Starting phenix.real_space_refine on Mon Mar 25 10:18:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/03_2024/8fvg_29486.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/03_2024/8fvg_29486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/03_2024/8fvg_29486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/03_2024/8fvg_29486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/03_2024/8fvg_29486.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvg_29486/03_2024/8fvg_29486.pdb" } resolution = 3.1 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= 0.001 sd= 0.007 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 156 5.16 5 C 30225 2.51 5 N 8125 2.21 5 O 9503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 213": "OD1" <-> "OD2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 332": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 332": "OD1" <-> "OD2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C ASP 501": "OD1" <-> "OD2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 332": "OD1" <-> "OD2" Residue "E ASP 371": "OD1" <-> "OD2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E ASP 501": "OD1" <-> "OD2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 332": "OD1" <-> "OD2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F ASP 501": "OD1" <-> "OD2" Residue "G ASP 213": "OD1" <-> "OD2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 332": "OD1" <-> "OD2" Residue "G ASP 371": "OD1" <-> "OD2" Residue "G TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 498": "OE1" <-> "OE2" Residue "G ASP 501": "OD1" <-> "OD2" Residue "H ASP 213": "OD1" <-> "OD2" Residue "H PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 302": "OE1" <-> "OE2" Residue "H PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 332": "OD1" <-> "OD2" Residue "H ASP 371": "OD1" <-> "OD2" Residue "H TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H ASP 501": "OD1" <-> "OD2" Residue "I ASP 213": "OD1" <-> "OD2" Residue "I PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 332": "OD1" <-> "OD2" Residue "I ASP 371": "OD1" <-> "OD2" Residue "I TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 498": "OE1" <-> "OE2" Residue "I ASP 501": "OD1" <-> "OD2" Residue "J ASP 213": "OD1" <-> "OD2" Residue "J PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 302": "OE1" <-> "OE2" Residue "J PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 332": "OD1" <-> "OD2" Residue "J TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 371": "OD1" <-> "OD2" Residue "J TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 498": "OE1" <-> "OE2" Residue "J ASP 501": "OD1" <-> "OD2" Residue "K ASP 213": "OD1" <-> "OD2" Residue "K PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 302": "OE1" <-> "OE2" Residue "K PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 332": "OD1" <-> "OD2" Residue "K ASP 371": "OD1" <-> "OD2" Residue "K TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 498": "OE1" <-> "OE2" Residue "K ASP 501": "OD1" <-> "OD2" Residue "L ASP 213": "OD1" <-> "OD2" Residue "L PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 302": "OE1" <-> "OE2" Residue "L PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 332": "OD1" <-> "OD2" Residue "L TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 371": "OD1" <-> "OD2" Residue "L TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 498": "OE1" <-> "OE2" Residue "L ASP 501": "OD1" <-> "OD2" Residue "M ASP 213": "OD1" <-> "OD2" Residue "M PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 302": "OE1" <-> "OE2" Residue "M PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 332": "OD1" <-> "OD2" Residue "M ASP 371": "OD1" <-> "OD2" Residue "M TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 498": "OE1" <-> "OE2" Residue "M ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48009 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3693 Classifications: {'peptide': 493} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain breaks: 11 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 23.78, per 1000 atoms: 0.50 Number of scatterers: 48009 At special positions: 0 Unit cell: (275.52, 273.28, 286.72, 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 156 16.00 O 9503 8.00 N 8125 7.00 C 30225 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: 17.40 Conformation dependent library (CDL) restraints added in 8.6 seconds 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11908 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 91 sheets defined 33.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN A 254 " --> pdb=" O TRP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 399 Processing helix chain 'A' and resid 405 through 427 Proline residue: A 418 - end of helix removed outlier: 3.609A pdb=" N ALA A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'B' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN B 254 " --> pdb=" O TRP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 399 Processing helix chain 'B' and resid 405 through 427 Proline residue: B 418 - end of helix removed outlier: 3.609A pdb=" N ALA B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 Processing helix chain 'C' and resid 153 through 158 removed outlier: 4.362A pdb=" N GLN C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN C 254 " --> pdb=" O TRP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 4.124A pdb=" N GLY C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS C 341 " --> pdb=" O ASN C 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER C 342 " --> pdb=" O THR C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 399 Processing helix chain 'C' and resid 405 through 427 Proline residue: C 418 - end of helix removed outlier: 3.609A pdb=" N ALA C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 149 Processing helix chain 'D' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 254 removed outlier: 3.801A pdb=" N GLN D 254 " --> pdb=" O TRP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS D 341 " --> pdb=" O ASN D 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D 342 " --> pdb=" O THR D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 399 Processing helix chain 'D' and resid 405 through 427 Proline residue: D 418 - end of helix removed outlier: 3.609A pdb=" N ALA D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'E' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 149 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN E 158 " --> pdb=" O PRO E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL E 225 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN E 254 " --> pdb=" O TRP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 342 " --> pdb=" O THR E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 399 Processing helix chain 'E' and resid 405 through 427 Proline residue: E 418 - end of helix removed outlier: 3.608A pdb=" N ALA E 425 " --> pdb=" O ASP E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 447 Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN E 455 " --> pdb=" O ARG E 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 149 Processing helix chain 'F' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN F 254 " --> pdb=" O TRP F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS F 341 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER F 342 " --> pdb=" O THR F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 405 through 427 Proline residue: F 418 - end of helix removed outlier: 3.609A pdb=" N ALA F 425 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 447 Processing helix chain 'F' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN F 455 " --> pdb=" O ARG F 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 7 Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'G' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL G 225 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER G 226 " --> pdb=" O SER G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN G 254 " --> pdb=" O TRP G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR G 307 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS G 341 " --> pdb=" O ASN G 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER G 342 " --> pdb=" O THR G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 399 Processing helix chain 'G' and resid 405 through 427 Proline residue: G 418 - end of helix removed outlier: 3.609A pdb=" N ALA G 425 " --> pdb=" O ASP G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 447 Processing helix chain 'G' and resid 451 through 456 removed outlier: 3.560A pdb=" N GLN G 455 " --> pdb=" O ARG G 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 7 Processing helix chain 'H' and resid 48 through 55 Processing helix chain 'H' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 149 Processing helix chain 'H' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 226 " --> pdb=" O SER H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN H 254 " --> pdb=" O TRP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 4.124A pdb=" N GLY H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 307 removed outlier: 3.556A pdb=" N THR H 307 " --> pdb=" O ILE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS H 341 " --> pdb=" O ASN H 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER H 342 " --> pdb=" O THR H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 399 Processing helix chain 'H' and resid 405 through 427 Proline residue: H 418 - end of helix removed outlier: 3.609A pdb=" N ALA H 425 " --> pdb=" O ASP H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 447 Processing helix chain 'H' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN H 455 " --> pdb=" O ARG H 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA I 66 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 149 Processing helix chain 'I' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN I 158 " --> pdb=" O PRO I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER I 226 " --> pdb=" O SER I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 254 removed outlier: 3.801A pdb=" N GLN I 254 " --> pdb=" O TRP I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY I 270 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR I 307 " --> pdb=" O ILE I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS I 341 " --> pdb=" O ASN I 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER I 342 " --> pdb=" O THR I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 399 Processing helix chain 'I' and resid 405 through 427 Proline residue: I 418 - end of helix removed outlier: 3.609A pdb=" N ALA I 425 " --> pdb=" O ASP I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 447 Processing helix chain 'I' and resid 451 through 456 removed outlier: 3.560A pdb=" N GLN I 455 " --> pdb=" O ARG I 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 7 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 149 Processing helix chain 'J' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN J 158 " --> pdb=" O PRO J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL J 225 " --> pdb=" O LYS J 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN J 254 " --> pdb=" O TRP J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY J 270 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR J 271 " --> pdb=" O ALA J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 307 removed outlier: 3.555A pdb=" N THR J 307 " --> pdb=" O ILE J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS J 341 " --> pdb=" O ASN J 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER J 342 " --> pdb=" O THR J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 399 Processing helix chain 'J' and resid 405 through 427 Proline residue: J 418 - end of helix removed outlier: 3.609A pdb=" N ALA J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 447 Processing helix chain 'J' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN J 455 " --> pdb=" O ARG J 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 7 Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 149 Processing helix chain 'K' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN K 158 " --> pdb=" O PRO K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL K 225 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER K 226 " --> pdb=" O SER K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN K 254 " --> pdb=" O TRP K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR K 307 " --> pdb=" O ILE K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS K 341 " --> pdb=" O ASN K 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER K 342 " --> pdb=" O THR K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 399 Processing helix chain 'K' and resid 405 through 427 Proline residue: K 418 - end of helix removed outlier: 3.610A pdb=" N ALA K 425 " --> pdb=" O ASP K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 447 Processing helix chain 'K' and resid 451 through 456 removed outlier: 3.560A pdb=" N GLN K 455 " --> pdb=" O ARG K 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 48 through 55 Processing helix chain 'L' and resid 58 through 68 removed outlier: 3.632A pdb=" N ALA L 66 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 149 Processing helix chain 'L' and resid 153 through 158 removed outlier: 4.364A pdb=" N GLN L 158 " --> pdb=" O PRO L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 226 removed outlier: 3.735A pdb=" N VAL L 225 " --> pdb=" O LYS L 221 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 226 " --> pdb=" O SER L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 254 removed outlier: 3.801A pdb=" N GLN L 254 " --> pdb=" O TRP L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 271 " --> pdb=" O ALA L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.554A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 342 removed outlier: 3.617A pdb=" N LYS L 341 " --> pdb=" O ASN L 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER L 342 " --> pdb=" O THR L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 399 Processing helix chain 'L' and resid 405 through 427 Proline residue: L 418 - end of helix removed outlier: 3.609A pdb=" N ALA L 425 " --> pdb=" O ASP L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 447 Processing helix chain 'L' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN L 455 " --> pdb=" O ARG L 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 7 Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 58 through 68 removed outlier: 3.631A pdb=" N ALA M 66 " --> pdb=" O GLN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 149 Processing helix chain 'M' and resid 153 through 158 removed outlier: 4.363A pdb=" N GLN M 158 " --> pdb=" O PRO M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 226 removed outlier: 3.736A pdb=" N VAL M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER M 226 " --> pdb=" O SER M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 254 removed outlier: 3.800A pdb=" N GLN M 254 " --> pdb=" O TRP M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 272 removed outlier: 4.123A pdb=" N GLY M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 307 removed outlier: 3.556A pdb=" N THR M 307 " --> pdb=" O ILE M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 342 removed outlier: 3.618A pdb=" N LYS M 341 " --> pdb=" O ASN M 337 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER M 342 " --> pdb=" O THR