 340 through 358 Processing helix chain 'IA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRIA 365 " --> pdb=" O LYSIA 361 " (cutoff:3.500A) Processing helix chain 'IA' and resid 435 through 452 Processing helix chain 'IA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUIA 457 " --> pdb=" O LEUIA 454 " (cutoff:3.500A) Processing helix chain 'JA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRJA 238 " --> pdb=" O GLYJA 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILEJA 239 " --> pdb=" O METJA 235 " (cutoff:3.500A) Processing helix chain 'JA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSJA 266 " --> pdb=" O SERJA 262 " (cutoff:3.500A) Processing helix chain 'JA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEJA 286 " --> pdb=" O SERJA 282 " (cutoff:3.500A) Processing helix chain 'JA' and resid 340 through 358 Processing helix chain 'JA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRJA 365 " --> pdb=" O LYSJA 361 " (cutoff:3.500A) Processing helix chain 'JA' and resid 435 through 452 Processing helix chain 'JA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUJA 457 " --> pdb=" O LEUJA 454 " (cutoff:3.500A) Processing helix chain 'KA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRKA 238 " --> pdb=" O GLYKA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEKA 239 " --> pdb=" O METKA 235 " (cutoff:3.500A) Processing helix chain 'KA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSKA 266 " --> pdb=" O SERKA 262 " (cutoff:3.500A) Processing helix chain 'KA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEKA 286 " --> pdb=" O SERKA 282 " (cutoff:3.500A) Processing helix chain 'KA' and resid 340 through 358 Processing helix chain 'KA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRKA 365 " --> pdb=" O LYSKA 361 " (cutoff:3.500A) Processing helix chain 'KA' and resid 435 through 452 Processing helix chain 'KA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUKA 457 " --> pdb=" O LEUKA 454 " (cutoff:3.500A) Processing helix chain 'LA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRLA 238 " --> pdb=" O GLYLA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILELA 239 " --> pdb=" O METLA 235 " (cutoff:3.500A) Processing helix chain 'LA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSLA 266 " --> pdb=" O SERLA 262 " (cutoff:3.500A) Processing helix chain 'LA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHELA 286 " --> pdb=" O SERLA 282 " (cutoff:3.500A) Processing helix chain 'LA' and resid 340 through 358 Processing helix chain 'LA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRLA 365 " --> pdb=" O LYSLA 361 " (cutoff:3.500A) Processing helix chain 'LA' and resid 435 through 452 Processing helix chain 'LA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEULA 457 " --> pdb=" O LEULA 454 " (cutoff:3.500A) Processing helix chain 'MA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRMA 238 " --> pdb=" O GLYMA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEMA 239 " --> pdb=" O METMA 235 " (cutoff:3.500A) Processing helix chain 'MA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSMA 266 " --> pdb=" O SERMA 262 " (cutoff:3.500A) Processing helix chain 'MA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEMA 286 " --> pdb=" O SERMA 282 " (cutoff:3.500A) Processing helix chain 'MA' and resid 340 through 358 Processing helix chain 'MA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRMA 365 " --> pdb=" O LYSMA 361 " (cutoff:3.500A) Processing helix chain 'MA' and resid 435 through 452 Processing helix chain 'MA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUMA 457 " --> pdb=" O LEUMA 454 " (cutoff:3.500A) Processing helix chain 'NA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRNA 238 " --> pdb=" O GLYNA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILENA 239 " --> pdb=" O METNA 235 " (cutoff:3.500A) Processing helix chain 'NA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSNA 266 " --> pdb=" O SERNA 262 " (cutoff:3.500A) Processing helix chain 'NA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHENA 286 " --> pdb=" O SERNA 282 " (cutoff:3.500A) Processing helix chain 'NA' and resid 340 through 358 Processing helix chain 'NA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRNA 365 " --> pdb=" O LYSNA 361 " (cutoff:3.500A) Processing helix chain 'NA' and resid 435 through 452 Processing helix chain 'NA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUNA 457 " --> pdb=" O LEUNA 454 " (cutoff:3.500A) Processing helix chain 'OA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THROA 238 " --> pdb=" O GLYOA 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILEOA 239 " --> pdb=" O METOA 235 " (cutoff:3.500A) Processing helix chain 'OA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSOA 266 " --> pdb=" O SEROA 262 " (cutoff:3.500A) Processing helix chain 'OA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEOA 286 " --> pdb=" O SEROA 282 " (cutoff:3.500A) Processing helix chain 'OA' and resid 340 through 358 Processing helix chain 'OA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYROA 365 " --> pdb=" O LYSOA 361 " (cutoff:3.500A) Processing helix chain 'OA' and resid 435 through 452 Processing helix chain 'OA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUOA 457 " --> pdb=" O LEUOA 454 " (cutoff:3.500A) Processing helix chain 'PA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRPA 238 " --> pdb=" O GLYPA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEPA 239 " --> pdb=" O METPA 235 " (cutoff:3.500A) Processing helix chain 'PA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSPA 266 " --> pdb=" O SERPA 262 " (cutoff:3.500A) Processing helix chain 'PA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEPA 286 " --> pdb=" O SERPA 282 " (cutoff:3.500A) Processing helix chain 'PA' and resid 340 through 358 Processing helix chain 'PA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRPA 365 " --> pdb=" O LYSPA 361 " (cutoff:3.500A) Processing helix chain 'PA' and resid 435 through 452 Processing helix chain 'PA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUPA 457 " --> pdb=" O LEUPA 454 " (cutoff:3.500A) Processing helix chain 'QA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRQA 238 " --> pdb=" O GLYQA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEQA 239 " --> pdb=" O METQA 235 " (cutoff:3.500A) Processing helix chain 'QA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSQA 266 " --> pdb=" O SERQA 262 " (cutoff:3.500A) Processing helix chain 'QA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEQA 286 " --> pdb=" O SERQA 282 " (cutoff:3.500A) Processing helix chain 'QA' and resid 340 through 358 Processing helix chain 'QA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRQA 365 " --> pdb=" O LYSQA 361 " (cutoff:3.500A) Processing helix chain 'QA' and resid 435 through 452 Processing helix chain 'QA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUQA 457 " --> pdb=" O LEUQA 454 " (cutoff:3.500A) Processing helix chain 'RA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRRA 238 " --> pdb=" O GLYRA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILERA 239 " --> pdb=" O METRA 235 " (cutoff:3.500A) Processing helix chain 'RA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSRA 266 " --> pdb=" O SERRA 262 " (cutoff:3.500A) Processing helix chain 'RA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHERA 286 " --> pdb=" O SERRA 282 " (cutoff:3.500A) Processing helix chain 'RA' and resid 340 through 358 Processing helix chain 'RA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRRA 365 " --> pdb=" O LYSRA 361 " (cutoff:3.500A) Processing helix chain 'RA' and resid 435 through 452 Processing helix chain 'RA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEURA 457 " --> pdb=" O LEURA 454 " (cutoff:3.500A) Processing helix chain 'SA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRSA 238 " --> pdb=" O GLYSA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILESA 239 " --> pdb=" O METSA 235 " (cutoff:3.500A) Processing helix chain 'SA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSSA 266 " --> pdb=" O SERSA 262 " (cutoff:3.500A) Processing helix chain 'SA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHESA 286 " --> pdb=" O SERSA 282 " (cutoff:3.500A) Processing helix chain 'SA' and resid 340 through 358 Processing helix chain 'SA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRSA 365 " --> pdb=" O LYSSA 361 " (cutoff:3.500A) Processing helix chain 'SA' and resid 435 through 452 Processing helix chain 'SA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUSA 457 " --> pdb=" O LEUSA 454 " (cutoff:3.500A) Processing helix chain 'TA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRTA 238 " --> pdb=" O GLYTA 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILETA 239 " --> pdb=" O METTA 235 " (cutoff:3.500A) Processing helix chain 'TA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSTA 266 " --> pdb=" O SERTA 262 " (cutoff:3.500A) Processing helix chain 'TA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHETA 286 " --> pdb=" O SERTA 282 " (cutoff:3.500A) Processing helix chain 'TA' and resid 340 through 358 Processing helix chain 'TA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRTA 365 " --> pdb=" O LYSTA 361 " (cutoff:3.500A) Processing helix chain 'TA' and resid 435 through 452 Processing helix chain 'TA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUTA 457 " --> pdb=" O LEUTA 454 " (cutoff:3.500A) Processing helix chain 'UA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRUA 238 " --> pdb=" O GLYUA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEUA 239 " --> pdb=" O METUA 235 " (cutoff:3.500A) Processing helix chain 'UA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSUA 266 " --> pdb=" O SERUA 262 " (cutoff:3.500A) Processing helix chain 'UA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEUA 286 " --> pdb=" O SERUA 282 " (cutoff:3.500A) Processing helix chain 'UA' and resid 340 through 358 Processing helix chain 'UA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRUA 365 " --> pdb=" O LYSUA 361 " (cutoff:3.500A) Processing helix chain 'UA' and resid 435 through 452 Processing helix chain 'UA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUUA 457 " --> pdb=" O LEUUA 454 " (cutoff:3.500A) Processing helix chain 'VA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRVA 238 " --> pdb=" O GLYVA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEVA 239 " --> pdb=" O METVA 235 " (cutoff:3.500A) Processing helix chain 'VA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSVA 266 " --> pdb=" O SERVA 262 " (cutoff:3.500A) Processing helix chain 'VA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEVA 286 " --> pdb=" O SERVA 282 " (cutoff:3.500A) Processing helix chain 'VA' and resid 340 through 358 Processing helix chain 'VA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRVA 365 " --> pdb=" O LYSVA 361 " (cutoff:3.500A) Processing helix chain 'VA' and resid 435 through 452 Processing helix chain 'VA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUVA 457 " --> pdb=" O LEUVA 454 " (cutoff:3.500A) Processing helix chain 'WA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRWA 238 " --> pdb=" O GLYWA 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEWA 239 " --> pdb=" O METWA 235 " (cutoff:3.500A) Processing helix chain 'WA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSWA 266 " --> pdb=" O SERWA 262 " (cutoff:3.500A) Processing helix chain 'WA' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEWA 286 " --> pdb=" O SERWA 282 " (cutoff:3.500A) Processing helix chain 'WA' and resid 340 through 358 Processing helix chain 'WA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRWA 365 " --> pdb=" O LYSWA 361 " (cutoff:3.500A) Processing helix chain 'WA' and resid 435 through 452 Processing helix chain 'WA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUWA 457 " --> pdb=" O LEUWA 454 " (cutoff:3.500A) Processing helix chain 'XA' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRXA 238 " --> pdb=" O GLYXA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEXA 239 " --> pdb=" O METXA 235 " (cutoff:3.500A) Processing helix chain 'XA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSXA 266 " --> pdb=" O SERXA 262 " (cutoff:3.500A) Processing helix chain 'XA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEXA 286 " --> pdb=" O SERXA 282 " (cutoff:3.500A) Processing helix chain 'XA' and resid 340 through 358 Processing helix chain 'XA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRXA 365 " --> pdb=" O LYSXA 361 " (cutoff:3.500A) Processing helix chain 'XA' and resid 435 through 452 Processing helix chain 'XA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUXA 457 " --> pdb=" O LEUXA 454 " (cutoff:3.500A) Processing helix chain 'YA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRYA 238 " --> pdb=" O GLYYA 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILEYA 239 " --> pdb=" O METYA 235 " (cutoff:3.500A) Processing helix chain 'YA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSYA 266 " --> pdb=" O SERYA 262 " (cutoff:3.500A) Processing helix chain 'YA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEYA 286 " --> pdb=" O SERYA 282 " (cutoff:3.500A) Processing helix chain 'YA' and resid 340 through 358 Processing helix chain 'YA' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRYA 365 " --> pdb=" O LYSYA 361 " (cutoff:3.500A) Processing helix chain 'YA' and resid 435 through 452 Processing helix chain 'YA' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUYA 457 " --> pdb=" O LEUYA 454 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRZA 238 " --> pdb=" O GLYZA 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEZA 239 " --> pdb=" O METZA 235 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSZA 266 " --> pdb=" O SERZA 262 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEZA 286 " --> pdb=" O SERZA 282 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 340 through 358 Processing helix chain 'ZA' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRZA 365 " --> pdb=" O LYSZA 361 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 435 through 452 Processing helix chain 'ZA' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUZA 457 " --> pdb=" O LEUZA 454 " (cutoff:3.500A) Processing helix chain 'AB' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRAB 238 " --> pdb=" O GLYAB 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEAB 239 " --> pdb=" O METAB 235 " (cutoff:3.500A) Processing helix chain 'AB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSAB 266 " --> pdb=" O SERAB 262 " (cutoff:3.500A) Processing helix chain 'AB' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEAB 286 " --> pdb=" O SERAB 282 " (cutoff:3.500A) Processing helix chain 'AB' and resid 340 through 358 Processing helix chain 'AB' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRAB 365 " --> pdb=" O LYSAB 361 " (cutoff:3.500A) Processing helix chain 'AB' and resid 435 through 452 Processing helix chain 'AB' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUAB 457 " --> pdb=" O LEUAB 454 " (cutoff:3.500A) Processing helix chain 'BB' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRBB 238 " --> pdb=" O GLYBB 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEBB 239 " --> pdb=" O METBB 235 " (cutoff:3.500A) Processing helix chain 'BB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSBB 266 " --> pdb=" O SERBB 262 " (cutoff:3.500A) Processing helix chain 'BB' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEBB 286 " --> pdb=" O SERBB 282 " (cutoff:3.500A) Processing helix chain 'BB' and resid 340 through 358 Processing helix chain 'BB' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRBB 365 " --> pdb=" O LYSBB 361 " (cutoff:3.500A) Processing helix chain 'BB' and resid 435 through 452 Processing helix chain 'BB' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUBB 457 " --> pdb=" O LEUBB 454 " (cutoff:3.500A) Processing helix chain 'CB' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRCB 238 " --> pdb=" O GLYCB 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILECB 239 " --> pdb=" O METCB 235 " (cutoff:3.500A) Processing helix chain 'CB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSCB 266 " --> pdb=" O SERCB 262 " (cutoff:3.500A) Processing helix chain 'CB' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHECB 286 " --> pdb=" O SERCB 282 " (cutoff:3.500A) Processing helix chain 'CB' and resid 340 through 358 Processing helix chain 'CB' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRCB 365 " --> pdb=" O LYSCB 361 " (cutoff:3.500A) Processing helix chain 'CB' and resid 435 through 452 Processing helix chain 'CB' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUCB 457 " --> pdb=" O LEUCB 454 " (cutoff:3.500A) Processing helix chain 'DB' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRDB 238 " --> pdb=" O GLYDB 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILEDB 239 " --> pdb=" O METDB 235 " (cutoff:3.500A) Processing helix chain 'DB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSDB 266 " --> pdb=" O SERDB 262 " (cutoff:3.500A) Processing helix chain 'DB' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEDB 286 " --> pdb=" O SERDB 282 " (cutoff:3.500A) Processing helix chain 'DB' and resid 340 through 358 Processing helix chain 'DB' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRDB 365 " --> pdb=" O LYSDB 361 " (cutoff:3.500A) Processing helix chain 'DB' and resid 435 through 452 Processing helix chain 'DB' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUDB 457 " --> pdb=" O LEUDB 454 " (cutoff:3.500A) Processing helix chain 'EB' and resid 234 through 250 removed outlier: 3.841A pdb=" N THREB 238 " --> pdb=" O GLYEB 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEEB 239 " --> pdb=" O METEB 235 " (cutoff:3.500A) Processing helix chain 'EB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSEB 266 " --> pdb=" O SEREB 262 " (cutoff:3.500A) Processing helix chain 'EB' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEEB 286 " --> pdb=" O SEREB 282 " (cutoff:3.500A) Processing helix chain 'EB' and resid 340 through 358 Processing helix chain 'EB' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYREB 365 " --> pdb=" O LYSEB 361 " (cutoff:3.500A) Processing helix chain 'EB' and resid 435 through 452 Processing helix chain 'EB' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUEB 457 " --> pdb=" O LEUEB 454 " (cutoff:3.500A) Processing helix chain 'FB' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRFB 238 " --> pdb=" O GLYFB 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEFB 239 " --> pdb=" O METFB 235 " (cutoff:3.500A) Processing helix chain 'FB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSFB 266 " --> pdb=" O SERFB 262 " (cutoff:3.500A) Processing helix chain 'FB' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEFB 286 " --> pdb=" O SERFB 282 " (cutoff:3.500A) Processing helix chain 'FB' and resid 340 through 358 Processing helix chain 'FB' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRFB 365 " --> pdb=" O LYSFB 361 " (cutoff:3.500A) Processing helix chain 'FB' and resid 435 through 452 Processing helix chain 'FB' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUFB 457 " --> pdb=" O LEUFB 454 " (cutoff:3.500A) Processing helix chain 'GB' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRGB 238 " --> pdb=" O GLYGB 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEGB 239 " --> pdb=" O METGB 235 " (cutoff:3.500A) Processing helix chain 'GB' and resid 261 through 274 removed outlier: 3.640A pdb=" N LYSGB 266 " --> pdb=" O SERGB 262 " (cutoff:3.500A) Processing helix chain 'GB' and resid 282 through 298 removed outlier: 3.909A pdb=" N PHEGB 286 " --> pdb=" O SERGB 282 " (cutoff:3.500A) Processing helix chain 'GB' and resid 340 through 358 Processing helix chain 'GB' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRGB 365 " --> pdb=" O