M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 399 Processing helix chain 'M' and resid 405 through 427 Proline residue: M 418 - end of helix removed outlier: 3.609A pdb=" N ALA M 425 " --> pdb=" O ASP M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 447 Processing helix chain 'M' and resid 451 through 456 removed outlier: 3.559A pdb=" N GLN M 455 " --> pdb=" O ARG M 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL A 29 " --> pdb=" O ALA A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU A 172 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE A 117 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR A 260 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 285 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 262 " --> pdb=" O ASN A 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 465 Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR A 470 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL B 29 " --> pdb=" O ALA B 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU B 172 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE B 117 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR B 260 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN B 285 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 262 " --> pdb=" O ASN B 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AB4, first strand: chain 'B' and resid 461 through 465 Processing sheet with id=AB5, first strand: chain 'B' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR B 470 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL C 29 " --> pdb=" O ALA C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU C 172 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE C 117 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR C 260 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN C 285 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 262 " --> pdb=" O ASN C 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 347 through 348 Processing sheet with id=AC2, first strand: chain 'C' and resid 461 through 465 Processing sheet with id=AC3, first strand: chain 'C' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR C 470 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL D 29 " --> pdb=" O ALA D 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU D 172 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE D 117 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR D 260 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN D 285 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 262 " --> pdb=" O ASN D 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AC9, first strand: chain 'D' and resid 461 through 465 Processing sheet with id=AD1, first strand: chain 'D' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR D 470 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL E 29 " --> pdb=" O ALA E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU E 172 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 123 through 125 removed outlier: 4.715A pdb=" N ILE E 117 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR E 260 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN E 285 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL E 262 " --> pdb=" O ASN E 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 347 through 348 Processing sheet with id=AD7, first strand: chain 'E' and resid 461 through 465 Processing sheet with id=AD8, first strand: chain 'E' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR E 470 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL F 29 " --> pdb=" O ALA F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU F 172 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE F 117 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR F 260 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN F 285 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL F 262 " --> pdb=" O ASN F 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 347 through 348 Processing sheet with id=AE5, first strand: chain 'F' and resid 461 through 465 Processing sheet with id=AE6, first strand: chain 'F' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR F 470 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL G 29 " --> pdb=" O ALA G 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU G 172 " --> pdb=" O VAL G 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE G 117 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR G 260 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN G 285 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL G 262 " --> pdb=" O ASN G 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 347 through 348 Processing sheet with id=AF3, first strand: chain 'G' and resid 461 through 465 Processing sheet with id=AF4, first strand: chain 'G' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR G 470 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL H 29 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU H 172 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE H 117 " --> pdb=" O ALA H 185 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR H 260 " --> pdb=" O ALA H 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN H 285 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL H 262 " --> pdb=" O ASN H 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'H' and resid 347 through 348 Processing sheet with id=AG1, first strand: chain 'H' and resid 461 through 465 Processing sheet with id=AG2, first strand: chain 'H' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR H 470 " --> pdb=" O GLU H 479 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.443A pdb=" N VAL I 29 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'I' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU I 172 " --> pdb=" O VAL I 95 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE I 117 " --> pdb=" O ALA I 185 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR I 260 " --> pdb=" O ALA I 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN I 285 " --> pdb=" O TYR I 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL I 262 " --> pdb=" O ASN I 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'I' and resid 347 through 348 Processing sheet with id=AG8, first strand: chain 'I' and resid 461 through 465 Processing sheet with id=AG9, first strand: chain 'I' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR I 470 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL J 29 " --> pdb=" O ALA J 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'J' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU J 172 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 123 through 125 removed outlier: 4.715A pdb=" N ILE J 117 " --> pdb=" O ALA J 185 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR J 260 " --> pdb=" O ALA J 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN J 285 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL J 262 " --> pdb=" O ASN J 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'J' and resid 347 through 348 Processing sheet with id=AH6, first strand: chain 'J' and resid 461 through 465 Processing sheet with id=AH7, first strand: chain 'J' and resid 478 through 479 removed outlier: 3.688A pdb=" N TYR J 470 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL K 29 " --> pdb=" O ALA K 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'K' and resid 160 through 163 removed outlier: 3.638A pdb=" N LEU K 172 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 123 through 125 removed outlier: 4.716A pdb=" N ILE K 117 " --> pdb=" O ALA K 185 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 260 through 264 removed outlier: 6.281A pdb=" N TYR K 260 " --> pdb=" O ALA K 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN K 285 " --> pdb=" O TYR K 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL K 262 " --> pdb=" O ASN K 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'K' and resid 347 through 348 Processing sheet with id=AI4, first strand: chain 'K' and resid 461 through 465 Processing sheet with id=AI5, first strand: chain 'K' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR K 470 " --> pdb=" O GLU K 479 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.443A pdb=" N VAL L 29 " --> pdb=" O ALA L 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'L' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU L 172 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 123 through 125 removed outlier: 4.717A pdb=" N ILE L 117 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR L 260 " --> pdb=" O ALA L 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN L 285 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL L 262 " --> pdb=" O ASN L 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'L' and resid 347 through 348 Processing sheet with id=AJ2, first strand: chain 'L' and resid 461 through 465 Processing sheet with id=AJ3, first strand: chain 'L' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR L 470 " --> pdb=" O GLU L 479 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.442A pdb=" N VAL M 29 " --> pdb=" O ALA M 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'M' and resid 160 through 163 removed outlier: 3.639A pdb=" N LEU M 172 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 123 through 125 removed outlier: 4.717A pdb=" N ILE M 117 " --> pdb=" O ALA M 185 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 260 through 264 removed outlier: 6.282A pdb=" N TYR M 260 " --> pdb=" O ALA M 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN M 285 " --> pdb=" O TYR M 260 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL M 262 " --> pdb=" O ASN M 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'M' and resid 347 through 348 Processing sheet with id=AJ9, first strand: chain 'M' and resid 461 through 465 Processing sheet with id=AK1, first strand: chain 'M' and resid 478 through 479 removed outlier: 3.687A pdb=" N TYR M 470 " --> pdb=" O GLU M 479 " (cutoff:3.500A) 1560 hydrogen bonds defined for protein. 4329 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: 19.27 Time building geometry restraints manager: 18.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15885 1.34 - 1.46: 10424 1.46 - 1.58: 22155 1.58 - 1.69: 0 1.69 - 1.81: 286 Bond restraints: 48750 Sorted by residual: bond pdb=" CA GLY C 22 " pdb=" C GLY C 22 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 1.84e+00 bond pdb=" CB MET J 137 " pdb=" CG MET J 137 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB MET L 137 " pdb=" CG MET L 137 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB MET F 137 " pdb=" CG MET F 137 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB MET A 137 " pdb=" CG MET A 137 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 ... (remaining 48745 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 1092 106.92 - 113.69: 27584 113.69 - 120.46: 17491 120.46 - 127.22: 19808 127.22 - 133.99: 403 Bond angle restraints: 66378 Sorted by residual: angle pdb=" C SER E 74 " pdb=" N VAL E 75 " pdb=" CA VAL E 75 " ideal model delta sigma weight residual 121.70 126.93 -5.23 1.80e+00 3.09e-01 8.45e+00 angle pdb=" C SER I 74 " pdb=" N VAL I 75 " pdb=" CA VAL I 75 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.25e+00 angle pdb=" C SER K 74 " pdb=" N VAL K 75 " pdb=" CA VAL K 75 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" C SER G 74 " pdb=" N VAL G 75 " pdb=" CA VAL G 75 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.22e+00 angle pdb=" C SER C 74 " pdb=" N VAL C 75 " pdb=" CA VAL C 75 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.21e+00 ... (remaining 66373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 26156 17.71 - 35.43: 2067 35.43 - 53.14: 285 53.14 - 70.86: 131 70.86 - 88.57: 52 Dihedral angle restraints: 28691 sinusoidal: 10296 harmonic: 18395 Sorted by residual: dihedral pdb=" CA ALA M 196 " pdb=" C ALA M 196 " pdb=" N LEU M 197 " pdb=" CA LEU M 197 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA J 196 " pdb=" C ALA J 196 " pdb=" N LEU J 197 " pdb=" CA LEU J 197 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA G 196 " pdb=" C ALA G 196 " pdb=" N LEU G 197 " pdb=" CA LEU G 197 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 28688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4141 0.029 - 0.058: 2249 0.058 - 0.087: 703 0.087 - 0.116: 613 0.116 - 0.144: 172 Chirality restraints: 7878 Sorted by residual: chirality pdb=" CB VAL J 456 " pdb=" CA VAL J 456 " pdb=" CG1 VAL J 456 " pdb=" CG2 VAL J 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CB VAL I 456 " pdb=" CA VAL I 456 " pdb=" CG1 VAL I 456 " pdb=" CG2 VAL I 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB VAL B 456 " pdb=" CA VAL B 456 " pdb=" CG1 VAL B 456 " pdb=" CG2 VAL B 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 7875 not shown) Planarity restraints: 8567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 153 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO J 154 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 37 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO E 38 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 153 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 154 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.018 5.00e-02 4.00e+02 ... (remaining 8564 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 712 2.66 - 3.22: 45991 3.22 - 3.78: 68771 3.78 - 4.34: 91678 4.34 - 4.90: 154362 Nonbonded interactions: 361514 Sorted by model distance: nonbonded pdb=" OD1 ASP B 394 " pdb=" ND2 ASN B 398 " model vdw 2.106 2.520 nonbonded pdb=" OD1 ASP D 394 " pdb=" ND2 ASN D 398 " model vdw 2.106 2.520 nonbonded pdb=" OD1 ASP C 394 " pdb=" ND2 ASN C 398 " model vdw 2.106 2.520 nonbonded pdb=" OD1 ASP J 394 " pdb=" ND2 ASN J 398 " model vdw 2.106 2.520 nonbonded pdb=" OD1 ASP E 394 " pdb=" ND2 ASN E 398 " model vdw 2.106 2.520 ... (remaining 361509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 0.010 Normalize map: mean=0, sd=1: 1.460 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: 0.030 Extract box with map and model: 8.930 Check model and map are aligned: 0.700 Set scattering table: 0.440 Process input model: 118.490 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 0.039 48750 Z= 0.279 Angle : 0.657 6.647 66378 Z= 0.372 Chirality : 0.047 0.144 7878 Planarity : 0.004 0.033 8567 Dihedral : 14.205 88.571 16783 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 6110 helix: 1.38 (0.12), residues: 2041 sheet: 0.25 (0.19), residues: 936 loop : -1.96 (0.10), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 480 PHE 0.012 0.002 PHE K 258 TYR 0.020 0.002 TYR K 321 ARG 0.004 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1203 time to evaluate : 5.