LYSGB 361 " (cutoff:3.500A) Processing helix chain 'GB' and resid 435 through 452 Processing helix chain 'GB' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUGB 457 " --> pdb=" O LEUGB 454 " (cutoff:3.500A) Processing helix chain 'HB' and resid 234 through 250 removed outlier: 3.840A pdb=" N THRHB 238 " --> pdb=" O GLYHB 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEHB 239 " --> pdb=" O METHB 235 " (cutoff:3.500A) Processing helix chain 'HB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSHB 266 " --> pdb=" O SERHB 262 " (cutoff:3.500A) Processing helix chain 'HB' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEHB 286 " --> pdb=" O SERHB 282 " (cutoff:3.500A) Processing helix chain 'HB' and resid 340 through 358 Processing helix chain 'HB' and resid 361 through 366 removed outlier: 3.785A pdb=" N TYRHB 365 " --> pdb=" O LYSHB 361 " (cutoff:3.500A) Processing helix chain 'HB' and resid 435 through 452 Processing helix chain 'HB' and resid 453 through 457 removed outlier: 3.509A pdb=" N LEUHB 457 " --> pdb=" O LEUHB 454 " (cutoff:3.500A) Processing helix chain 'IB' and resid 234 through 250 removed outlier: 3.841A pdb=" N THRIB 238 " --> pdb=" O GLYIB 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILEIB 239 " --> pdb=" O METIB 235 " (cutoff:3.500A) Processing helix chain 'IB' and resid 261 through 274 removed outlier: 3.641A pdb=" N LYSIB 266 " --> pdb=" O SERIB 262 " (cutoff:3.500A) Processing helix chain 'IB' and resid 282 through 298 removed outlier: 3.908A pdb=" N PHEIB 286 " --> pdb=" O SERIB 282 " (cutoff:3.500A) Processing helix chain 'IB' and resid 340 through 358 Processing helix chain 'IB' and resid 361 through 366 removed outlier: 3.784A pdb=" N TYRIB 365 " --> pdb=" O LYSIB 361 " (cutoff:3.500A) Processing helix chain 'IB' and resid 435 through 452 Processing helix chain 'IB' and resid 453 through 457 removed outlier: 3.508A pdb=" N LEUIB 457 " --> pdb=" O LEUIB 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER A 371 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER A 371 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.750A pdb=" N SER X 371 " --> pdb=" O ALA X 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 383 through 384 Processing sheet with id=AA6, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.749A pdb=" N SER B 371 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.749A pdb=" N SER B 371 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 324 Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERQA 371 " --> pdb=" O ALAQA 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AB2, first strand: chain 'C' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER C 371 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER C 371 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 322 through 324 Processing sheet with id=AB5, first strand: chain 'C' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERYA 371 " --> pdb=" O ALAYA 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=AB7, first strand: chain 'D' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER D 371 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER D 371 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AC1, first strand: chain 'D' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERIA 371 " --> pdb=" O ALAIA 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 383 through 384 Processing sheet with id=AC3, first strand: chain 'E' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER E 371 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER E 371 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 322 through 324 Processing sheet with id=AC6, first strand: chain 'E' and resid 383 through 384 removed outlier: 3.750A pdb=" N SER F 371 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 383 through 384 Processing sheet with id=AC8, first strand: chain 'F' and resid 322 through 324 Processing sheet with id=AC9, first strand: chain 'F' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERHA 371 " --> pdb=" O ALAHA 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 383 through 384 Processing sheet with id=AD2, first strand: chain 'G' and resid 332 through 333 removed outlier: 3.749A pdb=" N SER G 371 " --> pdb=" O ALA G 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 332 through 333 removed outlier: 3.749A pdb=" N SER G 371 " --> pdb=" O ALA G 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 322 through 324 Processing sheet with id=AD5, first strand: chain 'G' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERFB 371 " --> pdb=" O ALAFB 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 383 through 384 Processing sheet with id=AD7, first strand: chain 'H' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER H 371 " --> pdb=" O ALA H 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER H 371 " --> pdb=" O ALA H 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 322 through 324 Processing sheet with id=AE1, first strand: chain 'H' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERDB 371 " --> pdb=" O ALADB 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 383 through 384 Processing sheet with id=AE3, first strand: chain 'I' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER I 371 " --> pdb=" O ALA I 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER I 371 " --> pdb=" O ALA I 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 322 through 324 Processing sheet with id=AE6, first strand: chain 'I' and resid 383 through 384 removed outlier: 3.750A pdb=" N SER Y 371 " --> pdb=" O ALA Y 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 383 through 384 Processing sheet with id=AE8, first strand: chain 'J' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER J 371 " --> pdb=" O ALA J 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER J 371 " --> pdb=" O ALA J 394 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 322 through 324 Processing sheet with id=AF2, first strand: chain 'K' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER K 371 " --> pdb=" O ALA K 394 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER K 371 " --> pdb=" O ALA K 394 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 322 through 324 Processing sheet with id=AF5, first strand: chain 'K' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERMA 371 " --> pdb=" O ALAMA 394 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 383 through 384 Processing sheet with id=AF7, first strand: chain 'L' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER L 371 " --> pdb=" O ALA L 394 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER L 371 " --> pdb=" O ALA L 394 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 322 through 324 Processing sheet with id=AG1, first strand: chain 'L' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERVA 371 " --> pdb=" O ALAVA 394 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 383 through 384 Processing sheet with id=AG3, first strand: chain 'M' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER M 371 " --> pdb=" O ALA M 394 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER M 371 " --> pdb=" O ALA M 394 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 322 through 324 Processing sheet with id=AG6, first strand: chain 'M' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERTA 371 " --> pdb=" O ALATA 394 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 383 through 384 Processing sheet with id=AG8, first strand: chain 'N' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER N 371 " --> pdb=" O ALA N 394 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER N 371 " --> pdb=" O ALA N 394 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 322 through 324 Processing sheet with id=AH2, first strand: chain 'N' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERDA 371 " --> pdb=" O ALADA 394 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 383 through 384 Processing sheet with id=AH4, first strand: chain 'O' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER O 371 " --> pdb=" O ALA O 394 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER O 371 " --> pdb=" O ALA O 394 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 322 through 324 Processing sheet with id=AH7, first strand: chain 'O' and resid 383 through 384 removed outlier: 3.750A pdb=" N SER P 371 " --> pdb=" O ALA P 394 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 383 through 384 Processing sheet with id=AH9, first strand: chain 'P' and resid 322 through 324 Processing sheet with id=AI1, first strand: chain 'P' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERCA 371 " --> pdb=" O ALACA 394 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 383 through 384 Processing sheet with id=AI3, first strand: chain 'Q' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER Q 371 " --> pdb=" O ALA Q 394 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER Q 371 " --> pdb=" O ALA Q 394 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 322 through 324 Processing sheet with id=AI6, first strand: chain 'Q' and resid 383 through 384 removed outlier: 3.749A pdb=" N SERAB 371 " --> pdb=" O ALAAB 394 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 383 through 384 Processing sheet with id=AI8, first strand: chain 'R' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER R 371 " --> pdb=" O ALA R 394 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER R 371 " --> pdb=" O ALA R 394 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'R' and resid 322 through 324 Processing sheet with id=AJ2, first strand: chain 'R' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERIB 371 " --> pdb=" O ALAIB 394 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 383 through 384 Processing sheet with id=AJ4, first strand: chain 'S' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER S 371 " --> pdb=" O ALA S 394 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER S 371 " --> pdb=" O ALA S 394 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'S' and resid 322 through 324 Processing sheet with id=AJ7, first strand: chain 'S' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERNA 371 " --> pdb=" O ALANA 394 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 383 through 384 Processing sheet with id=AJ9, first strand: chain 'T' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER T 371 " --> pdb=" O ALA T 394 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER T 371 " --> pdb=" O ALA T 394 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 322 through 324 Processing sheet with id=AK3, first strand: chain 'V' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER V 371 " --> pdb=" O ALA V 394 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'V' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER V 371 " --> pdb=" O ALA V 394 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'V' and resid 322 through 324 Processing sheet with id=AK6, first strand: chain 'V' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERRA 371 " --> pdb=" O ALARA 394 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'V' and resid 383 through 384 Processing sheet with id=AK8, first strand: chain 'W' and resid 332 through 333 removed outlier: 3.749A pdb=" N SER W 371 " --> pdb=" O ALA W 394 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'W' and resid 332 through 333 removed outlier: 3.749A pdb=" N SER W 371 " --> pdb=" O ALA W 394 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'W' and resid 322 through 324 Processing sheet with id=AL2, first strand: chain 'X' and resid 322 through 324 Processing sheet with id=AL3, first strand: chain 'Y' and resid 322 through 324 Processing sheet with id=AL4, first strand: chain 'Y' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERCB 371 " --> pdb=" O ALACB 394 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Y' and resid 383 through 384 Processing sheet with id=AL6, first strand: chain 'Z' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER Z 371 " --> pdb=" O ALA Z 394 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Z' and resid 332 through 333 removed outlier: 3.750A pdb=" N SER Z 371 " --> pdb=" O ALA Z 394 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'Z' and resid 322 through 324 Processing sheet with id=AL9, first strand: chain 'Z' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERAA 371 " --> pdb=" O ALAAA 394 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Z' and resid 383 through 384 Processing sheet with id=AM2, first strand: chain 'AA' and resid 322 through 324 Processing sheet with id=AM3, first strand: chain 'AA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERBB 371 " --> pdb=" O ALABB 394 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'AA' and resid 383 through 384 Processing sheet with id=AM5, first strand: chain 'BA' and resid 332 through 333 removed outlier: 3.749A pdb=" N SERBA 371 " --> pdb=" O ALABA 394 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'BA' and resid 332 through 333 removed outlier: 3.749A pdb=" N SERBA 371 " --> pdb=" O ALABA 394 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'BA' and resid 322 through 324 Processing sheet with id=AM8, first strand: chain 'CA' and resid 322 through 324 Processing sheet with id=AM9, first strand: chain 'DA' and resid 322 through 324 Processing sheet with id=AN1, first strand: chain 'DA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERSA 371 " --> pdb=" O ALASA 394 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'DA' and resid 383 through 384 Processing sheet with id=AN3, first strand: chain 'EA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SEREA 371 " --> pdb=" O ALAEA 394 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'EA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SEREA 371 " --> pdb=" O ALAEA 394 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'EA' and resid 322 through 324 Processing sheet with id=AN6, first strand: chain 'FA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERFA 371 " --> pdb=" O ALAFA 394 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'FA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERFA 371 " --> pdb=" O ALAFA 394 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'FA' and resid 322 through 324 Processing sheet with id=AN9, first strand: chain 'FA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERGB 371 " --> pdb=" O ALAGB 394 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'FA' and resid 383 through 384 Processing sheet with id=AO2, first strand: chain 'GA' and resid 332 through 333 removed outlier: 3.749A pdb=" N SERGA 371 " --> pdb=" O ALAGA 394 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'GA' and resid 332 through 333 removed outlier: 3.749A pdb=" N SERGA 371 " --> pdb=" O ALAGA 394 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'GA' and resid 322 through 324 Processing sheet with id=AO5, first strand: chain 'HA' and resid 322 through 324 Processing sheet with id=AO6, first strand: chain 'IA' and resid 322 through 324 Processing sheet with id=AO7, first strand: chain 'IA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERXA 371 " --> pdb=" O ALAXA 394 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'IA' and resid 383 through 384 Processing sheet with id=AO9, first strand: chain 'JA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERJA 371 " --> pdb=" O ALAJA 394 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'JA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERJA 371 " --> pdb=" O ALAJA 394 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'JA' and resid 322 through 324 Processing sheet with id=AP3, first strand: chain 'JA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERKA 371 " --> pdb=" O ALAKA 394 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'JA' and resid 383 through 384 Processing sheet with id=AP5, first strand: chain 'KA' and resid 322 through 324 Processing sheet with id=AP6, first strand: chain 'KA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERWA 371 " --> pdb=" O ALAWA 394 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'KA' and resid 383 through 384 Processing sheet with id=AP8, first strand: chain 'LA' and resid 332 through 333 removed outlier: 3.749A pdb=" N SERLA 371 " --> pdb=" O ALALA 394 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'LA' and resid 332 through 333 removed outlier: 3.749A pdb=" N SERLA 371 " --> pdb=" O ALALA 394 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'LA' and resid 322 through 324 Processing sheet with id=AQ2, first strand: chain 'MA' and resid 322 through 324 Processing sheet with id=AQ3, first strand: chain 'NA' and resid 322 through 324 Processing sheet with id=AQ4, first strand: chain 'NA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERHB 371 " --> pdb=" O ALAHB 394 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'NA' and resid 383 through 384 Processing sheet with id=AQ6, first strand: chain 'OA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SEROA 371 " --> pdb=" O ALAOA 394 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'OA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SEROA 371 " --> pdb=" O ALAOA 394 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'OA' and resid 322 through 324 Processing sheet with id=AQ9, first strand: chain 'PA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERPA 371 " --> pdb=" O ALAPA 394 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'PA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERPA 371 " --> pdb=" O ALAPA 394 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'PA' and resid 322 through 324 Processing sheet with id=AR3, first strand: chain 'QA' and resid 322 through 324 Processing sheet with id=AR4, first strand: chain 'RA' and resid 322 through 324 Processing sheet with id=AR5, first strand: chain 'SA' and resid 322 through 324 Processing sheet with id=AR6, first strand: chain 'TA' and resid 322 through 324 Processing sheet with id=AR7, first strand: chain 'TA' and resid 383 through 384 removed outlier: 3.750A pdb=" N SERUA 371 " --> pdb=" O ALAUA 394 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'TA' and resid 383 through 384 Processing sheet with id=AR9, first strand: chain 'UA' and resid 322 through 324 Processing sheet with id=AS1, first strand: chain 'VA' and resid 322 through 324 Processing sheet with id=AS2, first strand: chain 'WA' and resid 322 through 324 Processing sheet with id=AS3, first strand: chain 'XA' and resid 322 through 324 Processing sheet with id=AS4, first strand: chain 'YA' and resid 322 through 324 Processing sheet with id=AS5, first strand: chain 'ZA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERZA 371 " --> pdb=" O ALAZA 394 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'ZA' and resid 332 through 333 removed outlier: 3.750A pdb=" N SERZA 371 " --> pdb=" O ALAZA 394 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'ZA' and resid 322 through 324 Processing sheet with id=AS8, first strand: chain 'AB' and resid 322 through 324 Processing sheet with id=AS9, first strand: chain 'BB' and resid 322 through 324 Processing sheet with id=AT1, first strand: chain 'CB' and resid 322 through 324 Processing sheet with id=AT2, first strand: chain 'DB' and resid 322 through 324 Processing sheet with id=AT3, first strand: chain 'DB' and resid 383 through 384 removed outlier: 3.750A pdb=" N SEREB 371 " --> pdb=" O ALAEB 394 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'DB' and resid 383 through 384 Processing sheet with id=AT5, first strand: chain 'EB' and resid 322 through 324 Processing sheet with id=AT6, first strand: chain 'FB' and resid 322 through 324 Processing sheet with id=AT7, first strand: chain 'GB' and resid 322 through 324 Processing sheet with id=AT8, first strand: chain 'HB' and resid 322 through 324 Processing sheet with id=AT9, first strand: chain 'IB' and resid 322 through 324 6390 hydrogen bonds defined for protein. 