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4909 (ttt) cc_final: 0.4452 (ttt) REVERT: A 24 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7542 (mtpt) REVERT: A 332 ASP cc_start: 0.6401 (m-30) cc_final: 0.6140 (m-30) REVERT: B 9 ARG cc_start: 0.6434 (ttt180) cc_final: 0.6209 (pmt-80) REVERT: B 24 LYS cc_start: 0.7228 (mtmt) cc_final: 0.6972 (tmtt) REVERT: B 69 LYS cc_start: 0.7980 (pttt) cc_final: 0.7537 (mmtp) REVERT: B 162 THR cc_start: 0.8012 (t) cc_final: 0.7792 (p) REVERT: B 211 SER cc_start: 0.7394 (p) cc_final: 0.7094 (t) REVERT: B 332 ASP cc_start: 0.6751 (m-30) cc_final: 0.6304 (t0) REVERT: B 481 LYS cc_start: 0.7635 (pttp) cc_final: 0.6528 (tppt) REVERT: B 489 SER cc_start: 0.7968 (p) cc_final: 0.7758 (t) REVERT: B 490 LYS cc_start: 0.7819 (ptpp) cc_final: 0.6581 (mptt) REVERT: C 30 MET cc_start: 0.8065 (mmm) cc_final: 0.7641 (mmm) REVERT: C 311 GLU cc_start: 0.4407 (mt-10) cc_final: 0.4092 (mt-10) REVERT: D 1 MET cc_start: 0.4703 (ttt) cc_final: 0.4266 (mmt) REVERT: D 69 LYS cc_start: 0.7587 (pttt) cc_final: 0.7082 (mmmt) REVERT: D 115 LEU cc_start: 0.7947 (mm) cc_final: 0.7524 (tt) REVERT: D 287 LEU cc_start: 0.7635 (mt) cc_final: 0.7412 (tp) REVERT: D 398 ASN cc_start: 0.7941 (m-40) cc_final: 0.7658 (m-40) REVERT: D 481 LYS cc_start: 0.7977 (pttp) cc_final: 0.6643 (tptt) REVERT: D 490 LYS cc_start: 0.7270 (ptpp) cc_final: 0.5649 (mptt) REVERT: E 1 MET cc_start: 0.5052 (ttt) cc_final: 0.4462 (ttt) REVERT: E 69 LYS cc_start: 0.8024 (pttt) cc_final: 0.7304 (mmtt) REVERT: E 221 LYS cc_start: 0.8584 (mttm) cc_final: 0.8364 (mmpt) REVERT: E 481 LYS cc_start: 0.7673 (pttp) cc_final: 0.6317 (tptt) REVERT: F 12 SER cc_start: 0.8026 (t) cc_final: 0.7813 (m) REVERT: F 69 LYS cc_start: 0.8160 (pttt) cc_final: 0.6685 (mmtt) REVERT: F 465 ILE cc_start: 0.7490 (mm) cc_final: 0.7168 (mp) REVERT: G 69 LYS cc_start: 0.8107 (pttt) cc_final: 0.7556 (mmtt) REVERT: G 117 ILE cc_start: 0.8121 (mt) cc_final: 0.7524 (tt) REVERT: G 255 ASN cc_start: 0.5961 (p0) cc_final: 0.5529 (t0) REVERT: G 481 LYS cc_start: 0.7314 (pttp) cc_final: 0.6484 (tptp) REVERT: G 492 ASP cc_start: 0.6181 (m-30) cc_final: 0.5807 (m-30) REVERT: H 24 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7715 (mtmt) REVERT: H 69 LYS cc_start: 0.8551 (pttt) cc_final: 0.7226 (mttt) REVERT: H 117 ILE cc_start: 0.8294 (mt) cc_final: 0.8043 (tp) REVERT: H 213 ASP cc_start: 0.6281 (t70) cc_final: 0.5960 (t0) REVERT: H 295 PHE cc_start: 0.6045 (p90) cc_final: 0.5340 (p90) REVERT: H 315 SER cc_start: 0.6839 (p) cc_final: 0.6448 (m) REVERT: H 481 LYS cc_start: 0.7508 (pttp) cc_final: 0.5639 (mmtp) REVERT: H 503 MET cc_start: 0.7190 (mmt) cc_final: 0.6851 (mmm) REVERT: I 481 LYS cc_start: 0.6970 (pttp) cc_final: 0.6649 (tptt) REVERT: I 490 LYS cc_start: 0.7293 (ptpp) cc_final: 0.6353 (mptt) REVERT: I 503 MET cc_start: 0.5448 (mmt) cc_final: 0.5163 (mmm) REVERT: J 24 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7290 (tmtt) REVERT: J 69 LYS cc_start: 0.8277 (pttt) cc_final: 0.7194 (mmtp) REVERT: J 165 GLN cc_start: 0.7435 (tp40) cc_final: 0.7143 (tp-100) REVERT: J 328 ILE cc_start: 0.8674 (mm) cc_final: 0.8412 (tp) REVERT: J 449 ASP cc_start: 0.5988 (t70) cc_final: 0.5774 (t0) REVERT: J 474 ASN cc_start: 0.6248 (m-40) cc_final: 0.5867 (m110) REVERT: J 481 LYS cc_start: 0.6828 (pttp) cc_final: 0.5399 (tptt) REVERT: K 194 SER cc_start: 0.8528 (m) cc_final: 0.8148 (p) REVERT: K 203 ASN cc_start: 0.5897 (p0) cc_final: 0.5610 (p0) REVERT: K 299 CYS cc_start: 0.7124 (m) cc_final: 0.6815 (m) REVERT: L 30 MET cc_start: 0.7200 (mmm) cc_final: 0.6824 (mmt) REVERT: L 181 VAL cc_start: 0.7488 (t) cc_final: 0.7195 (p) REVERT: L 332 ASP cc_start: 0.5532 (m-30) cc_final: 0.5288 (m-30) REVERT: L 479 GLU cc_start: 0.3245 (tp30) cc_final: 0.2990 (tt0) REVERT: L 503 MET cc_start: 0.6551 (mmt) cc_final: 0.6191 (mmt) REVERT: M 1 MET cc_start: 0.3318 (ttt) cc_final: 0.2856 (ptm) REVERT: M 9 ARG cc_start: 0.6911 (ttt180) cc_final: 0.6609 (pmt-80) REVERT: M 69 LYS cc_start: 0.7654 (pttt) cc_final: 0.7441 (mmtp) REVERT: M 94 MET cc_start: 0.6678 (mtt) cc_final: 0.6466 (mtp) REVERT: M 195 THR cc_start: 0.7038 (m) cc_final: 0.6589 (m) REVERT: M 409 GLU cc_start: 0.7156 (mp0) cc_final: 0.6946 (mp0) REVERT: M 481 LYS cc_start: 0.7097 (pttp) cc_final: 0.5363 (mmtt) REVERT: M 490 LYS cc_start: 0.7518 (ptpp) cc_final: 0.7094 (mptt) REVERT: M 503 MET cc_start: 0.6267 (mmt) cc_final: 0.5985 (mmm) outliers start: 0 outliers final: 0 residues processed: 1203 average time/residue: 0.5632 time to fit residues: 1125.5054 Evaluate side-chains 543 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 6.9990 chunk 482 optimal weight: 9.9990 chunk 267 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 257 optimal weight: 0.3980 chunk 499 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 303 optimal weight: 0.0060 chunk 371 optimal weight: 4.9990 chunk 578 optimal weight: 7.9990 overall best weight: 4.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN B 139 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN C 4 GLN C 48 ASN C 124 GLN C 155 GLN C 191 GLN C 361 GLN C 398 ASN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 124 GLN D 125 ASN D 191 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 GLN H 4 GLN H 165 GLN H 361 GLN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN I 124 GLN I 166 ASN I 361 GLN I 417 GLN ** I 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN J 124 GLN J 361 GLN ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 GLN J 441 GLN K 33 ASN K 99 ASN K 243 GLN K 251 ASN L 4 GLN L 361 GLN M 257 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48750 Z= 0.195 Angle : 0.538 10.234 66378 Z= 0.292 Chirality : 0.045 0.186 7878 Planarity : 0.003 0.039 8567 Dihedral : 4.697 23.053 6669 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.83 % Allowed : 8.97 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 6110 helix: 1.51 (0.11), residues: 2080 sheet: 0.47 (0.19), residues: 936 loop : -1.78 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 383 PHE 0.017 0.001 PHE B 323 TYR 0.017 0.002 TYR H 484 ARG 0.009 0.000 ARG K 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 609 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7539 (mtpt) REVERT: A 186 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6783 (tmtm) REVERT: B 9 ARG cc_start: 0.6728 (ttt180) cc_final: 0.6344 (pmt-80) REVERT: B 24 LYS cc_start: 0.7396 (mtmt) cc_final: 0.6923 (tmtt) REVERT: B 69 LYS cc_start: 0.7978 (pttt) cc_final: 0.7522 (mmtp) REVERT: B 162 THR cc_start: 0.7789 (t) cc_final: 0.7531 (p) REVERT: B 186 LYS cc_start: 0.6962 (tptp) cc_final: 0.5758 (ttmt) REVERT: B 481 LYS cc_start: 0.7604 (pttp) cc_final: 0.6550 (tptt) REVERT: B 489 SER cc_start: 0.8034 (p) cc_final: 0.7808 (t) REVERT: C 30 MET cc_start: 0.8063 (mmm) cc_final: 0.7620 (mmm) REVERT: C 114 VAL cc_start: 0.5461 (t) cc_final: 0.5186 (t) REVERT: D 1 MET cc_start: 0.4108 (ttt) cc_final: 0.3323 (mmm) REVERT: D 69 LYS cc_start: 0.7659 (pttt) cc_final: 0.7026 (mmtt) REVERT: D 147 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6079 (tp30) REVERT: D 179 THR cc_start: 0.6706 (m) cc_final: 0.6467 (p) REVERT: D 287 LEU cc_start: 0.7393 (mt) cc_final: 0.7182 (tp) REVERT: D 381 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5175 (tt0) REVERT: D 398 ASN cc_start: 0.7590 (m-40) cc_final: 0.7200 (m110) REVERT: E 1 MET cc_start: 0.5073 (ttt) cc_final: 0.4861 (ttt) REVERT: E 481 LYS cc_start: 0.7470 (pttp) cc_final: 0.6327 (tptt) REVERT: F 69 LYS cc_start: 0.8162 (pttt) cc_final: 0.6870 (mmtp) REVERT: G 1 MET cc_start: 0.5278 (ttt) cc_final: 0.4550 (tpt) REVERT: G 69 LYS cc_start: 0.8117 (pttt) cc_final: 0.7492 (mmtm) REVERT: G 255 ASN cc_start: 0.5897 (p0) cc_final: 0.5339 (t0) REVERT: G 381 GLU cc_start: 0.7263 (tp30) cc_final: 0.6844 (mt-10) REVERT: G 481 LYS cc_start: 0.6951 (pttp) cc_final: 0.6362 (tptt) REVERT: H 1 MET cc_start: 0.4158 (ttt) cc_final: 0.3346 (tmm) REVERT: H 24 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7728 (mtmt) REVERT: H 295 PHE cc_start: 0.6184 (p90) cc_final: 0.5085 (p90) REVERT: H 315 SER cc_start: 0.6865 (p) cc_final: 0.6424 (m) REVERT: H 481 LYS cc_start: 0.7129 (pttp) cc_final: 0.5603 (mmtt) REVERT: H 503 MET cc_start: 0.6903 (mmt) cc_final: 0.6587 (mmm) REVERT: I 311 GLU cc_start: 0.4606 (mt-10) cc_final: 0.4345 (mt-10) REVERT: I 490 LYS cc_start: 0.7369 (ptpp) cc_final: 0.6175 (mptt) REVERT: I 503 MET cc_start: 0.5407 (mmt) cc_final: 0.4992 (mmm) REVERT: J 24 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7363 (tmtt) REVERT: J 165 GLN cc_start: 0.7361 (tp40) cc_final: 0.7090 (tp-100) REVERT: J 474 ASN cc_start: 0.6350 (m-40) cc_final: 0.6003 (m-40) REVERT: K 100 LEU cc_start: 0.7434 (pp) cc_final: 0.7207 (mp) REVERT: L 181 VAL cc_start: 0.7729 (t) cc_final: 0.7466 (p) REVERT: L 332 ASP cc_start: 0.5427 (m-30) cc_final: 0.5223 (m-30) REVERT: M 1 MET cc_start: 0.3209 (ttt) cc_final: 0.2964 (ptm) REVERT: M 9 ARG cc_start: 0.7001 (ttt180) cc_final: 0.6569 (pmt-80) REVERT: M 94 MET cc_start: 0.6785 (mtt) cc_final: 0.6566 (mtp) REVERT: M 302 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6008 (mt-10) REVERT: M 355 GLN cc_start: 0.6386 (mm110) cc_final: 0.6180 (mt0) REVERT: M 481 LYS cc_start: 0.7067 (pttp) cc_final: 0.5871 (mmtt) REVERT: M 503 MET cc_start: 0.6050 (mmt) cc_final: 0.5792 (mmm) outliers start: 93 outliers final: 68 residues processed: 675 average time/residue: 0.5651 time to fit residues: 643.1387 Evaluate side-chains 566 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 496 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 321 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 481 optimal weight: 9.9990 chunk 393 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 579 optimal weight: 30.0000 chunk 626 optimal weight: 9.9990 chunk 516 optimal weight: 5.9990 chunk 574 optimal weight: 30.0000 chunk 197 optimal weight: 30.0000 chunk 464 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 293 ASN B 151 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 298 GLN C 398 ASN C 441 GLN D 124 GLN D 151 ASN E 124 GLN E 139 ASN E 293 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 191 GLN G 293 ASN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 361 GLN ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 151 ASN K 191 GLN K 251 ASN ** K 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 ASN L 316 GLN L 426 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 48750 Z= 0.305 Angle : 0.606 6.784 66378 Z= 0.331 Chirality : 0.047 0.203 7878 Planarity : 0.004 0.041 8567 Dihedral : 5.092 24.539 6669 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.32 % Allowed : 12.51 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 6110 helix: 1.50 (0.12), residues: 1989 sheet: 0.42 (0.19), residues: 910 loop : -1.87 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 383 PHE 0.026 0.002 PHE D 234 TYR 0.019 0.002 TYR H 360 ARG 0.011 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 513 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7432 (mtpt) REVERT: A 498 GLU cc_start: 0.6828 (tp30) cc_final: 0.6561 (tp30) REVERT: B 24 LYS cc_start: 0.7514 (mtmt) cc_final: 0.7053 (tmtt) REVERT: B 162 THR cc_start: 0.7945 (t) cc_final: 0.7737 (p) REVERT: B 193 MET cc_start: 0.7068 (mtm) cc_final: 0.6801 (mtm) REVERT: B 321 TYR cc_start: 0.4005 (t80) cc_final: 0.3760 (t80) REVERT: C 30 MET cc_start: 0.8223 (mmm) cc_final: 0.7806 (mmm) REVERT: D 1 MET cc_start: 0.3593 (ttt) cc_final: 0.3029 (mmm) REVERT: D 381 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5237 (tt0) REVERT: D 398 ASN cc_start: 0.7950 (m-40) cc_final: 0.7624 (m110) REVERT: E 130 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6544 (t70) REVERT: E 194 SER cc_start: 0.7504 (m) cc_final: 0.7032 (p) REVERT: E 481 LYS cc_start: 0.7671 (pttp) cc_final: 0.6536 (tptt) REVERT: F 69 LYS cc_start: 0.8197 (pttt) cc_final: 0.6701 (mmtp) REVERT: G 1 MET cc_start: 0.5655 (ttt) cc_final: 0.4907 (tpt) REVERT: G 255 ASN cc_start: 0.6277 (p0) cc_final: 0.5718 (t0) REVERT: G 381 GLU cc_start: 0.7233 (tp30) cc_final: 0.7001 (tp30) REVERT: G 481 LYS cc_start: 0.7255 (pttp) cc_final: 0.6411 (tptt) REVERT: H 1 MET cc_start: 0.4210 (ttt) cc_final: 0.2853 (tmm) REVERT: H 315 SER cc_start: 0.6906 (p) cc_final: 0.6461 (m) REVERT: H 461 TYR cc_start: 0.8642 (p90) cc_final: 0.8416 (p90) REVERT: H 481 LYS cc_start: 0.7492 (pttp) cc_final: 0.6052 (mmtp) REVERT: I 118 MET cc_start: 0.7114 (mpp) cc_final: 0.6731 (mpp) REVERT: I 216 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8018 (p0) REVERT: I 421 ASP cc_start: 0.6804 (m-30) cc_final: 0.6431 (m-30) REVERT: I 490 LYS cc_start: 0.7204 (ptpp) cc_final: 0.6204 (mptt) REVERT: I 503 MET cc_start: 0.5231 (mmt) cc_final: 0.4827 (mmm) REVERT: J 24 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7419 (tmtt) REVERT: J 165 GLN cc_start: 0.7535 (tp40) cc_final: 0.7271 (tp-100) REVERT: J 203 ASN cc_start: 0.6591 (OUTLIER) cc_final: 0.6376 (p0) REVERT: K 319 MET cc_start: 0.7652 (ttt) cc_final: 0.7269 (ttt) REVERT: L 24 LYS cc_start: 0.5871 (tttp) cc_final: 0.5623 (ttpp) REVERT: L 148 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7973 (mp) REVERT: L 181 VAL cc_start: 0.7822 (t) cc_final: 0.7616 (p) REVERT: M 1 MET cc_start: 0.3277 (ttt) cc_final: 0.2894 (ptm) REVERT: M 94 MET cc_start: 0.7011 (mtt) cc_final: 0.6761 (mtp) REVERT: M 271 THR cc_start: 0.8550 (p) cc_final: 0.8256 (p) REVERT: M 302 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6148 (mt-10) REVERT: M 450 ARG cc_start: 0.5858 (tmm-80) cc_final: 0.5340 (ttp-170) REVERT: M 481 LYS cc_start: 0.7091 (pttp) cc_final: 0.5933 (mmtt) outliers start: 169 outliers final: 123 residues processed: 652 average time/residue: 0.5514 time to fit residues: 608.5045 Evaluate side-chains 588 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 460 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 465 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 572 optimal weight: 20.0000 chunk 435 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 389 optimal weight: 8.9990 chunk 581 optimal weight: 8.9990 chunk 615 optimal weight: 40.0000 chunk 303 optimal weight: 8.9990 chunk 551 optimal weight: 8.9990 chunk 165 optimal weight: 50.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 316 GLN B 4 GLN C 165 GLN C 168 ASN E 145 GLN E 169 GLN E 257 GLN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 316 GLN G 293 ASN H 48 ASN H 361 GLN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 251 ASN K 256 ASN L 361 GLN L 426 ASN M 298 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 48750 Z= 0.308 Angle : 0.609 9.065 66378 Z= 0.333 Chirality : 0.047 0.191 7878 Planarity : 0.004 0.044 8567 Dihedral : 5.246 22.419 6669 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.03 % Allowed : 14.58 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.11), residues: 6110 helix: 1.39 (0.12), residues: 1976 sheet: 0.17 (0.19), residues: 910 loop : -1.95 (0.10), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 480 PHE 0.024 0.002 PHE D 234 TYR 0.016 0.002 TYR G 442 ARG 0.009 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 481 time to evaluate : 5.