17910 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: 64.89 Time building geometry restraints manager: 34.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 27318 1.33 - 1.45: 15630 1.45 - 1.57: 63312 1.57 - 1.68: 0 1.68 - 1.80: 480 Bond restraints: 106740 Sorted by residual: bond pdb=" C GLN A 402 " pdb=" O GLN A 402 " ideal model delta sigma weight residual 1.234 1.216 0.018 1.24e-02 6.50e+03 2.10e+00 bond pdb=" C GLN K 402 " pdb=" O GLN K 402 " ideal model delta sigma weight residual 1.234 1.216 0.018 1.24e-02 6.50e+03 2.10e+00 bond pdb=" C GLNFA 402 " pdb=" O GLNFA 402 " ideal model delta sigma weight residual 1.234 1.216 0.018 1.24e-02 6.50e+03 2.10e+00 bond pdb=" C GLNUA 402 " pdb=" O GLNUA 402 " ideal model delta sigma weight residual 1.234 1.216 0.018 1.24e-02 6.50e+03 2.10e+00 bond pdb=" C GLN F 402 " pdb=" O GLN F 402 " ideal model delta sigma weight residual 1.234 1.216 0.018 1.24e-02 6.50e+03 2.10e+00 ... (remaining 106735 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.18: 2940 106.18 - 113.14: 60921 113.14 - 120.09: 34042 120.09 - 127.05: 45725 127.05 - 134.01: 1152 Bond angle restraints: 144780 Sorted by residual: angle pdb=" CA GLU R 411 " pdb=" CB GLU R 411 " pdb=" CG GLU R 411 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.49e+00 angle pdb=" CA GLU C 411 " pdb=" CB GLU C 411 " pdb=" CG GLU C 411 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.49e+00 angle pdb=" CA GLUHA 411 " pdb=" CB GLUHA 411 " pdb=" CG GLUHA 411 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.49e+00 angle pdb=" CA GLUCA 411 " pdb=" CB GLUCA 411 " pdb=" CG GLUCA 411 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.49e+00 angle pdb=" CA GLURA 411 " pdb=" CB GLURA 411 " pdb=" CG GLURA 411 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.49e+00 ... (remaining 144775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 58394 14.68 - 29.35: 5521 29.35 - 44.03: 1305 44.03 - 58.70: 300 58.70 - 73.38: 60 Dihedral angle restraints: 65580 sinusoidal: 25740 harmonic: 39840 Sorted by residual: dihedral pdb=" CA ASPIA 307 " pdb=" CB ASPIA 307 " pdb=" CG ASPIA 307 " pdb=" OD1 ASPIA 307 " ideal model delta sinusoidal sigma weight residual -30.00 -86.50 56.50 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP Z 307 " pdb=" CB ASP Z 307 " pdb=" CG ASP Z 307 " pdb=" OD1 ASP Z 307 " ideal model delta sinusoidal sigma weight residual -30.00 -86.49 56.49 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASPEA 307 " pdb=" CB ASPEA 307 " pdb=" CG ASPEA 307 " pdb=" OD1 ASPEA 307 " ideal model delta sinusoidal sigma weight residual -30.00 -86.49 56.49 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 65577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 10964 0.038 - 0.075: 3970 0.075 - 0.113: 1845 0.113 - 0.150: 381 0.150 - 0.188: 120 Chirality restraints: 17280 Sorted by residual: chirality pdb=" CB VALLA 309 " pdb=" CA VALLA 309 " pdb=" CG1 VALLA 309 " pdb=" CG2 VALLA 309 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB VALVA 309 " pdb=" CA VALVA 309 " pdb=" CG1 VALVA 309 " pdb=" CG2 VALVA 309 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB VAL W 309 " pdb=" CA VAL W 309 " pdb=" CG1 VAL W 309 " pdb=" CG2 VAL W 309 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 17277 not shown) Planarity restraints: 18540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALGA 230 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PROGA 231 " -0.084 5.00e-02 4.00e+02 pdb=" CA PROGA 231 " 0.025 5.00e-02 4.00e+02 pdb=" CD PROGA 231 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL W 230 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO W 231 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO W 231 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO W 231 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 230 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO G 231 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 231 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 231 " 0.027 5.00e-02 4.00e+02 ... (remaining 18537 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 33960 2.86 - 3.37: 89565 3.37 - 3.88: 173353 3.88 - 4.39: 189216 4.39 - 4.90: 336524 Nonbonded interactions: 822618 Sorted by model distance: nonbonded pdb=" O SERGA 274 " pdb=" OG SERGA 274 " model vdw 2.346 2.440 nonbonded pdb=" O SER W 274 " pdb=" OG SER W 274 " model vdw 2.346 2.440 nonbonded pdb=" O SERLA 274 " pdb=" OG SERLA 274 " model vdw 2.346 2.440 nonbonded pdb=" O SERQA 274 " pdb=" OG SERQA 274 " model vdw 2.346 2.440 nonbonded pdb=" O SER Q 274 " pdb=" OG SER Q 274 " model vdw 2.346 2.440 ... (remaining 822613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.140 Extract box with map and model: 15.160 Check model and map are aligned: 1.140 Set scattering table: 0.720 Process input model: 237.100 Find NCS groups from input model: 5.900 Set up NCS constraints: 1.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.004 0.042 106740 Z= 0.242 Angle : 0.741 7.916 144780 Z= 0.425 Chirality : 0.049 0.188 17280 Planarity : 0.006 0.049 18540 Dihedral : 12.549 73.379 39780 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.52 % Allowed : 7.25 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.13 (0.06), residues: 13800 helix: -1.37 (0.05), residues: 4920 sheet: -0.66 (0.08), residues: 2760 loop : -1.70 (0.07), residues: 6120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 419 HIS 0.001 0.001 HIS Z 252 PHE 0.014 0.002 PHE M 253 TYR 0.008 0.002 TYRIB 365 ARG 0.002 0.000 ARG O 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2340 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 2280 time to evaluate : 9.275 Fit side-chains REVERT: A 245 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6238 (mt-10) REVERT: A 291 MET cc_start: 0.8552 (mtp) cc_final: 0.8234 (mtp) REVERT: A 310 ILE cc_start: 0.8367 (mm) cc_final: 0.7870 (tt) REVERT: A 402 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: A 452 ASN cc_start: 0.8123 (m110) cc_final: 0.7855 (m-40) REVERT: B 310 ILE cc_start: 0.8226 (mm) cc_final: 0.7673 (tt) REVERT: B 402 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: C 310 ILE cc_start: 0.8286 (mm) cc_final: 0.7726 (tt) REVERT: E 389 ASN cc_start: 0.8679 (m110) cc_final: 0.8374 (m110) REVERT: F 245 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6243 (mt-10) REVERT: F 291 MET cc_start: 0.8549 (mtp) cc_final: 0.8235 (mtp) REVERT: F 310 ILE cc_start: 0.8364 (mm) cc_final: 0.7867 (tt) REVERT: F 402 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: F 452 ASN cc_start: 0.8115 (m110) cc_final: 0.7847 (m-40) REVERT: G 310 ILE cc_start: 0.8220 (mm) cc_final: 0.7670 (tt) REVERT: G 402 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: H 310 ILE cc_start: 0.8281 (mm) cc_final: 0.7720 (tt) REVERT: J 389 ASN cc_start: 0.8680 (m110) cc_final: 0.8372 (m110) REVERT: K 245 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6240 (mt-10) REVERT: K 291 MET cc_start: 0.8551 (mtp) cc_final: 0.8237 (mtp) REVERT: K 310 ILE cc_start: 0.8364 (mm) cc_final: 0.7870 (tt) REVERT: K 402 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: K 452 ASN cc_start: 0.8116 (m110) cc_final: 0.7847 (m-40) REVERT: L 310 ILE cc_start: 0.8224 (mm) cc_final: 0.7671 (tt) REVERT: L 402 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: M 310 ILE cc_start: 0.8286 (mm) cc_final: 0.7728 (tt) REVERT: O 389 ASN cc_start: 0.8677 (m110) cc_final: 0.8370 (m110) REVERT: P 245 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6239 (mt-10) REVERT: P 291 MET cc_start: 0.8551 (mtp) cc_final: 0.8238 (mtp) REVERT: P 310 ILE cc_start: 0.8362 (mm) cc_final: 0.7866 (tt) REVERT: P 402 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: P 452 ASN cc_start: 0.8122 (m110) cc_final: 0.7852 (m-40) REVERT: Q 310 ILE cc_start: 0.8224 (mm) cc_final: 0.7672 (tt) REVERT: Q 402 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: R 310 ILE cc_start: 0.8282 (mm) cc_final: 0.7723 (tt) REVERT: T 389 ASN cc_start: 0.8678 (m110) cc_final: 0.8370 (m110) REVERT: V 245 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6243 (mt-10) REVERT: V 291 MET cc_start: 0.8549 (mtp) cc_final: 0.8235 (mtp) REVERT: V 310 ILE cc_start: 0.8364 (mm) cc_final: 0.7867 (tt) REVERT: V 402 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: V 452 ASN cc_start: 0.8115 (m110) cc_final: 0.7848 (m-40) REVERT: W 310 ILE cc_start: 0.8220 (mm) cc_final: 0.7670 (tt) REVERT: W 402 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: X 310 ILE cc_start: 0.8281 (mm) cc_final: 0.7720 (tt) REVERT: Z 389 ASN cc_start: 0.8680 (m110) cc_final: 0.8373 (m110) REVERT: AA 245 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6238 (mt-10) REVERT: AA 291 MET cc_start: 0.8552 (mtp) cc_final: 0.8234 (mtp) REVERT: AA 310 ILE cc_start: 0.8368 (mm) cc_final: 0.7871 (tt) REVERT: AA 402 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: AA 452 ASN cc_start: 0.8123 (m110) cc_final: 0.7855 (m-40) REVERT: BA 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7673 (tt) REVERT: BA 402 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: CA 310 ILE cc_start: 0.8286 (mm) cc_final: 0.7727 (tt) REVERT: EA 389 ASN cc_start: 0.8679 (m110) cc_final: 0.8374 (m110) REVERT: FA 245 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6239 (mt-10) REVERT: FA 291 MET cc_start: 0.8551 (mtp) cc_final: 0.8237 (mtp) REVERT: FA 310 ILE cc_start: 0.8362 (mm) cc_final: 0.7865 (tt) REVERT: FA 402 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: FA 452 ASN cc_start: 0.8122 (m110) cc_final: 0.7852 (m-40) REVERT: GA 310 ILE cc_start: 0.8224 (mm) cc_final: 0.7673 (tt) REVERT: GA 402 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: HA 310 ILE cc_start: 0.8282 (mm) cc_final: 0.7722 (tt) REVERT: JA 389 ASN cc_start: 0.8678 (m110) cc_final: 0.8370 (m110) REVERT: KA 245 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6240 (mt-10) REVERT: KA 291 MET cc_start: 0.8551 (mtp) cc_final: 0.8237 (mtp) REVERT: KA 310 ILE cc_start: 0.8363 (mm) cc_final: 0.7870 (tt) REVERT: KA 402 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: KA 452 ASN cc_start: 0.8116 (m110) cc_final: 0.7847 (m-40) REVERT: LA 310 ILE cc_start: 0.8224 (mm) cc_final: 0.7671 (tt) REVERT: LA 402 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: MA 310 ILE cc_start: 0.8286 (mm) cc_final: 0.7728 (tt) REVERT: OA 389 ASN cc_start: 0.8678 (m110) cc_final: 0.8370 (m110) REVERT: PA 245 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6239 (mt-10) REVERT: PA 291 MET cc_start: 0.8551 (mtp) cc_final: 0.8237 (mtp) REVERT: PA 310 ILE cc_start: 0.8362 (mm) cc_final: 0.7866 (tt) REVERT: PA 402 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: PA 452 ASN cc_start: 0.8122 (m110) cc_final: 0.7852 (m-40) REVERT: QA 310 ILE cc_start: 0.8224 (mm) cc_final: 0.7672 (tt) REVERT: QA 402 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: RA 310 ILE cc_start: 0.8282 (mm) cc_final: 0.7723 (tt) REVERT: TA 389 ASN cc_start: 0.8678 (m110) cc_final: 0.8370 (m110) REVERT: UA 245 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6241 (mt-10) REVERT: UA 291 MET cc_start: 0.8551 (mtp) cc_final: 0.8237 (mtp) REVERT: UA 310 ILE cc_start: 0.8363 (mm) cc_final: 0.7869 (tt) REVERT: UA 402 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: UA 452 ASN cc_start: 0.8116 (m110) cc_final: 0.7847 (m-40) REVERT: VA 310 ILE cc_start: 0.8224 (mm) cc_final: 0.7670 (tt) REVERT: VA 402 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: WA 310 ILE cc_start: 0.8286 (mm) cc_final: 0.7728 (tt) REVERT: YA 389 ASN cc_start: 0.8678 (m110) cc_final: 0.8370 (m110) REVERT: ZA 245 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6243 (mt-10) REVERT: ZA 291 MET cc_start: 0.8549 (mtp) cc_final: 0.8235 (mtp) REVERT: ZA 310 ILE cc_start: 0.8364 (mm) cc_final: 0.7868 (tt) REVERT: ZA 402 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: ZA 452 ASN cc_start: 0.8115 (m110) cc_final: 0.7848 (m-40) REVERT: AB 310 ILE cc_start: 0.8220 (mm) cc_final: 0.7670 (tt) REVERT: AB 402 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: BB 310 ILE cc_start: 0.8281 (mm) cc_final: 0.7720 (tt) REVERT: DB 389 ASN cc_start: 0.8680 (m110) cc_final: 0.8373 (m110) REVERT: EB 245 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6237 (mt-10) REVERT: EB 291 MET cc_start: 0.8552 (mtp) cc_final: 0.8234 (mtp) REVERT: EB 310 ILE cc_start: 0.8368 (mm) cc_final: 0.7871 (tt) REVERT: EB 402 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: EB 452 ASN cc_start: 0.8123 (m110) cc_final: 0.7855 (m-40) REVERT: FB 310 ILE cc_start: 0.8226 (mm) cc_final: 0.7673 (tt) REVERT: FB 402 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: GB 310 ILE cc_start: 0.8285 (mm) cc_final: 0.7726 (tt) REVERT: IB 389 ASN cc_start: 0.8679 (m110) cc_final: 0.8374 (m110) outliers start: 60 outliers final: 0 residues processed: 2340 average time/residue: 1.8871 time to fit residues: 5972.5616 Evaluate side-chains 1446 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1422 time to evaluate : 8.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 402 GLN Chi-restraints excluded: chain K residue 402 GLN Chi-restraints excluded: chain L residue 402 GLN Chi-restraints excluded: chain P residue 402 GLN Chi-restraints excluded: chain Q residue 402 GLN Chi-restraints excluded: chain V residue 402 GLN Chi-restraints excluded: chain W residue 402 GLN Chi-restraints excluded: chain AA residue 402 GLN Chi-restraints excluded: chain BA residue 402 GLN Chi-restraints excluded: chain FA residue 402 GLN Chi-restraints excluded: chain GA residue 402 GLN Chi-restraints excluded: chain KA residue 402 GLN Chi-restraints excluded: chain LA residue 402 GLN Chi-restraints excluded: chain PA residue 402 GLN Chi-restraints excluded: chain QA residue 402 GLN Chi-restraints excluded: chain UA residue 402 GLN Chi-restraints excluded: chain VA residue 402 GLN Chi-restraints excluded: chain ZA residue 402 GLN Chi-restraints excluded: chain AB residue 402 GLN Chi-restraints excluded: chain EB residue 402 GLN Chi-restraints excluded: chain FB residue 402 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1165 optimal weight: 2.9990 chunk 1045 optimal weight: 0.9980 chunk 580 optimal weight: 0.6980 chunk 357 optimal weight: 3.9990 chunk 705 optimal weight: 2.9990 chunk 558 optimal weight: 5.9990 chunk 1081 optimal weight: 1.9990 chunk 418 optimal weight: 0.9990 chunk 657 optimal weight: 20.0000 chunk 805 optimal weight: 30.0000 chunk 1253 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 250 ASN B 252 HIS B 269 GLN C 252 HIS C 269 GLN D 250 ASN D 252 HIS E 250 ASN E 269 GLN F 269 GLN G 250 ASN G 252 HIS G 269 GLN H 252 HIS H 269 GLN I 250 ASN I 252 HIS J 250 ASN J 269 GLN K 269 GLN L 250 ASN L 252 HIS L 269 GLN M 252 HIS M 269 GLN N 250 ASN N 252 HIS O 250 ASN O 269 GLN P 269 GLN Q 250 ASN Q 252 HIS Q 269 GLN R 252 HIS R 269 GLN S 250 ASN S 252 HIS T 250 ASN T 269 GLN V 269 GLN W 250 ASN W 252 HIS W 269 GLN X 252 HIS X 269 GLN Y 250 ASN Y 252 HIS Z 250 ASN Z 269 GLN AA 269 GLN BA 250 ASN BA 252 HIS BA 269 GLN CA 252 HIS CA 269 GLN DA 250 ASN DA 252 HIS EA 250 ASN EA 269 GLN FA 269 GLN GA 250 ASN GA 252 HIS GA 269 GLN HA 252 HIS HA 269 GLN IA 250 ASN IA 252 HIS JA 250 ASN JA 269 GLN KA 269 GLN LA 250 ASN LA 252 HIS LA 269 GLN MA 252 HIS MA 269 GLN NA 250 ASN NA 252 HIS OA 250 ASN OA 269 GLN PA 269 GLN QA 250 ASN QA 252 HIS QA 269 GLN RA 252 HIS RA 269 GLN SA 250 ASN SA 252 HIS TA 250 ASN TA 269 GLN UA 269 GLN VA 250 ASN VA 252 HIS VA 269 GLN WA 252 HIS WA 269 GLN XA 250 ASN XA 252 HIS YA 250 ASN YA 269 GLN ZA 250 ASN ZA 269 GLN AB 250 ASN AB 252 HIS AB 269 GLN BB 252 HIS BB 269 GLN CB 250 ASN CB 252 HIS DB 250 ASN DB 269 GLN EB 250 ASN EB 269 GLN FB 250 ASN FB 252 HIS FB 269 GLN GB 269 GLN HB 250 ASN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 106740 Z= 0.162 Angle : 0.474 8.339 144780 Z= 0.244 Chirality : 0.044 0.136 17280 Planarity : 0.004 0.032 18540 Dihedral : 5.029 52.389 14652 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.76 % Allowed : 13.46 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.18 (0.06), residues: 13800 helix: 1.39 (0.07), residues: 4860 sheet: -0.27 (0.09), residues: 2820 loop : -1.27 (0.07), residues: 6120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPGA 419 HIS 0.003 0.001 HISFA 252 PHE 0.012 0.002 PHE E 384 TYR 0.017 0.002 TYR O 365 ARG 0.002 0.000 ARGOA 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1497 time to evaluate : 9.022 Fit side-chains REVERT: A 291 MET cc_start: 0.8484 (mtp) cc_final: 0.8124 (mtp) REVERT: A 310 ILE cc_start: 0.8301 (mm) cc_final: 0.7659 (tt) REVERT: B 310 ILE cc_start: 0.8223 (mm) cc_final: 0.7572 (tt) REVERT: B 326 ASN cc_start: 0.6954 (t0) cc_final: 0.6692 (t0) REVERT: B 375 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8066 (mtm) REVERT: B 445 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: C 310 ILE cc_start: 0.8244 (mm) cc_final: 0.7616 (tt) REVERT: C 353 LYS cc_start: 0.8041 (ttpp) cc_final: 0.7823 (ttpt) REVERT: D 297 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: D 375 MET cc_start: 0.8348 (mtt) cc_final: 0.8118 (mtt) REVERT: D 402 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: F 291 MET cc_start: 0.8483 (mtp) cc_final: 0.8128 (mtp) REVERT: F 310 ILE cc_start: 0.8297 (mm) cc_final: 0.7654 (tt) REVERT: G 310 ILE cc_start: 0.8218 (mm) cc_final: 0.7567 (tt) REVERT: G 326 ASN cc_start: 0.6950 (t0) cc_final: 0.6696 (t0) REVERT: G 375 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: G 445 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: H 310 ILE cc_start: 0.8240 (mm) cc_final: 0.7612 (tt) REVERT: H 353 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7817 (ttpt) REVERT: I 297 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7399 (mtt-85) REVERT: I 375 MET cc_start: 0.8342 (mtt) cc_final: 0.8110 (mtt) REVERT: I 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: K 291 MET cc_start: 0.8484 (mtp) cc_final: 0.8125 (mtp) REVERT: K 310 ILE cc_start: 0.8297 (mm) cc_final: 0.7653 (tt) REVERT: L 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7570 (tt) REVERT: L 326 ASN cc_start: 0.6945 (t0) cc_final: 0.6687 (t0) REVERT: L 375 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8065 (mtm) REVERT: L 445 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: M 310 ILE cc_start: 0.8248 (mm) cc_final: 0.7622 (tt) REVERT: M 353 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7821 (ttpt) REVERT: N 297 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: N 375 MET cc_start: 0.8346 (mtt) cc_final: 0.8117 (mtt) REVERT: N 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: P 291 MET cc_start: 0.8487 (mtp) cc_final: 0.8130 (mtp) REVERT: P 310 ILE cc_start: 0.8295 (mm) cc_final: 0.7650 (tt) REVERT: Q 310 ILE cc_start: 0.8223 (mm) cc_final: 0.7571 (tt) REVERT: Q 326 ASN cc_start: 0.6950 (t0) cc_final: 0.6691 (t0) REVERT: Q 375 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: Q 445 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: R 310 ILE cc_start: 0.8242 (mm) cc_final: 0.7615 (tt) REVERT: R 353 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7826 (ttpt) REVERT: S 297 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7402 (mtt-85) REVERT: S 375 MET cc_start: 0.8349 (mtt) cc_final: 0.8121 (mtt) REVERT: S 402 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: V 291 MET cc_start: 0.8480 (mtp) cc_final: 0.8125 (mtp) REVERT: V 310 ILE cc_start: 0.8297 (mm) cc_final: 0.7654 (tt) REVERT: W 310 ILE cc_start: 0.8219 (mm) cc_final: 0.7569 (tt) REVERT: W 326 ASN cc_start: 0.6949 (t0) cc_final: 0.6696 (t0) REVERT: W 375 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: W 445 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: X 310 ILE cc_start: 0.8240 (mm) cc_final: 0.7612 (tt) REVERT: X 353 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7821 (ttpt) REVERT: Y 297 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7400 (mtt-85) REVERT: Y 375 MET cc_start: 0.8346 (mtt) cc_final: 0.8121 (mtt) REVERT: Y 402 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: AA 291 MET cc_start: 0.8488 (mtp) cc_final: 0.8127 (mtp) REVERT: AA 310 ILE cc_start: 0.8301 (mm) cc_final: 0.7659 (tt) REVERT: BA 310 ILE cc_start: 0.8223 (mm) cc_final: 0.7575 (tt) REVERT: BA 326 ASN cc_start: 0.6953 (t0) cc_final: 0.6693 (t0) REVERT: BA 375 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: BA 445 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: CA 310 ILE cc_start: 0.8244 (mm) cc_final: 0.7616 (tt) REVERT: CA 353 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7821 (ttpt) REVERT: DA 297 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: DA 375 MET cc_start: 0.8349 (mtt) cc_final: 0.8123 (mtt) REVERT: DA 402 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: FA 291 MET cc_start: 0.8484 (mtp) cc_final: 0.8126 (mtp) REVERT: FA 310 ILE cc_start: 0.8295 (mm) cc_final: 0.7650 (tt) REVERT: GA 310 ILE cc_start: 0.8223 (mm) cc_final: 0.7573 (tt) REVERT: GA 326 ASN cc_start: 0.6949 (t0) cc_final: 0.6692 (t0) REVERT: GA 375 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8067 (mtm) REVERT: GA 445 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: HA 310 ILE cc_start: 0.8244 (mm) cc_final: 0.7616 (tt) REVERT: HA 353 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7825 (ttpt) REVERT: IA 297 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7401 (mtt-85) REVERT: IA 375 MET cc_start: 0.8350 (mtt) cc_final: 0.8130 (mtt) REVERT: IA 402 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: KA 291 MET cc_start: 0.8487 (mtp) cc_final: 0.8131 (mtp) REVERT: KA 310 ILE cc_start: 0.8296 (mm) cc_final: 0.7652 (tt) REVERT: LA 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7573 (tt) REVERT: LA 326 ASN cc_start: 0.6944 (t0) cc_final: 0.6688 (t0) REVERT: LA 375 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: LA 445 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: MA 310 ILE cc_start: 0.8248 (mm) cc_final: 0.7622 (tt) REVERT: MA 353 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7818 (ttpt) REVERT: NA 297 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: NA 375 MET cc_start: 0.8348 (mtt) cc_final: 0.8126 (mtt) REVERT: NA 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: PA 291 MET cc_start: 0.8483 (mtp) cc_final: 0.8126 (mtp) REVERT: PA 310 ILE cc_start: 0.8295 (mm) cc_final: 0.7650 (tt) REVERT: QA 310 ILE cc_start: 0.8223 (mm) cc_final: 0.7573 (tt) REVERT: QA 326 ASN cc_start: 0.6948 (t0) cc_final: 0.6692 (t0) REVERT: QA 375 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: QA 445 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: RA 310 ILE cc_start: 0.8243 (mm) cc_final: 0.7616 (tt) REVERT: RA 353 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7825 (ttpt) REVERT: SA 297 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7402 (mtt-85) REVERT: SA 375 MET cc_start: 0.8350 (mtt) cc_final: 0.8127 (mtt) REVERT: SA 402 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: UA 291 MET cc_start: 0.8486 (mtp) cc_final: 0.8130 (mtp) REVERT: UA 310 ILE cc_start: 0.8295 (mm) cc_final: 0.7652 (tt) REVERT: VA 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7572 (tt) REVERT: VA 326 ASN cc_start: 0.6943 (t0) cc_final: 0.6688 (t0) REVERT: VA 375 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: VA 445 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: WA 310 ILE cc_start: 0.8248 (mm) cc_final: 0.7622 (tt) REVERT: WA 353 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7817 (ttpt) REVERT: XA 297 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7406 (mtt-85) REVERT: XA 375 MET cc_start: 0.8344 (mtt) cc_final: 0.8119 (mtt) REVERT: XA 402 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: ZA 291 MET cc_start: 0.8480 (mtp) cc_final: 0.8126 (mtp) REVERT: ZA 310 ILE cc_start: 0.8297 (mm) cc_final: 0.7654 (tt) REVERT: AB 310 ILE cc_start: 0.8218 (mm) cc_final: 0.7569 (tt) REVERT: AB 326 ASN cc_start: 0.6949 (t0) cc_final: 0.6696 (t0) REVERT: AB 375 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: AB 445 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: BB 310 ILE cc_start: 0.8240 (mm) cc_final: 0.7613 (tt) REVERT: BB 353 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7817 (ttpt) REVERT: CB 297 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7399 (mtt-85) REVERT: CB 375 MET cc_start: 0.8345 (mtt) cc_final: 0.8119 (mtt) REVERT: CB 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: EB 291 MET cc_start: 0.8487 (mtp) cc_final: 0.8129 (mtp) REVERT: EB 310 ILE cc_start: 0.8301 (mm) cc_final: 0.7658 (tt) REVERT: FB 310 ILE cc_start: 0.8223 (mm) cc_final: 0.7574 (tt) REVERT: FB 326 ASN cc_start: 0.6952 (t0) cc_final: 0.6692 (t0) REVERT: FB 375 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: FB 445 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: GB 310 ILE cc_start: 0.8245 (mm) cc_final: 0.7616 (tt) REVERT: GB 353 LYS cc_start: 0.8041 (ttpp) cc_final: 0.7820 (ttpt) REVERT: HB 297 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: HB 375 MET cc_start: 0.8347 (mtt) cc_final: 0.8121 (mtt) REVERT: HB 402 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7853 (mt0) outliers start: 204 outliers final: 24 residues processed: 1641 average time/residue: 1.7700 time to fit residues: 3974.5257 Evaluate side-chains 1368 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1296 time to evaluate : 9.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain G residue 445 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 297 ARG Chi-restraints excluded: chain I residue 402 GLN Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 402 GLN Chi-restraints excluded: chain Q residue 247 VAL Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain Q residue 445 GLU Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 297 ARG Chi-restraints excluded: chain S residue 402 GLN Chi-restraints excluded: chain W residue 247 VAL Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 445 GLU Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 297 ARG Chi-restraints excluded: chain Y residue 402 GLN Chi-restraints excluded: chain BA residue 247 VAL Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain BA residue 445 GLU Chi-restraints excluded: chain DA residue 247 VAL Chi-restraints excluded: chain DA residue 297 ARG Chi-restraints excluded: chain DA residue 402 GLN Chi-restraints excluded: chain GA residue 247 VAL Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain GA residue 445 GLU Chi-restraints excluded: chain IA residue 247 VAL Chi-restraints excluded: chain IA residue 297 ARG Chi-restraints excluded: chain IA residue 402 GLN Chi-restraints excluded: chain LA residue 247 VAL Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain LA residue 445 GLU Chi-restraints excluded: chain NA residue 247 VAL Chi-restraints excluded: chain NA residue 297 ARG Chi-restraints excluded: chain NA residue 402 GLN Chi-restraints excluded: chain QA residue 247 VAL Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain QA residue 445 GLU Chi-restraints excluded: chain SA residue 247 VAL Chi-restraints excluded: chain SA residue 297 ARG Chi-restraints excluded: chain SA residue 402 GLN Chi-restraints excluded: chain VA residue 247 VAL Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain VA residue 445 GLU Chi-restraints excluded: chain XA residue 247 VAL Chi-restraints excluded: chain XA residue 297 ARG Chi-restraints excluded: chain XA residue 402 GLN Chi-restraints excluded: chain AB residue 247 VAL Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain AB residue 445 GLU Chi-restraints excluded: chain CB residue 247 VAL Chi-restraints excluded: chain CB residue 297 ARG Chi-restraints excluded: chain CB residue 402 GLN Chi-restraints excluded: chain FB residue 247 VAL Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain FB residue 445 GLU Chi-restraints excluded: chain HB residue 247 VAL Chi-restraints excluded: chain HB residue 297 ARG Chi-restraints excluded: chain HB residue 402 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 696 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 1043 optimal weight: 0.3980 chunk 853 optimal weight: 0.9980 chunk 345 optimal weight: 30.0000 chunk 1255 optimal weight: 4.9990 chunk 1356 optimal weight: 0.7980 chunk 1118 optimal weight: 4.9990 chunk 1244 optimal weight: 4.9990 chunk 428 optimal weight: 0.3980 chunk 1007 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 250 ASN B 252 HIS B 269 GLN C 250 ASN C 252 HIS C 269 GLN D 252 HIS E 269 GLN F 250 ASN F 269 GLN G 250 ASN G 252 HIS G 269 GLN H 250 ASN H 252 HIS H 269 GLN I 252 HIS J 269 GLN K 250 ASN K 269 GLN L 250 ASN L 252 HIS L 269 GLN M 250 ASN M 252 HIS M 269 GLN N 252 HIS O 269 GLN P 269 GLN Q 250 ASN Q 252 HIS Q 269 GLN R 250 ASN R 252 HIS R 269 GLN S 252 HIS T 269 GLN V 250 ASN V 269 GLN W 250 ASN W 252 HIS W 269 GLN X 252 HIS X 269 GLN Y 252 HIS Z 269 GLN AA 269 GLN BA 250 ASN BA 252 HIS BA 269 GLN CA 250 ASN CA 252 HIS CA 269 GLN CA 326 ASN DA 252 HIS EA 269 GLN FA 250 ASN FA 269 GLN GA 250 ASN GA 252 HIS GA 269 GLN HA 250 ASN HA 252 HIS HA 269 GLN HA 326 ASN IA 252 HIS JA 269 GLN KA 250 ASN KA 269 GLN LA 250 ASN LA 252 HIS LA 269 GLN MA 252 HIS MA 269 GLN NA 252 HIS OA 269 GLN PA 250 ASN PA 269 GLN QA 250 ASN QA 252 HIS QA 269 GLN RA 250 ASN RA 252 HIS RA 269 GLN RA 326 ASN SA 252 HIS TA 269 GLN UA 250 ASN UA 269 GLN VA 250 ASN VA 252 HIS VA 269 GLN WA 250 ASN WA 252 HIS WA 269 GLN WA 326 ASN XA 252 HIS YA 250 ASN YA 269 GLN ZA 269 GLN AB 250 ASN AB 252 HIS AB 269 GLN BB 250 ASN BB 252 HIS BB 269 GLN CB 252 HIS DB 269 GLN EB 269 GLN FB 250 ASN FB 252 HIS FB 269 GLN GB 250 ASN GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 106740 Z= 0.174 Angle : 0.464 8.730 144780 Z= 0.238 Chirality : 0.044 0.134 17280 Planarity : 0.004 0.030 18540 Dihedral : 4.144 15.921 14580 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.87 % Allowed : 13.61 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.62 (0.07), residues: 13800 helix: 2.37 (0.07), residues: 4920 sheet: -0.06 (0.09), residues: 2820 loop : -1.04 (0.07), residues: 6060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 419 HIS 0.003 0.001 HISZA 252 PHE 0.012 0.002 PHEZA 429 TYR 0.018 0.002 TYROA 365 ARG 0.001 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1349 time to evaluate : 8.983 Fit side-chains REVERT: A 252 HIS cc_start: 0.8391 (m170) cc_final: 0.8093 (m-70) REVERT: A 291 MET cc_start: 0.8522 (mtp) cc_final: 0.8191 (mtp) REVERT: A 310 ILE cc_start: 0.8439 (mm) cc_final: 0.7808 (tt) REVERT: A 326 ASN cc_start: 0.6632 (t0) cc_final: 0.6417 (t0) REVERT: A 445 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: B 310 ILE cc_start: 0.8229 (mm) cc_final: 0.7623 (tt) REVERT: B 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: C 375 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8479 (mtm) REVERT: D 297 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7331 (mtt-85) REVERT: F 252 HIS cc_start: 0.8380 (m170) cc_final: 0.8106 (m-70) REVERT: F 291 MET cc_start: 0.8524 (mtp) cc_final: 0.8194 (mtp) REVERT: F 310 ILE cc_start: 0.8434 (mm) cc_final: 0.7801 (tt) REVERT: F 326 ASN cc_start: 0.6639 (t0) cc_final: 0.6417 (t0) REVERT: F 445 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: G 310 ILE cc_start: 0.8226 (mm) cc_final: 0.7620 (tt) REVERT: G 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8227 (mtt) REVERT: H 375 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: I 297 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7329 (mtt-85) REVERT: K 252 HIS cc_start: 0.8388 (m170) cc_final: 0.8091 (m-70) REVERT: K 291 MET cc_start: 0.8520 (mtp) cc_final: 0.8192 (mtp) REVERT: K 310 ILE cc_start: 0.8436 (mm) cc_final: 0.7803 (tt) REVERT: K 326 ASN cc_start: 0.6636 (t0) cc_final: 0.6412 (t0) REVERT: K 445 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: L 310 ILE cc_start: 0.8227 (mm) cc_final: 0.7618 (tt) REVERT: L 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8227 (mtt) REVERT: M 375 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8485 (mtm) REVERT: N 297 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7329 (mtt-85) REVERT: P 252 HIS cc_start: 0.8380 (m170) cc_final: 0.8107 (m-70) REVERT: P 291 MET cc_start: 0.8528 (mtp) cc_final: 0.8200 (mtp) REVERT: P 310 ILE cc_start: 0.8433 (mm) cc_final: 0.7799 (tt) REVERT: P 326 ASN cc_start: 0.6631 (t0) cc_final: 0.6420 (t0) REVERT: P 445 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: Q 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7621 (tt) REVERT: Q 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8228 (mtt) REVERT: R 375 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: S 297 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7331 (mtt-85) REVERT: V 252 HIS cc_start: 0.8385 (m170) cc_final: 0.8089 (m-70) REVERT: V 291 MET cc_start: 0.8521 (mtp) cc_final: 0.8191 (mtp) REVERT: V 310 ILE cc_start: 0.8434 (mm) cc_final: 0.7801 (tt) REVERT: V 326 ASN cc_start: 0.6637 (t0) cc_final: 0.6415 (t0) REVERT: V 445 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: W 310 ILE cc_start: 0.8226 (mm) cc_final: 0.7619 (tt) REVERT: W 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8223 (mtt) REVERT: X 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: Y 297 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7326 (mtt-85) REVERT: AA 252 HIS cc_start: 0.8382 (m170) cc_final: 0.8109 (m-70) REVERT: AA 291 MET cc_start: 0.8525 (mtp) cc_final: 0.8195 (mtp) REVERT: AA 310 ILE cc_start: 0.8439 (mm) cc_final: 0.7808 (tt) REVERT: AA 326 ASN cc_start: 0.6632 (t0) cc_final: 0.6418 (t0) REVERT: AA 445 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: BA 310 ILE cc_start: 0.8229 (mm) cc_final: 0.7623 (tt) REVERT: BA 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: CA 375 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: DA 297 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7326 (mtt-85) REVERT: FA 252 HIS cc_start: 0.8387 (m170) cc_final: 0.8091 (m-70) REVERT: FA 291 MET cc_start: 0.8525 (mtp) cc_final: 0.8196 (mtp) REVERT: FA 310 ILE cc_start: 0.8433 (mm) cc_final: 0.7799 (tt) REVERT: FA 326 ASN cc_start: 0.6630 (t0) cc_final: 0.6417 (t0) REVERT: FA 445 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: GA 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7621 (tt) REVERT: GA 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8223 (mtt) REVERT: HA 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8476 (mtm) REVERT: IA 297 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7327 (mtt-85) REVERT: KA 252 HIS cc_start: 0.8382 (m170) cc_final: 0.8106 (m-70) REVERT: KA 291 MET cc_start: 0.8524 (mtp) cc_final: 0.8195 (mtp) REVERT: KA 310 ILE cc_start: 0.8435 (mm) cc_final: 0.7803 (tt) REVERT: KA 326 ASN cc_start: 0.6637 (t0) cc_final: 0.6414 (t0) REVERT: KA 445 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: LA 310 ILE cc_start: 0.8226 (mm) cc_final: 0.7618 (tt) REVERT: LA 375 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8222 (mtt) REVERT: MA 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: NA 297 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7324 (mtt-85) REVERT: PA 252 HIS cc_start: 0.8387 (m170) cc_final: 0.8093 (m-70) REVERT: PA 291 MET cc_start: 0.8525 (mtp) cc_final: 0.8195 (mtp) REVERT: PA 310 ILE cc_start: 0.8433 (mm) cc_final: 0.7799 (tt) REVERT: PA 326 ASN cc_start: 0.6631 (t0) cc_final: 0.6419 (t0) REVERT: PA 445 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: QA 310 ILE cc_start: 0.8225 (mm) cc_final: 0.7621 (tt) REVERT: QA 375 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: RA 375 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8476 (mtm) REVERT: SA 297 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7327 (mtt-85) REVERT: UA 252 HIS cc_start: 0.8381 (m170) cc_final: 0.8107 (m-70) REVERT: UA 291 MET cc_start: 0.8523 (mtp) cc_final: 0.8194 (mtp) REVERT: UA 310 ILE cc_start: 0.8435 (mm) cc_final: 0.7803 (tt) REVERT: UA 326 ASN cc_start: 0.6636 (t0) cc_final: 0.6414 (t0) REVERT: UA 445 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: VA 310 ILE cc_start: 0.8227 (mm) cc_final: 0.7619 (tt) REVERT: VA 375 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: WA 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8476 (mtm) REVERT: XA 297 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7325 (mtt-85) REVERT: ZA 252 HIS cc_start: 0.8383 (m170) cc_final: 0.8089 (m-70) REVERT: ZA 291 MET cc_start: 0.8522 (mtp) cc_final: 0.8190 (mtp) REVERT: ZA 310 ILE cc_start: 0.8433 (mm) cc_final: 0.7805 (tt) REVERT: ZA 326 ASN cc_start: 0.6639 (t0) cc_final: 0.6416 (t0) REVERT: ZA 445 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: AB 310 ILE cc_start: 0.8226 (mm) cc_final: 0.7620 (tt) REVERT: AB 375 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8228 (mtt) REVERT: BB 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: CB 297 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7325 (mtt-85) REVERT: EB 252 HIS cc_start: 0.8381 (m170) cc_final: 0.8109 (m-70) REVERT: EB 291 MET cc_start: 0.8527 (mtp) cc_final: 0.8194 (mtp) REVERT: EB 310 ILE cc_start: 0.8437 (mm) cc_final: 0.7811 (tt) REVERT: EB 326 ASN cc_start: 0.6632 (t0) cc_final: 0.6418 (t0) REVERT: EB 445 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: FB 310 ILE cc_start: 0.8229 (mm) cc_final: 0.7623 (tt) REVERT: FB 375 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8232 (mtt) REVERT: GB 375 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: HB 297 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7328 (mtt-85) outliers start: 216 outliers final: 48 residues processed: 1505 average time/residue: 1.7497 time to fit residues: 3614.4621 Evaluate side-chains 1346 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1250 time to evaluate : 8.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 297 ARG Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain M residue 247 VAL Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 297 ARG Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 297 ARG Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain CA residue 247 VAL Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 247 VAL Chi-restraints excluded: chain DA residue 297 ARG Chi-restraints excluded: chain EA residue 247 VAL Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain HA residue 247 VAL Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 247 VAL Chi-restraints excluded: chain IA residue 297 ARG Chi-restraints excluded: chain JA residue 247 VAL Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain MA residue 247 VAL Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 247 VAL Chi-restraints excluded: chain NA residue 297 ARG Chi-restraints excluded: chain OA residue 247 VAL Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 247 VAL Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 247 VAL Chi-restraints excluded: chain SA residue 297 ARG Chi-restraints excluded: chain TA residue 247 VAL Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 247 VAL Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 247 VAL Chi-restraints excluded: chain XA residue 297 ARG Chi-restraints excluded: chain YA residue 247 VAL Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 247 VAL Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 247 VAL Chi-restraints excluded: chain CB residue 297 ARG Chi-restraints excluded: chain DB residue 247 VAL Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 247 VAL Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 247 VAL Chi-restraints excluded: chain HB residue 297 ARG Chi-restraints excluded: chain IB residue 247 VAL Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1240 optimal weight: 4.9990 chunk 943 optimal weight: 7.9990 chunk 651 optimal weight: 7.9990 chunk 138 optimal weight: 30.0000 chunk 599 optimal weight: 9.9990 chunk 843 optimal weight: 4.9990 chunk 1259 optimal weight: 1.9990 chunk 1333 optimal weight: 0.4980 chunk 658 optimal weight: 0.0270 chunk 1194 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 250 ASN B 269 GLN C 250 ASN C 252 HIS C 269 GLN D 252 HIS E 269 GLN F 269 GLN G 250 ASN G 269 GLN H 250 ASN H 252 HIS H 269 GLN I 252 HIS J 269 GLN K 269 GLN L 250 ASN L 269 GLN M 250 ASN M 252 HIS M 269 GLN N 252 HIS O 269 GLN P 269 GLN Q 250 ASN Q 269 GLN R 250 ASN R 252 HIS R 269 GLN S 252 HIS T 269 GLN V 269 GLN W 250 ASN W 269 GLN X 250 ASN X 252 HIS X 269 GLN Y 252 HIS Z 269 GLN AA 269 GLN BA 250 ASN BA 269 GLN CA 250 ASN CA 252 HIS CA 269 GLN DA 252 HIS EA 269 GLN FA 269 GLN GA 250 ASN GA 269 GLN HA 250 ASN HA 252 HIS HA 269 GLN IA 252 HIS JA 269 GLN KA 269 GLN LA 250 ASN LA 269 GLN MA 250 ASN MA 252 HIS MA 269 GLN NA 252 HIS OA 269 GLN PA 269 GLN QA 250 ASN QA 269 GLN RA 250 ASN RA 252 HIS RA 269 GLN RA 326 ASN SA 252 HIS TA 269 GLN UA 269 GLN VA 250 ASN VA 269 GLN WA 250 ASN WA 252 HIS WA 269 GLN WA 326 ASN XA 252 HIS YA 269 GLN ZA 269 GLN AB 250 ASN AB 269 GLN BB 250 ASN BB 252 HIS BB 269 GLN CB 252 HIS DB 269 GLN EB 269 GLN FB 250 ASN FB 269 GLN GB 250 ASN GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 97 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 106740 Z= 0.225 Angle : 0.473 8.901 144780 Z= 0.243 Chirality : 0.045 0.137 17280 Planarity : 0.004 0.036 18540 Dihedral : 4.212 17.798 14580 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.77 % Allowed : 13.70 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.86 (0.07), residues: 13800 helix: 2.64 (0.07), residues: 4920 sheet: 0.04 (0.09), residues: 2820 loop : -0.94 (0.07), residues: 6060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 419 HIS 0.003 0.001 HISZA 252 PHE 0.013 0.002 PHENA 253 TYR 0.019 0.002 TYR O 365 ARG 0.002 0.000 ARGFA 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1313 time to evaluate : 8.839 Fit side-chains REVERT: A 310 ILE cc_start: 0.8502 (mm) cc_final: 0.7873 (tt) REVERT: A 326 ASN cc_start: 0.6885 (t0) cc_final: 0.6588 (t0) REVERT: A 445 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: B 375 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8243 (mtt) REVERT: C 375 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: F 310 ILE cc_start: 0.8501 (mm) cc_final: 0.7875 (tt) REVERT: F 326 ASN cc_start: 0.6888 (t0) cc_final: 0.6592 (t0) REVERT: F 445 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: G 375 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: H 375 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: K 310 ILE cc_start: 0.8505 (mm) cc_final: 0.7879 (tt) REVERT: K 326 ASN cc_start: 0.6886 (t0) cc_final: 0.6586 (t0) REVERT: K 445 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: L 375 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: M 375 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8476 (mtm) REVERT: P 310 ILE cc_start: 0.8501 (mm) cc_final: 0.7875 (tt) REVERT: P 326 ASN cc_start: 0.6884 (t0) cc_final: 0.6593 (t0) REVERT: P 445 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: Q 375 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8244 (mtt) REVERT: R 375 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: V 310 ILE cc_start: 0.8503 (mm) cc_final: 0.7876 (tt) REVERT: V 326 ASN cc_start: 0.6886 (t0) cc_final: 0.6588 (t0) REVERT: V 445 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: W 375 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: X 375 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: AA 310 ILE cc_start: 0.8500 (mm) cc_final: 0.7873 (tt) REVERT: AA 326 ASN cc_start: 0.6886 (t0) cc_final: 0.6590 (t0) REVERT: AA 445 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: BA 375 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8240 (mtt) REVERT: CA 375 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8464 (mtm) REVERT: FA 310 ILE cc_start: 0.8501 (mm) cc_final: 0.7874 (tt) REVERT: FA 326 ASN cc_start: 0.6882 (t0) cc_final: 0.6589 (t0) REVERT: FA 445 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: GA 375 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8240 (mtt) REVERT: HA 375 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: KA 310 ILE cc_start: 0.8504 (mm) cc_final: 0.7879 (tt) REVERT: KA 326 ASN cc_start: 0.6888 (t0) cc_final: 0.6591 (t0) REVERT: KA 445 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: LA 375 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: MA 375 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: PA 310 ILE cc_start: 0.8501 (mm) cc_final: 0.7875 (tt) REVERT: PA 326 ASN cc_start: 0.6883 (t0) cc_final: 0.6589 (t0) REVERT: PA 445 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: QA 375 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8247 (mtt) REVERT: RA 375 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: UA 310 ILE cc_start: 0.8504 (mm) cc_final: 0.7879 (tt) REVERT: UA 326 ASN cc_start: 0.6887 (t0) cc_final: 0.6590 (t0) REVERT: UA 445 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: VA 375 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: WA 375 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8470 (mtm) REVERT: ZA 310 ILE cc_start: 0.8527 (mm) cc_final: 0.7918 (tt) REVERT: ZA 326 ASN cc_start: 0.6887 (t0) cc_final: 0.6589 (t0) REVERT: ZA 445 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: AB 375 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8260 (mtt) REVERT: BB 375 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: EB 310 ILE cc_start: 0.8527 (mm) cc_final: 0.7916 (tt) REVERT: EB 326 ASN cc_start: 0.6887 (t0) cc_final: 0.6589 (t0) REVERT: EB 445 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: FB 375 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8264 (mtt) REVERT: GB 375 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8464 (mtm) outliers start: 321 outliers final: 134 residues processed: 1550 average time/residue: 1.6196 time to fit residues: 3471.7988 Evaluate side-chains 1414 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1244 time to evaluate : 8.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 296 LYS Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 296 LYS Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain M residue 247 VAL Chi-restraints excluded: chain M residue 273 SER Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 315 THR Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 273 SER Chi-restraints excluded: chain O residue 296 LYS Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 247 VAL Chi-restraints excluded: chain Q residue 273 SER Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 273 SER Chi-restraints excluded: chain T residue 296 LYS Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 247 VAL Chi-restraints excluded: chain W residue 273 SER Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 273 SER Chi-restraints excluded: chain X residue 315 THR Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 273 SER Chi-restraints excluded: chain Z residue 296 LYS Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 247 VAL Chi-restraints excluded: chain BA residue 273 SER Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain CA residue 247 VAL Chi-restraints excluded: chain CA residue 273 SER Chi-restraints excluded: chain CA residue 315 THR Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 247 VAL Chi-restraints excluded: chain DA residue 315 THR Chi-restraints excluded: chain EA residue 247 VAL Chi-restraints excluded: chain EA residue 273 SER Chi-restraints excluded: chain EA residue 296 LYS Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 247 VAL Chi-restraints excluded: chain GA residue 273 SER Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain HA residue 247 VAL Chi-restraints excluded: chain HA residue 273 SER Chi-restraints excluded: chain HA residue 315 THR Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 247 VAL Chi-restraints excluded: chain IA residue 315 THR Chi-restraints excluded: chain JA residue 247 VAL Chi-restraints excluded: chain JA residue 273 SER Chi-restraints excluded: chain JA residue 296 LYS Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 247 VAL Chi-restraints excluded: chain LA residue 273 SER Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain MA residue 247 VAL Chi-restraints excluded: chain MA residue 273 SER Chi-restraints excluded: chain MA residue 315 THR Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 247 VAL Chi-restraints excluded: chain NA residue 315 THR Chi-restraints excluded: chain OA residue 247 VAL Chi-restraints excluded: chain OA residue 273 SER Chi-restraints excluded: chain OA residue 296 LYS Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 247 VAL Chi-restraints excluded: chain QA residue 273 SER Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 247 VAL Chi-restraints excluded: chain RA residue 273 SER Chi-restraints excluded: chain RA residue 315 THR Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 247 VAL Chi-restraints excluded: chain SA residue 315 THR Chi-restraints excluded: chain TA residue 247 VAL Chi-restraints excluded: chain TA residue 273 SER Chi-restraints excluded: chain TA residue 296 LYS Chi-restraints excluded: chain TA residue 307 ASP Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 247 VAL Chi-restraints excluded: chain VA residue 273 SER Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 247 VAL Chi-restraints excluded: chain WA residue 273 SER Chi-restraints excluded: chain WA residue 315 THR Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 247 VAL Chi-restraints excluded: chain XA residue 315 THR Chi-restraints excluded: chain YA residue 247 VAL Chi-restraints excluded: chain YA residue 273 SER Chi-restraints excluded: chain YA residue 296 LYS Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 247 VAL Chi-restraints excluded: chain AB residue 273 SER Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 247 VAL Chi-restraints excluded: chain BB residue 273 SER Chi-restraints excluded: chain BB residue 315 THR Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 247 VAL Chi-restraints excluded: chain CB residue 315 THR Chi-restraints excluded: chain DB residue 247 VAL Chi-restraints excluded: chain DB residue 273 SER Chi-restraints excluded: chain DB residue 296 LYS Chi-restraints excluded: chain DB residue 307 ASP Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 247 VAL Chi-restraints excluded: chain FB residue 273 SER Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 247 VAL Chi-restraints excluded: chain GB residue 273 SER Chi-restraints excluded: chain GB residue 315 THR Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 247 VAL Chi-restraints excluded: chain HB residue 315 THR Chi-restraints excluded: chain IB residue 247 VAL Chi-restraints excluded: chain IB residue 273 SER Chi-restraints excluded: chain IB residue 296 LYS Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1110 optimal weight: 3.9990 chunk 757 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 993 optimal weight: 0.6980 chunk 550 optimal weight: 8.9990 chunk 1138 optimal weight: 10.0000 chunk 922 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 681 optimal weight: 8.9990 chunk 1197 optimal weight: 10.0000 chunk 336 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN B 326 ASN C 250 ASN C 269 GLN D 252 HIS E 269 GLN E 326 ASN F 269 GLN G 269 GLN G 326 ASN H 250 ASN H 269 GLN I 252 HIS J 269 GLN J 326 ASN K 269 GLN L 269 GLN L 326 ASN M 250 ASN M 269 GLN N 252 HIS O 269 GLN O 326 ASN P 269 GLN Q 269 GLN Q 326 ASN R 250 ASN R 269 GLN S 252 HIS T 269 GLN T 326 ASN V 269 GLN W 269 GLN W 326 ASN X 250 ASN X 269 GLN Y 252 HIS Z 269 GLN Z 326 ASN AA 269 GLN BA 269 GLN BA 326 ASN CA 250 ASN CA 269 GLN DA 252 HIS EA 269 GLN EA 326 ASN FA 269 GLN GA 269 GLN GA 326 ASN HA 250 ASN HA 269 GLN IA 252 HIS JA 269 GLN JA 326 ASN KA 269 GLN LA 269 GLN LA 326 ASN MA 250 ASN MA 269 GLN NA 252 HIS OA 269 GLN OA 326 ASN PA 269 GLN QA 269 GLN QA 326 ASN RA 250 ASN RA 269 GLN SA 252 HIS TA 250 ASN TA 269 GLN TA 326 ASN UA 269 GLN VA 269 GLN VA 326 ASN WA 250 ASN WA 269 GLN XA 252 HIS YA 269 GLN YA 326 ASN ZA 269 GLN AB 269 GLN AB 326 ASN BB 250 ASN BB 269 GLN CB 252 HIS DB 269 GLN DB 326 ASN EB 269 GLN FB 269 GLN FB 326 ASN GB 269 GLN HB 252 HIS IB 269 GLN IB 326 ASN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 106740 Z= 0.178 Angle : 0.451 8.651 144780 Z= 0.231 Chirality : 0.045 0.136 17280 Planarity : 0.004 0.037 18540 Dihedral : 4.074 17.327 14580 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 15.77 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.10 (0.07), residues: 13800 helix: 2.84 (0.07), residues: 4980 sheet: 0.08 (0.09), residues: 2820 loop : -0.79 (0.07), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 419 HIS 0.004 0.001 HISPA 252 PHE 0.015 0.002 PHECB 253 TYR 0.020 0.002 TYR E 365 ARG 0.001 0.000 ARGDA 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1302 time to evaluate : 7.994 Fit side-chains REVERT: A 252 HIS cc_start: 0.8464 (m170) cc_final: 0.8191 (m-70) REVERT: A 326 ASN cc_start: 0.7228 (t0) cc_final: 0.6989 (t0) REVERT: A 445 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 375 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: C 350 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: C 375 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: D 297 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7251 (mtt-85) REVERT: D 402 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: F 326 ASN cc_start: 0.7237 (t0) cc_final: 0.6995 (t0) REVERT: F 445 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: G 375 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8275 (mtt) REVERT: H 350 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: H 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: I 297 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7249 (mtt-85) REVERT: I 402 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: K 252 HIS cc_start: 0.8464 (m170) cc_final: 0.8188 (m-70) REVERT: K 326 ASN cc_start: 0.7231 (t0) cc_final: 0.6989 (t0) REVERT: K 445 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: L 375 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: M 350 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: M 375 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8505 (mtm) REVERT: N 297 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7245 (mtt-85) REVERT: N 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: P 326 ASN cc_start: 0.7235 (t0) cc_final: 0.6996 (t0) REVERT: P 445 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: Q 375 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: R 350 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: R 375 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: S 297 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7246 (mtt-85) REVERT: S 402 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: V 252 HIS cc_start: 0.8463 (m170) cc_final: 0.8188 (m-70) REVERT: V 326 ASN cc_start: 0.7234 (t0) cc_final: 0.6990 (t0) REVERT: V 445 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: W 375 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: X 350 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: X 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8501 (mtm) REVERT: Y 297 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7252 (mtt-85) REVERT: Y 402 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: AA 326 ASN cc_start: 0.7232 (t0) cc_final: 0.6993 (t0) REVERT: AA 445 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: BA 375 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8273 (mtt) REVERT: CA 350 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: CA 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8498 (mtm) REVERT: DA 297 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7252 (mtt-85) REVERT: DA 402 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: FA 252 HIS cc_start: 0.8461 (m170) cc_final: 0.8188 (m-70) REVERT: FA 326 ASN cc_start: 0.7234 (t0) cc_final: 0.6994 (t0) REVERT: FA 445 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: GA 375 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8271 (mtt) REVERT: HA 350 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: HA 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: IA 297 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7248 (mtt-85) REVERT: IA 402 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: KA 326 ASN cc_start: 0.7237 (t0) cc_final: 0.6994 (t0) REVERT: KA 445 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: LA 375 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8266 (mtt) REVERT: MA 350 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: MA 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: NA 297 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7246 (mtt-85) REVERT: NA 402 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: PA 252 HIS cc_start: 0.8461 (m170) cc_final: 0.8189 (m-70) REVERT: PA 326 ASN cc_start: 0.7235 (t0) cc_final: 0.6994 (t0) REVERT: PA 445 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: QA 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8298 (mtt) REVERT: RA 350 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: RA 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: SA 297 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: SA 402 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: UA 326 ASN cc_start: 0.7237 (t0) cc_final: 0.6994 (t0) REVERT: UA 445 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: VA 375 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: WA 350 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: WA 375 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (mtm) REVERT: XA 297 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: XA 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: ZA 252 HIS cc_start: 0.8463 (m170) cc_final: 0.8193 (m-70) REVERT: ZA 326 ASN cc_start: 0.7233 (t0) cc_final: 0.6989 (t0) REVERT: ZA 445 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: AB 375 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: BB 350 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: BB 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8501 (mtm) REVERT: CB 297 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7251 (mtt-85) REVERT: CB 402 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: EB 252 HIS cc_start: 0.8391 (m170) cc_final: 0.8102 (m-70) REVERT: EB 326 ASN cc_start: 0.7230 (t0) cc_final: 0.6990 (t0) REVERT: EB 445 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: FB 375 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8298 (mtt) REVERT: GB 350 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: GB 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8497 (mtm) REVERT: HB 297 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7252 (mtt-85) REVERT: HB 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7683 (mt0) outliers start: 248 outliers final: 81 residues processed: 1502 average time/residue: 1.5518 time to fit residues: 3222.0267 Evaluate side-chains 1416 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1263 time to evaluate : 8.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 297 ARG Chi-restraints excluded: chain I residue 402 GLN Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain M residue 247 VAL Chi-restraints excluded: chain M residue 273 SER Chi-restraints excluded: chain M residue 350 GLU Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 402 GLN Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 307 ASP Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 247 VAL Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 350 GLU Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 297 ARG Chi-restraints excluded: chain S residue 402 GLN Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 273 SER Chi-restraints excluded: chain T residue 307 ASP Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 247 VAL Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 273 SER Chi-restraints excluded: chain X residue 350 GLU Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 258 ASN Chi-restraints excluded: chain Y residue 297 ARG Chi-restraints excluded: chain Y residue 402 GLN Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 307 ASP Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 247 VAL Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain CA residue 247 VAL Chi-restraints excluded: chain CA residue 273 SER Chi-restraints excluded: chain CA residue 350 GLU Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 258 ASN Chi-restraints excluded: chain DA residue 297 ARG Chi-restraints excluded: chain DA residue 402 GLN Chi-restraints excluded: chain EA residue 247 VAL Chi-restraints excluded: chain EA residue 307 ASP Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 247 VAL Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain HA residue 247 VAL Chi-restraints excluded: chain HA residue 273 SER Chi-restraints excluded: chain HA residue 350 GLU Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 258 ASN Chi-restraints excluded: chain IA residue 297 ARG Chi-restraints excluded: chain IA residue 402 GLN Chi-restraints excluded: chain JA residue 247 VAL Chi-restraints excluded: chain JA residue 307 ASP Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 247 VAL Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain MA residue 247 VAL Chi-restraints excluded: chain MA residue 273 SER Chi-restraints excluded: chain MA residue 350 GLU Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 258 ASN Chi-restraints excluded: chain NA residue 297 ARG Chi-restraints excluded: chain NA residue 402 GLN Chi-restraints excluded: chain OA residue 247 VAL Chi-restraints excluded: chain OA residue 273 SER Chi-restraints excluded: chain OA residue 307 ASP Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 247 VAL Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 247 VAL Chi-restraints excluded: chain RA residue 273 SER Chi-restraints excluded: chain RA residue 350 GLU Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 258 ASN Chi-restraints excluded: chain SA residue 297 ARG Chi-restraints excluded: chain SA residue 402 GLN Chi-restraints excluded: chain TA residue 247 VAL Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 247 VAL Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 247 VAL Chi-restraints excluded: chain WA residue 273 SER Chi-restraints excluded: chain WA residue 350 GLU Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 258 ASN Chi-restraints excluded: chain XA residue 297 ARG Chi-restraints excluded: chain XA residue 402 GLN Chi-restraints excluded: chain YA residue 307 ASP Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 247 VAL Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 247 VAL Chi-restraints excluded: chain BB residue 273 SER Chi-restraints excluded: chain BB residue 350 GLU Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 258 ASN Chi-restraints excluded: chain CB residue 297 ARG Chi-restraints excluded: chain CB residue 402 GLN Chi-restraints excluded: chain DB residue 247 VAL Chi-restraints excluded: chain DB residue 296 LYS Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 247 VAL Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 247 VAL Chi-restraints excluded: chain GB residue 273 SER Chi-restraints excluded: chain GB residue 350 GLU Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 258 ASN Chi-restraints excluded: chain HB residue 297 ARG Chi-restraints excluded: chain HB residue 402 GLN Chi-restraints excluded: chain IB residue 247 VAL Chi-restraints excluded: chain IB residue 307 ASP Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 448 optimal weight: 1.9990 chunk 1201 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 783 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 1335 optimal weight: 9.9990 chunk 1108 optimal weight: 1.9990 chunk 618 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 441 optimal weight: 3.9990 chunk 700 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 269 GLN B 326 ASN C 269 GLN D 252 HIS E 269 GLN F 250 ASN F 269 GLN G 269 GLN G 326 ASN H 269 GLN I 252 HIS J 269 GLN J 326 ASN K 250 ASN K 269 GLN L 269 GLN L 326 ASN M 269 GLN N 252 HIS O 269 GLN P 250 ASN P 269 GLN Q 269 GLN Q 326 ASN R 269 GLN S 252 HIS T 269 GLN T 326 ASN V 250 ASN V 269 GLN W 269 GLN W 326 ASN X 269 GLN Y 252 HIS Z 269 GLN Z 326 ASN AA 250 ASN AA 269 GLN BA 269 GLN BA 326 ASN CA 269 GLN DA 252 HIS EA 269 GLN FA 269 GLN GA 269 GLN GA 326 ASN HA 269 GLN IA 252 HIS JA 269 GLN KA 250 ASN KA 269 GLN LA 269 GLN LA 326 ASN MA 269 GLN NA 252 HIS OA 269 GLN OA 326 ASN PA 250 ASN PA 269 GLN QA 269 GLN QA 326 ASN RA 269 GLN SA 252 HIS TA 269 GLN UA 250 ASN UA 269 GLN VA 269 GLN VA 326 ASN WA 269 GLN XA 252 HIS YA 269 GLN ZA 250 ASN ZA 269 GLN AB 269 GLN AB 326 ASN BB 269 GLN CB 252 HIS DB 269 GLN DB 326 ASN EB 250 ASN EB 269 GLN FB 269 GLN FB 326 ASN GB 250 ASN GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 106740 Z= 0.249 Angle : 0.480 8.402 144780 Z= 0.249 Chirality : 0.046 0.134 17280 Planarity : 0.004 0.036 18540 Dihedral : 4.271 17.702 14580 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.21 % Allowed : 15.08 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.05 (0.07), residues: 13800 helix: 2.71 (0.07), residues: 4980 sheet: 0.12 (0.09), residues: 2820 loop : -0.77 (0.07), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPEB 419 HIS 0.004 0.001 HISKA 252 PHE 0.015 0.002 PHEDA 253 TYR 0.021 0.002 TYR O 365 ARG 0.002 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1324 time to evaluate : 8.118 Fit side-chains REVERT: A 326 ASN cc_start: 0.7322 (t0) cc_final: 0.7114 (t0) REVERT: A 445 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 375 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8283 (mtt) REVERT: C 350 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: C 375 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (mtm) REVERT: F 326 ASN cc_start: 0.7332 (t0) cc_final: 0.7117 (t0) REVERT: F 445 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: G 375 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: H 350 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: H 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8516 (mtm) REVERT: K 326 ASN cc_start: 0.7325 (t0) cc_final: 0.7117 (t0) REVERT: K 445 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: L 375 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: M 350 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: M 375 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8519 (mtm) REVERT: P 326 ASN cc_start: 0.7331 (t0) cc_final: 0.7119 (t0) REVERT: P 445 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: Q 375 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: R 350 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: R 375 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8518 (mtm) REVERT: V 326 ASN cc_start: 0.7330 (t0) cc_final: 0.7114 (t0) REVERT: V 445 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: W 375 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: X 350 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: X 375 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8038 (mtm) REVERT: AA 326 ASN cc_start: 0.7324 (t0) cc_final: 0.7115 (t0) REVERT: AA 445 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: BA 375 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: CA 350 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: CA 375 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8045 (mtm) REVERT: FA 326 ASN cc_start: 0.7330 (t0) cc_final: 0.7115 (t0) REVERT: FA 445 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: GA 375 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: HA 350 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: HA 375 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: KA 326 ASN cc_start: 0.7327 (t0) cc_final: 0.7119 (t0) REVERT: KA 445 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: LA 375 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: MA 350 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: MA 375 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8045 (mtm) REVERT: PA 326 ASN cc_start: 0.7330 (t0) cc_final: 0.7116 (t0) REVERT: PA 445 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: QA 375 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8292 (mtt) REVERT: RA 350 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: RA 375 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8489 (mtm) REVERT: UA 326 ASN cc_start: 0.7326 (t0) cc_final: 0.7119 (t0) REVERT: UA 445 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: VA 375 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: WA 350 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: WA 375 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (mtm) REVERT: ZA 326 ASN cc_start: 0.7331 (t0) cc_final: 0.7115 (t0) REVERT: ZA 445 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: AB 375 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: BB 350 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: BB 375 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: EB 326 ASN cc_start: 0.7322 (t0) cc_final: 0.7115 (t0) REVERT: EB 445 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: FB 375 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: GB 350 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: GB 375 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (mtm) outliers start: 372 outliers final: 152 residues processed: 1566 average time/residue: 1.5053 time to fit residues: 3277.7370 Evaluate side-chains 1462 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1262 time to evaluate : 7.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 285 ASP Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain M residue 247 VAL Chi-restraints excluded: chain M residue 273 SER Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 350 GLU Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain O residue 247 VAL Chi-restraints excluded: chain O residue 273 SER Chi-restraints excluded: chain O residue 307 ASP Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 247 VAL Chi-restraints excluded: chain Q residue 273 SER Chi-restraints excluded: chain Q residue 285 ASP Chi-restraints excluded: chain Q residue 315 THR Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 350 GLU Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 273 SER Chi-restraints excluded: chain T residue 307 ASP Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 247 VAL Chi-restraints excluded: chain W residue 273 SER Chi-restraints excluded: chain W residue 285 ASP Chi-restraints excluded: chain W residue 315 THR Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 273 SER Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 315 THR Chi-restraints excluded: chain X residue 350 GLU Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 247 VAL Chi-restraints excluded: chain Z residue 273 SER Chi-restraints excluded: chain Z residue 307 ASP Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 247 VAL Chi-restraints excluded: chain BA residue 273 SER Chi-restraints excluded: chain BA residue 285 ASP Chi-restraints excluded: chain BA residue 315 THR Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain CA residue 247 VAL Chi-restraints excluded: chain CA residue 273 SER Chi-restraints excluded: chain CA residue 285 ASP Chi-restraints excluded: chain CA residue 315 THR Chi-restraints excluded: chain CA residue 350 GLU Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 315 THR Chi-restraints excluded: chain EA residue 247 VAL Chi-restraints excluded: chain EA residue 273 SER Chi-restraints excluded: chain EA residue 307 ASP Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 247 VAL Chi-restraints excluded: chain GA residue 273 SER Chi-restraints excluded: chain GA residue 285 ASP Chi-restraints excluded: chain GA residue 315 THR Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain HA residue 247 VAL Chi-restraints excluded: chain HA residue 273 SER Chi-restraints excluded: chain HA residue 285 ASP Chi-restraints excluded: chain HA residue 315 THR Chi-restraints excluded: chain HA residue 350 GLU Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 315 THR Chi-restraints excluded: chain JA residue 247 VAL Chi-restraints excluded: chain JA residue 273 SER Chi-restraints excluded: chain JA residue 307 ASP Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 247 VAL Chi-restraints excluded: chain LA residue 273 SER Chi-restraints excluded: chain LA residue 285 ASP Chi-restraints excluded: chain LA residue 315 THR Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain MA residue 247 VAL Chi-restraints excluded: chain MA residue 273 SER Chi-restraints excluded: chain MA residue 285 ASP Chi-restraints excluded: chain MA residue 315 THR Chi-restraints excluded: chain MA residue 350 GLU Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 315 THR Chi-restraints excluded: chain OA residue 247 VAL Chi-restraints excluded: chain OA residue 273 SER Chi-restraints excluded: chain OA residue 307 ASP Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 247 VAL Chi-restraints excluded: chain QA residue 273 SER Chi-restraints excluded: chain QA residue 285 ASP Chi-restraints excluded: chain QA residue 315 THR Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 247 VAL Chi-restraints excluded: chain RA residue 273 SER Chi-restraints excluded: chain RA residue 285 ASP Chi-restraints excluded: chain RA residue 315 THR Chi-restraints excluded: chain RA residue 350 GLU Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 315 THR Chi-restraints excluded: chain TA residue 247 VAL Chi-restraints excluded: chain TA residue 273 SER Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 247 VAL Chi-restraints excluded: chain VA residue 273 SER Chi-restraints excluded: chain VA residue 285 ASP Chi-restraints excluded: chain VA residue 315 THR Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 247 VAL Chi-restraints excluded: chain WA residue 273 SER Chi-restraints excluded: chain WA residue 285 ASP Chi-restraints excluded: chain WA residue 315 THR Chi-restraints excluded: chain WA residue 350 GLU Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 315 THR Chi-restraints excluded: chain YA residue 247 VAL Chi-restraints excluded: chain YA residue 273 SER Chi-restraints excluded: chain YA residue 307 ASP Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 247 VAL Chi-restraints excluded: chain AB residue 273 SER Chi-restraints excluded: chain AB residue 285 ASP Chi-restraints excluded: chain AB residue 315 THR Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 247 VAL Chi-restraints excluded: chain BB residue 273 SER Chi-restraints excluded: chain BB residue 285 ASP Chi-restraints excluded: chain BB residue 315 THR Chi-restraints excluded: chain BB residue 350 GLU Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain DB residue 247 VAL Chi-restraints excluded: chain DB residue 273 SER Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 247 VAL Chi-restraints excluded: chain FB residue 273 SER Chi-restraints excluded: chain FB residue 285 ASP Chi-restraints excluded: chain FB residue 315 THR Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 247 VAL Chi-restraints excluded: chain GB residue 273 SER Chi-restraints excluded: chain GB residue 285 ASP Chi-restraints excluded: chain GB residue 315 THR Chi-restraints excluded: chain GB residue 350 GLU Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 315 THR Chi-restraints excluded: chain IB residue 247 VAL Chi-restraints excluded: chain IB residue 273 SER Chi-restraints excluded: chain IB residue 307 ASP Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1287 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 760 optimal weight: 20.0000 chunk 975 optimal weight: 0.6980 chunk 755 optimal weight: 2.9990 chunk 1123 optimal weight: 1.9990 chunk 745 optimal weight: 0.3980 chunk 1330 optimal weight: 1.9990 chunk 832 optimal weight: 0.7980 chunk 810 optimal weight: 0.4980 chunk 614 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 269 GLN B 326 ASN C 269 GLN D 252 HIS E 269 GLN F 269 GLN G 269 GLN G 326 ASN H 269 GLN I 252 HIS J 269 GLN K 250 ASN K 269 GLN L 269 GLN L 326 ASN M 269 GLN N 252 HIS O 269 GLN P 250 ASN P 269 GLN Q 269 GLN Q 326 ASN R 269 GLN S 252 HIS T 269 GLN V 269 GLN W 269 GLN W 326 ASN X 269 GLN Y 252 HIS Z 269 GLN AA 269 GLN BA 269 GLN BA 326 ASN CA 269 GLN DA 252 HIS EA 269 GLN FA 269 GLN GA 269 GLN GA 326 ASN HA 269 GLN IA 252 HIS JA 269 GLN KA 269 GLN LA 269 GLN LA 326 ASN MA 269 GLN NA 252 HIS OA 269 GLN PA 250 ASN PA 269 GLN QA 269 GLN QA 326 ASN RA 269 GLN SA 252 HIS TA 269 GLN UA 269 GLN VA 269 GLN VA 326 ASN WA 269 GLN XA 252 HIS YA 269 GLN ZA 269 GLN AB 269 GLN AB 326 ASN BB 269 GLN CB 252 HIS DB 269 GLN EB 250 ASN EB 269 GLN FB 269 GLN FB 326 ASN GB 252 HIS GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 106740 Z= 0.107 Angle : 0.426 9.309 144780 Z= 0.217 Chirality : 0.044 0.131 17280 Planarity : 0.003 0.036 18540 Dihedral : 3.882 16.002 14580 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.33 % Allowed : 15.52 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.60 (0.07), residues: 13800 helix: 3.31 (0.07), residues: 4980 sheet: 0.20 (0.09), residues: 2820 loop : -0.48 (0.08), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPKA 419 HIS 0.005 0.001 HISUA 252 PHE 0.014 0.002 PHEVA 253 TYR 0.021 0.002 TYRIB 365 ARG 0.001 0.000 ARGEB 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1293 time to evaluate : 7.527 Fit side-chains REVERT: A 445 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: C 375 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8524 (mtm) REVERT: D 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7161 (mtt-85) REVERT: D 402 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: F 445 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: G 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: H 375 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8525 (mtm) REVERT: I 297 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7159 (mtt-85) REVERT: I 402 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: K 445 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: L 375 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: M 375 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: N 297 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7160 (mtt-85) REVERT: N 402 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: P 445 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: Q 375 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: R 375 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8523 (mtm) REVERT: S 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7160 (mtt-85) REVERT: S 402 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: V 445 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: W 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8273 (mtt) REVERT: X 375 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8495 (mtm) REVERT: Y 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7161 (mtt-85) REVERT: Y 402 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: AA 445 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: BA 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: CA 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: DA 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7162 (mtt-85) REVERT: DA 402 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: FA 445 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: GA 375 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: HA 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: IA 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7161 (mtt-85) REVERT: IA 402 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: KA 445 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: LA 375 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: MA 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: NA 297 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7160 (mtt-85) REVERT: NA 402 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: PA 445 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: QA 375 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: RA 375 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: SA 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7160 (mtt-85) REVERT: SA 402 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: UA 445 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: VA 375 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8266 (mtt) REVERT: WA 375 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: XA 297 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7162 (mtt-85) REVERT: XA 402 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: ZA 445 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: AB 375 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: BB 375 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8497 (mtm) REVERT: CB 297 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7162 (mtt-85) REVERT: CB 402 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: EB 445 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: FB 375 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: GB 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8493 (mtm) REVERT: HB 297 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7163 (mtt-85) REVERT: HB 402 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7688 (mt0) outliers start: 270 outliers final: 72 residues processed: 1455 average time/residue: 1.4578 time to fit residues: 2931.5884 Evaluate side-chains 1352 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1220 time to evaluate : 7.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 297 ARG Chi-restraints excluded: chain I residue 402 GLN Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 307 ASP Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 285 ASP Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 258 ASN Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 402 GLN Chi-restraints excluded: chain O residue 273 SER Chi-restraints excluded: chain O residue 307 ASP Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 247 VAL Chi-restraints excluded: chain Q residue 285 ASP Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 258 ASN Chi-restraints excluded: chain S residue 297 ARG Chi-restraints excluded: chain S residue 402 GLN Chi-restraints excluded: chain T residue 307 ASP Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 247 VAL Chi-restraints excluded: chain W residue 285 ASP Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 297 ARG Chi-restraints excluded: chain Y residue 402 GLN Chi-restraints excluded: chain Z residue 273 SER Chi-restraints excluded: chain Z residue 307 ASP Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 247 VAL Chi-restraints excluded: chain BA residue 285 ASP Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain CA residue 285 ASP Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 297 ARG Chi-restraints excluded: chain DA residue 402 GLN Chi-restraints excluded: chain EA residue 273 SER Chi-restraints excluded: chain EA residue 307 ASP Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 247 VAL Chi-restraints excluded: chain GA residue 285 ASP Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain HA residue 285 ASP Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 297 ARG Chi-restraints excluded: chain IA residue 402 GLN Chi-restraints excluded: chain JA residue 273 SER Chi-restraints excluded: chain JA residue 307 ASP Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 247 VAL Chi-restraints excluded: chain LA residue 285 ASP Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain MA residue 285 ASP Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 297 ARG Chi-restraints excluded: chain NA residue 402 GLN Chi-restraints excluded: chain OA residue 307 ASP Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 247 VAL Chi-restraints excluded: chain QA residue 285 ASP Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 285 ASP Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 297 ARG Chi-restraints excluded: chain SA residue 402 GLN Chi-restraints excluded: chain TA residue 273 SER Chi-restraints excluded: chain TA residue 307 ASP Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 247 VAL Chi-restraints excluded: chain VA residue 285 ASP Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 285 ASP Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 297 ARG Chi-restraints excluded: chain XA residue 402 GLN Chi-restraints excluded: chain YA residue 273 SER Chi-restraints excluded: chain YA residue 307 ASP Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 247 VAL Chi-restraints excluded: chain AB residue 285 ASP Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 285 ASP Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 297 ARG Chi-restraints excluded: chain CB residue 402 GLN Chi-restraints excluded: chain DB residue 273 SER Chi-restraints excluded: chain DB residue 307 ASP Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 247 VAL Chi-restraints excluded: chain FB residue 285 ASP Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 285 ASP Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 297 ARG Chi-restraints excluded: chain HB residue 402 GLN Chi-restraints excluded: chain IB residue 273 SER Chi-restraints excluded: chain IB residue 307 ASP Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 822 optimal weight: 0.7980 chunk 531 optimal weight: 8.9990 chunk 794 optimal weight: 2.9990 chunk 400 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 845 optimal weight: 5.9990 chunk 906 optimal weight: 9.9990 chunk 657 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 1045 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 269 GLN C 269 GLN D 252 HIS E 269 GLN F 250 ASN F 252 HIS F 269 GLN G 269 GLN H 269 GLN I 252 HIS J 269 GLN K 250 ASN K 269 GLN L 269 GLN M 269 GLN N 252 HIS O 269 GLN P 250 ASN P 252 HIS P 269 GLN Q 269 GLN R 269 GLN S 252 HIS T 269 GLN V 250 ASN V 269 GLN W 269 GLN X 269 GLN Y 252 HIS Z 269 GLN AA 250 ASN AA 269 GLN BA 269 GLN CA 269 GLN DA 252 HIS EA 269 GLN FA 250 ASN FA 269 GLN GA 269 GLN HA 269 GLN IA 252 HIS JA 269 GLN KA 250 ASN KA 252 HIS KA 269 GLN LA 269 GLN MA 269 GLN NA 252 HIS OA 269 GLN PA 250 ASN PA 269 GLN QA 269 GLN RA 269 GLN SA 252 HIS TA 269 GLN UA 250 ASN UA 269 GLN VA 269 GLN WA 269 GLN XA 252 HIS YA 269 GLN ZA 250 ASN ZA 269 GLN AB 269 GLN BB 269 GLN CB 252 HIS DB 269 GLN EB 250 ASN EB 269 GLN FB 269 GLN GB 250 ASN GB 252 HIS GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 106740 Z= 0.204 Angle : 0.457 9.215 144780 Z= 0.235 Chirality : 0.045 0.133 17280 Planarity : 0.004 0.037 18540 Dihedral : 4.073 17.199 14580 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.44 % Allowed : 15.91 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.07), residues: 13800 helix: 3.18 (0.07), residues: 4980 sheet: 0.24 (0.09), residues: 2820 loop : -0.55 (0.08), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 419 HIS 0.005 0.001 HIS P 252 PHE 0.015 0.002 PHESA 253 TYR 0.021 0.002 TYR T 365 ARG 0.001 0.000 ARG M 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1250 time to evaluate : 7.578 Fit side-chains REVERT: A 445 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: B 375 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8288 (mtt) REVERT: C 375 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: D 297 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: D 402 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: E 389 ASN cc_start: 0.8753 (m110) cc_final: 0.8519 (m110) REVERT: F 445 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: G 375 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: H 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: I 402 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: J 389 ASN cc_start: 0.8780 (m110) cc_final: 0.8553 (m110) REVERT: K 445 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: L 375 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: M 375 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8478 (mtm) REVERT: N 402 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: O 389 ASN cc_start: 0.8754 (m110) cc_final: 0.8519 (m110) REVERT: P 445 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: Q 375 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: R 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: S 402 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: T 389 ASN cc_start: 0.8782 (m110) cc_final: 0.8554 (m110) REVERT: V 445 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: W 375 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: X 375 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8468 (mtm) REVERT: Y 402 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: Z 389 ASN cc_start: 0.8754 (m110) cc_final: 0.8515 (m110) REVERT: AA 445 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: BA 375 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: CA 375 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8071 (mtm) REVERT: DA 402 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: EA 389 ASN cc_start: 0.8781 (m110) cc_final: 0.8556 (m110) REVERT: FA 445 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: GA 375 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8288 (mtt) REVERT: HA 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: IA 402 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: JA 389 ASN cc_start: 0.8755 (m110) cc_final: 0.8519 (m110) REVERT: KA 445 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: LA 375 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8286 (mtt) REVERT: MA 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: NA 402 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: OA 389 ASN cc_start: 0.8779 (m110) cc_final: 0.8554 (m110) REVERT: PA 445 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: QA 375 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8314 (mtt) REVERT: RA 375 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8072 (mtm) REVERT: SA 402 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: UA 445 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: VA 375 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: WA 375 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: XA 402 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: ZA 445 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: AB 375 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: BB 375 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8468 (mtm) REVERT: CB 402 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: EB 445 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: FB 375 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8314 (mtt) REVERT: GB 375 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8463 (mtm) REVERT: HB 402 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: IB 389 ASN cc_start: 0.8780 (m110) cc_final: 0.8554 (m110) outliers start: 282 outliers final: 99 residues processed: 1444 average time/residue: 1.4248 time to fit residues: 2860.1428 Evaluate side-chains 1393 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1245 time to evaluate : 7.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 343 SER Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain I residue 402 GLN Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 285 ASP Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 273 SER Chi-restraints excluded: chain N residue 315 THR Chi-restraints excluded: chain N residue 402 GLN Chi-restraints excluded: chain O residue 273 SER Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 247 VAL Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 ASP Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain R residue 343 SER Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 273 SER Chi-restraints excluded: chain S residue 402 GLN Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 247 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain W residue 285 ASP Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 343 SER Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 273 SER Chi-restraints excluded: chain Y residue 402 GLN Chi-restraints excluded: chain Z residue 273 SER Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 247 VAL Chi-restraints excluded: chain BA residue 281 LEU Chi-restraints excluded: chain BA residue 285 ASP Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain CA residue 285 ASP Chi-restraints excluded: chain CA residue 343 SER Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 258 ASN Chi-restraints excluded: chain DA residue 273 SER Chi-restraints excluded: chain DA residue 402 GLN Chi-restraints excluded: chain EA residue 273 SER Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 247 VAL Chi-restraints excluded: chain GA residue 281 LEU Chi-restraints excluded: chain GA residue 285 ASP Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain HA residue 285 ASP Chi-restraints excluded: chain HA residue 343 SER Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 273 SER Chi-restraints excluded: chain IA residue 402 GLN Chi-restraints excluded: chain JA residue 273 SER Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 247 VAL Chi-restraints excluded: chain LA residue 281 LEU Chi-restraints excluded: chain LA residue 285 ASP Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain MA residue 285 ASP Chi-restraints excluded: chain MA residue 343 SER Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 258 ASN Chi-restraints excluded: chain NA residue 402 GLN Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 247 VAL Chi-restraints excluded: chain QA residue 281 LEU Chi-restraints excluded: chain QA residue 285 ASP Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 285 ASP Chi-restraints excluded: chain RA residue 343 SER Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 273 SER Chi-restraints excluded: chain SA residue 402 GLN Chi-restraints excluded: chain TA residue 273 SER Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 247 VAL Chi-restraints excluded: chain VA residue 281 LEU Chi-restraints excluded: chain VA residue 285 ASP Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 285 ASP Chi-restraints excluded: chain WA residue 343 SER Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 273 SER Chi-restraints excluded: chain XA residue 402 GLN Chi-restraints excluded: chain YA residue 273 SER Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 247 VAL Chi-restraints excluded: chain AB residue 281 LEU Chi-restraints excluded: chain AB residue 285 ASP Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 285 ASP Chi-restraints excluded: chain BB residue 343 SER Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 258 ASN Chi-restraints excluded: chain CB residue 273 SER Chi-restraints excluded: chain CB residue 315 THR Chi-restraints excluded: chain CB residue 402 GLN Chi-restraints excluded: chain DB residue 273 SER Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 247 VAL Chi-restraints excluded: chain FB residue 281 LEU Chi-restraints excluded: chain FB residue 285 ASP Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 285 ASP Chi-restraints excluded: chain GB residue 343 SER Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 258 ASN Chi-restraints excluded: chain HB residue 273 SER Chi-restraints excluded: chain HB residue 402 GLN Chi-restraints excluded: chain IB residue 273 SER Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1209 optimal weight: 20.0000 chunk 1274 optimal weight: 0.6980 chunk 1162 optimal weight: 1.9990 chunk 1239 optimal weight: 6.9990 chunk 1273 optimal weight: 0.0770 chunk 746 optimal weight: 2.9990 chunk 539 optimal weight: 4.9990 chunk 973 optimal weight: 0.9980 chunk 380 optimal weight: 0.8980 chunk 1120 optimal weight: 2.9990 chunk 1172 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 269 GLN C 269 GLN D 252 HIS E 269 GLN F 250 ASN F 252 HIS F 269 GLN G 269 GLN H 269 GLN I 252 HIS J 269 GLN K 250 ASN K 269 GLN L 269 GLN M 269 GLN N 252 HIS O 269 GLN P 250 ASN P 252 HIS P 269 GLN Q 269 GLN R 269 GLN S 252 HIS T 269 GLN V 250 ASN V 269 GLN W 269 GLN X 269 GLN Y 252 HIS Z 269 GLN AA 250 ASN AA 269 GLN BA 269 GLN CA 269 GLN DA 252 HIS EA 269 GLN FA 250 ASN FA 269 GLN GA 269 GLN HA 269 GLN IA 252 HIS JA 269 GLN KA 250 ASN KA 269 GLN LA 269 GLN MA 269 GLN NA 252 HIS OA 269 GLN PA 250 ASN PA 269 GLN QA 269 GLN RA 269 GLN SA 252 HIS TA 269 GLN UA 250 ASN UA 269 GLN VA 269 GLN WA 269 GLN XA 252 HIS YA 269 GLN ZA 250 ASN ZA 269 GLN AB 269 GLN BB 269 GLN CB 252 HIS DB 269 GLN EB 250 ASN EB 269 GLN FB 269 GLN GB 252 HIS GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 106740 Z= 0.132 Angle : 0.427 9.481 144780 Z= 0.218 Chirality : 0.044 0.130 17280 Planarity : 0.003 0.034 18540 Dihedral : 3.893 16.424 14580 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.54 % Allowed : 17.05 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.71 (0.07), residues: 13800 helix: 3.41 (0.07), residues: 4980 sheet: 0.29 (0.09), residues: 2820 loop : -0.43 (0.08), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP V 419 HIS 0.006 0.001 HISAA 252 PHE 0.013 0.002 PHEQA 253 TYR 0.021 0.002 TYRTA 365 ARG 0.001 0.000 ARGZA 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1236 time to evaluate : 7.566 Fit side-chains REVERT: A 445 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: B 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8298 (mtt) REVERT: C 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: D 297 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7205 (mtt-85) REVERT: E 389 ASN cc_start: 0.8731 (m110) cc_final: 0.8477 (m110) REVERT: F 445 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: G 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8292 (mtt) REVERT: H 375 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: I 297 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7204 (mtt-85) REVERT: J 389 ASN cc_start: 0.8741 (m110) cc_final: 0.8485 (m110) REVERT: K 445 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: L 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8295 (mtt) REVERT: M 375 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8493 (mtm) REVERT: N 297 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7206 (mtt-85) REVERT: O 389 ASN cc_start: 0.8732 (m110) cc_final: 0.8477 (m110) REVERT: P 445 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: Q 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8298 (mtt) REVERT: R 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8490 (mtm) REVERT: S 297 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7206 (mtt-85) REVERT: T 389 ASN cc_start: 0.8742 (m110) cc_final: 0.8485 (m110) REVERT: V 445 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: W 375 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: X 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: Y 297 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7210 (mtt-85) REVERT: Y 402 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: Z 389 ASN cc_start: 0.8732 (m110) cc_final: 0.8476 (m110) REVERT: AA 445 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: BA 375 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8292 (mtt) REVERT: CA 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8065 (mtm) REVERT: DA 297 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7212 (mtt-85) REVERT: DA 402 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: EA 389 ASN cc_start: 0.8739 (m110) cc_final: 0.8484 (m110) REVERT: FA 445 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: GA 375 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: HA 375 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: IA 297 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7209 (mtt-85) REVERT: IA 402 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: JA 389 ASN cc_start: 0.8735 (m110) cc_final: 0.8477 (m110) REVERT: KA 445 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: LA 375 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: MA 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: NA 297 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7209 (mtt-85) REVERT: NA 402 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: OA 389 ASN cc_start: 0.8739 (m110) cc_final: 0.8485 (m110) REVERT: PA 445 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: QA 375 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8283 (mtt) REVERT: RA 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: SA 297 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7213 (mtt-85) REVERT: SA 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: UA 445 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: VA 375 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8273 (mtt) REVERT: WA 375 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8066 (mtm) REVERT: XA 297 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7214 (mtt-85) REVERT: XA 402 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: ZA 445 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: AB 375 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: BB 375 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8060 (mtm) REVERT: CB 297 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7210 (mtt-85) REVERT: EB 445 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: FB 375 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: GB 375 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8065 (mtm) REVERT: HB 297 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7217 (mtt-85) REVERT: HB 402 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: IB 389 ASN cc_start: 0.8736 (m110) cc_final: 0.8482 (m110) outliers start: 178 outliers final: 72 residues processed: 1341 average time/residue: 1.4029 time to fit residues: 2619.7678 Evaluate side-chains 1324 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1197 time to evaluate : 7.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain G residue 377 MET Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 297 ARG Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 285 ASP Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain L residue 377 MET Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain O residue 273 SER Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 ASP Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain Q residue 377 MET Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 297 ARG Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain W residue 285 ASP Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 273 SER Chi-restraints excluded: chain Y residue 297 ARG Chi-restraints excluded: chain Y residue 402 GLN Chi-restraints excluded: chain Z residue 273 SER Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 281 LEU Chi-restraints excluded: chain BA residue 285 ASP Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain BA residue 377 MET Chi-restraints excluded: chain CA residue 285 ASP Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 273 SER Chi-restraints excluded: chain DA residue 297 ARG Chi-restraints excluded: chain DA residue 402 GLN Chi-restraints excluded: chain EA residue 273 SER Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 281 LEU Chi-restraints excluded: chain GA residue 285 ASP Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain GA residue 377 MET Chi-restraints excluded: chain HA residue 285 ASP Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 297 ARG Chi-restraints excluded: chain IA residue 402 GLN Chi-restraints excluded: chain JA residue 273 SER Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 281 LEU Chi-restraints excluded: chain LA residue 285 ASP Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain LA residue 377 MET Chi-restraints excluded: chain MA residue 285 ASP Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 273 SER Chi-restraints excluded: chain NA residue 297 ARG Chi-restraints excluded: chain NA residue 402 GLN Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 281 LEU Chi-restraints excluded: chain QA residue 285 ASP Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 285 ASP Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 273 SER Chi-restraints excluded: chain SA residue 297 ARG Chi-restraints excluded: chain SA residue 402 GLN Chi-restraints excluded: chain TA residue 273 SER Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 281 LEU Chi-restraints excluded: chain VA residue 285 ASP Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 285 ASP Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 297 ARG Chi-restraints excluded: chain XA residue 402 GLN Chi-restraints excluded: chain YA residue 273 SER Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 281 LEU Chi-restraints excluded: chain AB residue 285 ASP Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 285 ASP Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 297 ARG Chi-restraints excluded: chain DB residue 273 SER Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 281 LEU Chi-restraints excluded: chain FB residue 285 ASP Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 285 ASP Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 273 SER Chi-restraints excluded: chain HB residue 297 ARG Chi-restraints excluded: chain HB residue 402 GLN Chi-restraints excluded: chain IB residue 273 SER Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1235 optimal weight: 8.9990 chunk 813 optimal weight: 2.9990 chunk 1310 optimal weight: 9.9990 chunk 799 optimal weight: 1.9990 chunk 621 optimal weight: 0.9980 chunk 911 optimal weight: 3.9990 chunk 1374 optimal weight: 0.9980 chunk 1265 optimal weight: 0.9990 chunk 1094 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 845 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 269 GLN C 269 GLN D 252 HIS E 269 GLN F 252 HIS F 269 GLN G 269 GLN H 269 GLN I 252 HIS J 269 GLN K 250 ASN K 269 GLN L 269 GLN M 269 GLN N 252 HIS O 269 GLN P 252 HIS P 269 GLN Q 269 GLN R 269 GLN S 252 HIS T 269 GLN V 250 ASN V 269 GLN W 269 GLN X 269 GLN Y 252 HIS Z 269 GLN AA 252 HIS AA 269 GLN BA 269 GLN CA 269 GLN DA 252 HIS EA 269 GLN FA 250 ASN FA 269 GLN GA 269 GLN HA 269 GLN IA 252 HIS JA 269 GLN KA 252 HIS KA 269 GLN LA 269 GLN MA 269 GLN NA 252 HIS OA 269 GLN PA 250 ASN PA 269 GLN QA 269 GLN RA 269 GLN SA 252 HIS TA 269 GLN UA 252 HIS UA 269 GLN VA 269 GLN WA 269 GLN XA 252 HIS YA 269 GLN ZA 250 ASN ZA 269 GLN AB 269 GLN BB 269 GLN CB 252 HIS DB 269 GLN EB 250 ASN EB 252 HIS EB 269 GLN FB 269 GLN GB 250 ASN GB 252 HIS GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 106740 Z= 0.149 Angle : 0.429 8.969 144780 Z= 0.219 Chirality : 0.044 0.131 17280 Planarity : 0.003 0.034 18540 Dihedral : 3.919 16.768 14580 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.50 % Allowed : 17.60 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.75 (0.07), residues: 13800 helix: 3.45 (0.07), residues: 4980 sheet: 0.31 (0.09), residues: 2820 loop : -0.42 (0.08), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPEB 419 HIS 0.007 0.001 HIS F 252 PHE 0.014 0.002 PHEIA 253 TYR 0.022 0.002 TYR E 365 ARG 0.001 0.000 ARG I 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27600 Ramachandran restraints generated. 13800 Oldfield, 0 Emsley, 13800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1182 time to evaluate : 7.553 Fit side-chains REVERT: A 445 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: B 375 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: C 375 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: D 297 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7223 (mtt-85) REVERT: D 402 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: E 389 ASN cc_start: 0.8736 (m110) cc_final: 0.8470 (m110) REVERT: F 445 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: G 375 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: H 375 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: I 297 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7224 (mtt-85) REVERT: I 402 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: J 389 ASN cc_start: 0.8743 (m110) cc_final: 0.8475 (m110) REVERT: K 445 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: L 375 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8292 (mtt) REVERT: M 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8507 (mtm) REVERT: N 297 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7222 (mtt-85) REVERT: N 402 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: O 389 ASN cc_start: 0.8735 (m110) cc_final: 0.8470 (m110) REVERT: P 445 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: Q 375 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8297 (mtt) REVERT: R 375 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8505 (mtm) REVERT: S 297 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7222 (mtt-85) REVERT: S 402 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: T 389 ASN cc_start: 0.8744 (m110) cc_final: 0.8477 (m110) REVERT: V 445 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: W 375 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: X 375 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: Y 297 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7224 (mtt-85) REVERT: Y 402 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: Z 389 ASN cc_start: 0.8736 (m110) cc_final: 0.8468 (m110) REVERT: AA 445 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: BA 375 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: CA 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8482 (mtm) REVERT: DA 297 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7226 (mtt-85) REVERT: DA 402 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: EA 389 ASN cc_start: 0.8742 (m110) cc_final: 0.8475 (m110) REVERT: FA 445 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: GA 375 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8280 (mtt) REVERT: HA 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8489 (mtm) REVERT: IA 297 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7224 (mtt-85) REVERT: IA 402 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: JA 389 ASN cc_start: 0.8739 (m110) cc_final: 0.8471 (m110) REVERT: KA 445 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: LA 375 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: MA 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: NA 297 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7223 (mtt-85) REVERT: NA 402 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: OA 389 ASN cc_start: 0.8742 (m110) cc_final: 0.8476 (m110) REVERT: PA 445 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: QA 375 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: RA 375 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (mtm) REVERT: SA 297 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7224 (mtt-85) REVERT: SA 402 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: UA 445 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: VA 375 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: WA 375 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: XA 297 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7224 (mtt-85) REVERT: XA 402 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: ZA 445 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: AB 375 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8292 (mtt) REVERT: BB 375 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8484 (mtm) REVERT: CB 297 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7225 (mtt-85) REVERT: CB 402 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: EB 445 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: FB 375 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8295 (mtt) REVERT: GB 375 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: HB 297 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7226 (mtt-85) REVERT: HB 402 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: IB 389 ASN cc_start: 0.8740 (m110) cc_final: 0.8477 (m110) outliers start: 174 outliers final: 81 residues processed: 1282 average time/residue: 1.3692 time to fit residues: 2464.7619 Evaluate side-chains 1304 residues out of total 11580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1163 time to evaluate : 7.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain G residue 377 MET Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 343 SER Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain I residue 297 ARG Chi-restraints excluded: chain I residue 402 GLN Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 285 ASP Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain L residue 377 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 375 MET Chi-restraints excluded: chain N residue 273 SER Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 402 GLN Chi-restraints excluded: chain O residue 273 SER Chi-restraints excluded: chain O residue 375 MET Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 ASP Chi-restraints excluded: chain Q residue 375 MET Chi-restraints excluded: chain Q residue 377 MET Chi-restraints excluded: chain R residue 343 SER Chi-restraints excluded: chain R residue 375 MET Chi-restraints excluded: chain S residue 273 SER Chi-restraints excluded: chain S residue 297 ARG Chi-restraints excluded: chain S residue 402 GLN Chi-restraints excluded: chain T residue 375 MET Chi-restraints excluded: chain V residue 445 GLU Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain W residue 285 ASP Chi-restraints excluded: chain W residue 375 MET Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain X residue 343 SER Chi-restraints excluded: chain X residue 375 MET Chi-restraints excluded: chain Y residue 273 SER Chi-restraints excluded: chain Y residue 297 ARG Chi-restraints excluded: chain Y residue 402 GLN Chi-restraints excluded: chain Z residue 273 SER Chi-restraints excluded: chain Z residue 375 MET Chi-restraints excluded: chain AA residue 445 GLU Chi-restraints excluded: chain BA residue 281 LEU Chi-restraints excluded: chain BA residue 285 ASP Chi-restraints excluded: chain BA residue 375 MET Chi-restraints excluded: chain BA residue 377 MET Chi-restraints excluded: chain CA residue 285 ASP Chi-restraints excluded: chain CA residue 343 SER Chi-restraints excluded: chain CA residue 375 MET Chi-restraints excluded: chain DA residue 273 SER Chi-restraints excluded: chain DA residue 297 ARG Chi-restraints excluded: chain DA residue 402 GLN Chi-restraints excluded: chain EA residue 273 SER Chi-restraints excluded: chain EA residue 375 MET Chi-restraints excluded: chain FA residue 445 GLU Chi-restraints excluded: chain GA residue 281 LEU Chi-restraints excluded: chain GA residue 285 ASP Chi-restraints excluded: chain GA residue 375 MET Chi-restraints excluded: chain GA residue 377 MET Chi-restraints excluded: chain HA residue 343 SER Chi-restraints excluded: chain HA residue 375 MET Chi-restraints excluded: chain IA residue 273 SER Chi-restraints excluded: chain IA residue 297 ARG Chi-restraints excluded: chain IA residue 402 GLN Chi-restraints excluded: chain JA residue 273 SER Chi-restraints excluded: chain JA residue 375 MET Chi-restraints excluded: chain KA residue 445 GLU Chi-restraints excluded: chain LA residue 281 LEU Chi-restraints excluded: chain LA residue 285 ASP Chi-restraints excluded: chain LA residue 375 MET Chi-restraints excluded: chain LA residue 377 MET Chi-restraints excluded: chain MA residue 285 ASP Chi-restraints excluded: chain MA residue 343 SER Chi-restraints excluded: chain MA residue 375 MET Chi-restraints excluded: chain NA residue 273 SER Chi-restraints excluded: chain NA residue 297 ARG Chi-restraints excluded: chain NA residue 402 GLN Chi-restraints excluded: chain OA residue 375 MET Chi-restraints excluded: chain PA residue 445 GLU Chi-restraints excluded: chain QA residue 281 LEU Chi-restraints excluded: chain QA residue 285 ASP Chi-restraints excluded: chain QA residue 375 MET Chi-restraints excluded: chain RA residue 343 SER Chi-restraints excluded: chain RA residue 375 MET Chi-restraints excluded: chain SA residue 273 SER Chi-restraints excluded: chain SA residue 297 ARG Chi-restraints excluded: chain SA residue 402 GLN Chi-restraints excluded: chain TA residue 273 SER Chi-restraints excluded: chain TA residue 375 MET Chi-restraints excluded: chain UA residue 445 GLU Chi-restraints excluded: chain VA residue 281 LEU Chi-restraints excluded: chain VA residue 285 ASP Chi-restraints excluded: chain VA residue 375 MET Chi-restraints excluded: chain WA residue 343 SER Chi-restraints excluded: chain WA residue 375 MET Chi-restraints excluded: chain XA residue 273 SER Chi-restraints excluded: chain XA residue 297 ARG Chi-restraints excluded: chain XA residue 402 GLN Chi-restraints excluded: chain YA residue 273 SER Chi-restraints excluded: chain YA residue 375 MET Chi-restraints excluded: chain ZA residue 445 GLU Chi-restraints excluded: chain AB residue 281 LEU Chi-restraints excluded: chain AB residue 285 ASP Chi-restraints excluded: chain AB residue 375 MET Chi-restraints excluded: chain BB residue 343 SER Chi-restraints excluded: chain BB residue 375 MET Chi-restraints excluded: chain CB residue 273 SER Chi-restraints excluded: chain CB residue 297 ARG Chi-restraints excluded: chain CB residue 402 GLN Chi-restraints excluded: chain DB residue 273 SER Chi-restraints excluded: chain DB residue 375 MET Chi-restraints excluded: chain EB residue 445 GLU Chi-restraints excluded: chain FB residue 281 LEU Chi-restraints excluded: chain FB residue 285 ASP Chi-restraints excluded: chain FB residue 375 MET Chi-restraints excluded: chain GB residue 343 SER Chi-restraints excluded: chain GB residue 375 MET Chi-restraints excluded: chain HB residue 273 SER Chi-restraints excluded: chain HB residue 297 ARG Chi-restraints excluded: chain HB residue 402 GLN Chi-restraints excluded: chain IB residue 273 SER Chi-restraints excluded: chain IB residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 671 optimal weight: 4.9990 chunk 869 optimal weight: 0.9980 chunk 1166 optimal weight: 1.9990 chunk 335 optimal weight: 20.0000 chunk 1009 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 304 optimal weight: 6.9990 chunk 1096 optimal weight: 2.9990 chunk 458 optimal weight: 5.9990 chunk 1125 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 269 GLN B 269 GLN C 269 GLN D 252 HIS E 269 GLN F 252 HIS F 269 GLN G 269 GLN H 269 GLN I 252 HIS J 269 GLN K 250 ASN K 269 GLN L 269 GLN M 269 GLN N 252 HIS O 269 GLN P 252 HIS P 269 GLN Q 269 GLN R 269 GLN S 252 HIS T 269 GLN V 250 ASN V 269 GLN W 269 GLN X 269 GLN Y 252 HIS Z 269 GLN AA 252 HIS AA 269 GLN BA 269 GLN CA 269 GLN DA 252 HIS EA 269 GLN FA 250 ASN FA 269 GLN GA 269 GLN HA 269 GLN IA 252 HIS JA 269 GLN KA 252 HIS KA 269 GLN LA 269 GLN MA 269 GLN NA 252 HIS OA 269 GLN PA 250 ASN PA 269 GLN QA 269 GLN RA 269 GLN SA 252 HIS TA 269 GLN UA 252 HIS UA 269 GLN VA 269 GLN WA 269 GLN XA 252 HIS YA 269 GLN ZA 250 ASN ZA 269 GLN AB 269 GLN BB 269 GLN CB 252 HIS DB 269 GLN EB 250 ASN EB 252 HIS EB 269 GLN FB 269 GLN GB 250 ASN GB 269 GLN HB 252 HIS IB 269 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111635 restraints weight = 124617.392| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.10 r_work: 0.3074 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 106740 Z= 0.355 Angle : 0.528 7.931 144780 Z= 0.275 Chirality : 0.048 0.139 17280 Planarity : 0.004 0.033 18540 Dihedral : 4.436 18.405 14580 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.72 % Allowed : 17.34 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.14 (0.07), residues: 13800 helix: 2.75 (0.07), residues: 4980 sheet: 0.24 (0.09), residues: 2820 loop : -0.73 (0.07), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRPKA 419 HIS 0.008 0.001 HIS P 252 PHE 0.017 0.002 PHE Y 253 TYR 0.022 0.003 TYR E 365 ARG 0.003 0.000 ARGCA 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43937.58 seconds wall clock time: 756 minutes 17.55 seconds (45377.55 seconds total)