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7644 (mtmt) cc_final: 0.7140 (ttpp) REVERT: A 498 GLU cc_start: 0.6944 (tp30) cc_final: 0.6680 (tp30) REVERT: B 24 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7172 (tmtt) REVERT: B 189 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.5888 (m-30) REVERT: B 321 TYR cc_start: 0.4337 (t80) cc_final: 0.3822 (t80) REVERT: C 30 MET cc_start: 0.8325 (mmm) cc_final: 0.7939 (mmm) REVERT: D 1 MET cc_start: 0.3796 (ttt) cc_final: 0.3277 (mmm) REVERT: D 88 ASN cc_start: 0.7845 (t0) cc_final: 0.7603 (t0) REVERT: D 381 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5281 (tt0) REVERT: E 194 SER cc_start: 0.7648 (m) cc_final: 0.7157 (p) REVERT: E 255 ASN cc_start: 0.5436 (p0) cc_final: 0.5098 (t0) REVERT: E 481 LYS cc_start: 0.7794 (pttp) cc_final: 0.6605 (tptt) REVERT: F 69 LYS cc_start: 0.8185 (pttt) cc_final: 0.6799 (mmtp) REVERT: G 1 MET cc_start: 0.5654 (ttt) cc_final: 0.4966 (tpt) REVERT: G 255 ASN cc_start: 0.6362 (p0) cc_final: 0.5989 (t0) REVERT: G 295 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.4961 (p90) REVERT: G 316 GLN cc_start: 0.6528 (tt0) cc_final: 0.6303 (tt0) REVERT: G 481 LYS cc_start: 0.7278 (pttp) cc_final: 0.6364 (tptt) REVERT: H 1 MET cc_start: 0.4502 (ttt) cc_final: 0.2918 (tmm) REVERT: H 228 ASN cc_start: 0.6209 (m-40) cc_final: 0.5776 (t0) REVERT: H 316 GLN cc_start: 0.6526 (tt0) cc_final: 0.6321 (tt0) REVERT: H 461 TYR cc_start: 0.8687 (p90) cc_final: 0.8246 (p90) REVERT: I 118 MET cc_start: 0.7185 (mpp) cc_final: 0.6912 (mpp) REVERT: I 216 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8008 (p0) REVERT: I 371 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: I 396 PHE cc_start: 0.7995 (m-10) cc_final: 0.7103 (t80) REVERT: I 421 ASP cc_start: 0.6730 (m-30) cc_final: 0.6517 (m-30) REVERT: I 490 LYS cc_start: 0.7003 (ptpp) cc_final: 0.6017 (mptt) REVERT: I 503 MET cc_start: 0.5508 (mmt) cc_final: 0.5084 (mmm) REVERT: J 1 MET cc_start: 0.3639 (ttt) cc_final: 0.0665 (tpt) REVERT: J 24 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7388 (tmtt) REVERT: J 203 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6798 (p0) REVERT: K 114 VAL cc_start: 0.6705 (t) cc_final: 0.6475 (m) REVERT: K 319 MET cc_start: 0.7739 (ttt) cc_final: 0.7440 (ttt) REVERT: L 24 LYS cc_start: 0.5384 (tttp) cc_final: 0.5155 (ttpp) REVERT: L 148 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7997 (mp) REVERT: L 422 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8149 (ttmm) REVERT: M 1 MET cc_start: 0.3081 (ttt) cc_final: 0.2694 (ptm) REVERT: M 450 ARG cc_start: 0.5934 (tmm-80) cc_final: 0.5435 (ttp-170) REVERT: M 481 LYS cc_start: 0.7223 (pttp) cc_final: 0.5768 (mmtt) outliers start: 205 outliers final: 147 residues processed: 651 average time/residue: 0.5507 time to fit residues: 609.2573 Evaluate side-chains 586 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 431 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 492 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain I residue 433 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 512 optimal weight: 9.9990 chunk 349 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 458 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 525 optimal weight: 0.4980 chunk 425 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 0.0670 chunk 552 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN B 4 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 316 GLN E 99 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 GLN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 GLN I 417 GLN K 33 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 ASN L 169 GLN L 361 GLN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 48750 Z= 0.129 Angle : 0.480 7.661 66378 Z= 0.258 Chirality : 0.043 0.173 7878 Planarity : 0.003 0.040 8567 Dihedral : 4.440 20.704 6669 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.34 % Allowed : 17.39 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6110 helix: 1.80 (0.12), residues: 1976 sheet: 0.55 (0.19), residues: 910 loop : -1.86 (0.10), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 383 PHE 0.008 0.001 PHE F 295 TYR 0.016 0.001 TYR H 484 ARG 0.006 0.000 ARG L 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 520 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7611 (mtmt) cc_final: 0.7117 (ttpp) REVERT: B 24 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7304 (tmtt) REVERT: B 162 THR cc_start: 0.8082 (t) cc_final: 0.7830 (p) REVERT: B 321 TYR cc_start: 0.4227 (t80) cc_final: 0.3841 (t80) REVERT: B 451 ARG cc_start: 0.6690 (mmm160) cc_final: 0.6219 (mmm160) REVERT: C 30 MET cc_start: 0.8218 (mmm) cc_final: 0.7830 (mmm) REVERT: D 1 MET cc_start: 0.3584 (ttt) cc_final: 0.3115 (mmm) REVERT: D 69 LYS cc_start: 0.7823 (pttt) cc_final: 0.7158 (mmtp) REVERT: D 88 ASN cc_start: 0.7778 (t0) cc_final: 0.7549 (t0) REVERT: D 381 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5066 (tt0) REVERT: E 255 ASN cc_start: 0.5243 (p0) cc_final: 0.4909 (t0) REVERT: E 381 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5541 (tt0) REVERT: E 481 LYS cc_start: 0.7529 (pttp) cc_final: 0.6503 (tptt) REVERT: F 69 LYS cc_start: 0.7846 (pttt) cc_final: 0.6790 (mmtp) REVERT: F 481 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.5455 (tptt) REVERT: G 110 PHE cc_start: 0.8239 (m-10) cc_final: 0.8020 (m-10) REVERT: G 295 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.4160 (p90) REVERT: G 481 LYS cc_start: 0.7096 (pttp) cc_final: 0.6295 (tptt) REVERT: H 1 MET cc_start: 0.4158 (ttt) cc_final: 0.2439 (mmm) REVERT: H 228 ASN cc_start: 0.6465 (m-40) cc_final: 0.6199 (t0) REVERT: H 295 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.4871 (p90) REVERT: H 316 GLN cc_start: 0.6210 (tt0) cc_final: 0.5914 (tt0) REVERT: I 118 MET cc_start: 0.7161 (mpp) cc_final: 0.6916 (mpp) REVERT: I 222 SER cc_start: 0.8239 (t) cc_final: 0.7976 (p) REVERT: I 396 PHE cc_start: 0.8069 (m-10) cc_final: 0.7286 (t80) REVERT: I 490 LYS cc_start: 0.7152 (ptpp) cc_final: 0.6219 (mptt) REVERT: J 1 MET cc_start: 0.3634 (ttt) cc_final: 0.0640 (tpt) REVERT: J 24 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7571 (tmtt) REVERT: J 203 ASN cc_start: 0.6717 (OUTLIER) cc_final: 0.6481 (p0) REVERT: J 440 GLN cc_start: 0.7331 (mt0) cc_final: 0.7074 (mt0) REVERT: K 98 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.6035 (m-30) REVERT: K 114 VAL cc_start: 0.6515 (t) cc_final: 0.6288 (m) REVERT: K 295 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.5750 (p90) REVERT: K 299 CYS cc_start: 0.6804 (m) cc_final: 0.6474 (m) REVERT: K 319 MET cc_start: 0.7715 (ttt) cc_final: 0.7310 (ttt) REVERT: L 59 GLU cc_start: 0.6766 (tt0) cc_final: 0.6529 (tt0) REVERT: L 60 GLU cc_start: 0.8217 (mp0) cc_final: 0.8010 (mp0) REVERT: L 148 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7921 (mp) REVERT: L 337 ASN cc_start: 0.6250 (m-40) cc_final: 0.5899 (m110) REVERT: L 422 LYS cc_start: 0.8270 (ttpt) cc_final: 0.8013 (ttmm) REVERT: M 1 MET cc_start: 0.2889 (ttt) cc_final: 0.2579 (ptm) REVERT: M 94 MET cc_start: 0.6953 (mtp) cc_final: 0.6644 (mtp) REVERT: M 295 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.4228 (p90) REVERT: M 302 GLU cc_start: 0.6495 (mt-10) cc_final: 0.5854 (mt-10) REVERT: M 450 ARG cc_start: 0.5836 (tmm-80) cc_final: 0.5335 (ttp-170) REVERT: M 481 LYS cc_start: 0.7210 (pttp) cc_final: 0.5845 (mmtt) outliers start: 119 outliers final: 78 residues processed: 606 average time/residue: 0.6128 time to fit residues: 632.5108 Evaluate side-chains 535 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 447 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 20.0000 chunk 554 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 361 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 616 optimal weight: 8.9990 chunk 511 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 203 optimal weight: 0.9990 chunk 323 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN D 155 GLN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN G 151 ASN G 255 ASN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 169 GLN K 251 ASN K 256 ASN K 426 ASN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 426 ASN ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48750 Z= 0.208 Angle : 0.530 8.291 66378 Z= 0.286 Chirality : 0.044 0.162 7878 Planarity : 0.003 0.040 8567 Dihedral : 4.636 21.935 6669 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.46 % Allowed : 17.33 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.11), residues: 6110 helix: 1.68 (0.12), residues: 2002 sheet: 0.49 (0.18), residues: 910 loop : -1.91 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 PHE 0.018 0.001 PHE D 234 TYR 0.017 0.001 TYR G 442 ARG 0.009 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 449 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7146 (ttpp) REVERT: A 498 GLU cc_start: 0.6761 (tp30) cc_final: 0.6514 (tp30) REVERT: B 24 LYS cc_start: 0.7579 (mtmt) cc_final: 0.7288 (tmtt) REVERT: B 189 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6029 (m-30) REVERT: B 321 TYR cc_start: 0.4068 (t80) cc_final: 0.3531 (t80) REVERT: C 30 MET cc_start: 0.8343 (mmm) cc_final: 0.7875 (mmm) REVERT: D 1 MET cc_start: 0.4121 (ttt) cc_final: 0.2959 (mmm) REVERT: D 88 ASN cc_start: 0.7828 (t0) cc_final: 0.7553 (t0) REVERT: D 381 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5196 (tt0) REVERT: E 255 ASN cc_start: 0.5397 (OUTLIER) cc_final: 0.5153 (t0) REVERT: E 481 LYS cc_start: 0.7690 (pttp) cc_final: 0.6596 (tptt) REVERT: E 504 ILE cc_start: 0.5601 (mt) cc_final: 0.5308 (mt) REVERT: F 189 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6990 (t70) REVERT: G 295 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.4447 (p90) REVERT: G 321 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: G 481 LYS cc_start: 0.7221 (pttp) cc_final: 0.6316 (tptp) REVERT: H 1 MET cc_start: 0.4258 (ttt) cc_final: 0.2165 (mmm) REVERT: H 228 ASN cc_start: 0.6145 (m-40) cc_final: 0.5804 (t0) REVERT: H 295 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5188 (p90) REVERT: H 461 TYR cc_start: 0.8635 (p90) cc_final: 0.8257 (p90) REVERT: I 340 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: I 396 PHE cc_start: 0.8076 (m-10) cc_final: 0.7213 (t80) REVERT: I 490 LYS cc_start: 0.7007 (ptpp) cc_final: 0.6035 (mptt) REVERT: J 1 MET cc_start: 0.3604 (ttt) cc_final: 0.0505 (tpt) REVERT: J 24 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7467 (tmtt) REVERT: J 501 ASP cc_start: 0.6480 (p0) cc_final: 0.6216 (p0) REVERT: K 118 MET cc_start: 0.6472 (ptp) cc_final: 0.6032 (ptp) REVERT: K 295 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.5746 (p90) REVERT: K 319 MET cc_start: 0.7701 (ttt) cc_final: 0.7382 (ttt) REVERT: L 148 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7904 (mp) REVERT: L 337 ASN cc_start: 0.6154 (m-40) cc_final: 0.5761 (m110) REVERT: M 1 MET cc_start: 0.3084 (ttt) cc_final: 0.2655 (ptm) REVERT: M 94 MET cc_start: 0.6986 (mtp) cc_final: 0.6709 (mtp) REVERT: M 295 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.4194 (p90) REVERT: M 302 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5964 (mt-10) REVERT: M 450 ARG cc_start: 0.5918 (tmm-80) cc_final: 0.5398 (ttp-170) REVERT: M 481 LYS cc_start: 0.7380 (pttp) cc_final: 0.5996 (mmtt) outliers start: 176 outliers final: 133 residues processed: 590 average time/residue: 0.5414 time to fit residues: 544.2657 Evaluate side-chains 572 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 428 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 321 TYR Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 351 optimal weight: 30.0000 chunk 450 optimal weight: 5.9990 chunk 348 optimal weight: 0.4980 chunk 518 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 613 optimal weight: 20.0000 chunk 384 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN C 168 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN K 33 ASN L 4 GLN L 165 GLN L 206 ASN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 426 ASN ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48750 Z= 0.198 Angle : 0.519 8.266 66378 Z= 0.280 Chirality : 0.044 0.160 7878 Planarity : 0.003 0.040 8567 Dihedral : 4.620 20.652 6669 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.78 % Allowed : 17.33 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 6110 helix: 1.68 (0.12), residues: 2002 sheet: 0.45 (0.18), residues: 910 loop : -1.93 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 383 PHE 0.014 0.001 PHE B 234 TYR 0.011 0.001 TYR H 360 ARG 0.007 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 436 time to evaluate : 5.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7101 (ttpp) REVERT: A 498 GLU cc_start: 0.6758 (tp30) cc_final: 0.6518 (tp30) REVERT: B 24 LYS cc_start: 0.7578 (mtmt) cc_final: 0.7300 (tmtt) REVERT: B 189 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.5991 (m-30) REVERT: B 321 TYR cc_start: 0.4157 (t80) cc_final: 0.3521 (t80) REVERT: C 30 MET cc_start: 0.8350 (mmm) cc_final: 0.7965 (mmm) REVERT: D 1 MET cc_start: 0.4409 (ttt) cc_final: 0.3173 (mmm) REVERT: D 30 MET cc_start: 0.7367 (mmm) cc_final: 0.7025 (mmm) REVERT: D 88 ASN cc_start: 0.7828 (t0) cc_final: 0.7526 (t0) REVERT: D 321 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.7231 (t80) REVERT: D 327 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7734 (p0) REVERT: D 381 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5160 (tt0) REVERT: E 1 MET cc_start: 0.4863 (ttt) cc_final: 0.2714 (tpt) REVERT: E 255 ASN cc_start: 0.5497 (OUTLIER) cc_final: 0.5237 (t0) REVERT: E 481 LYS cc_start: 0.7646 (pttp) cc_final: 0.6598 (tptt) REVERT: E 504 ILE cc_start: 0.5360 (mt) cc_final: 0.5073 (mt) REVERT: F 189 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6959 (t70) REVERT: F 481 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.5424 (tptt) REVERT: G 295 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.4368 (p90) REVERT: G 481 LYS cc_start: 0.7231 (pttp) cc_final: 0.6300 (tptp) REVERT: H 1 MET cc_start: 0.4159 (OUTLIER) cc_final: 0.2107 (mmm) REVERT: H 295 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.5045 (p90) REVERT: H 461 TYR cc_start: 0.8637 (p90) cc_final: 0.8264 (p90) REVERT: I 216 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7927 (p0) REVERT: I 396 PHE cc_start: 0.8045 (m-10) cc_final: 0.7243 (t80) REVERT: I 490 LYS cc_start: 0.7021 (ptpp) cc_final: 0.6032 (mptt) REVERT: J 1 MET cc_start: 0.3475 (ttt) cc_final: 0.0371 (tpt) REVERT: J 24 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7480 (tmtt) REVERT: J 440 GLN cc_start: 0.7310 (mt0) cc_final: 0.7093 (mt0) REVERT: K 118 MET cc_start: 0.6490 (ptp) cc_final: 0.5929 (mtm) REVERT: K 295 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.5727 (p90) REVERT: K 319 MET cc_start: 0.7723 (ttt) cc_final: 0.7398 (ttt) REVERT: L 148 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (mp) REVERT: L 337 ASN cc_start: 0.6127 (m-40) cc_final: 0.5724 (m110) REVERT: M 1 MET cc_start: 0.3051 (ttt) cc_final: 0.2658 (ptm) REVERT: M 94 MET cc_start: 0.6973 (mtp) cc_final: 0.6692 (mtp) REVERT: M 137 MET cc_start: 0.4329 (mmp) cc_final: 0.3847 (mmp) REVERT: M 295 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.4180 (p90) REVERT: M 302 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6010 (mt-10) REVERT: M 450 ARG cc_start: 0.5922 (tmm-80) cc_final: 0.5402 (ttp-170) REVERT: M 481 LYS cc_start: 0.7342 (pttp) cc_final: 0.6011 (mmtt) outliers start: 192 outliers final: 155 residues processed: 591 average time/residue: 0.5374 time to fit residues: 543.5130 Evaluate side-chains 593 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 424 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 311 GLU Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 418 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 482 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN B 151 ASN E 99 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN H 361 GLN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN K 33 ASN K 99 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 426 ASN ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 48750 Z= 0.275 Angle : 0.577 8.534 66378 Z= 0.313 Chirality : 0.046 0.234 7878 Planarity : 0.004 0.042 8567 Dihedral : 4.946 23.614 6669 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.17 % Allowed : 16.96 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 6110 helix: 1.51 (0.12), residues: 2002 sheet: 0.16 (0.19), residues: 910 loop : -1.94 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 383 PHE 0.021 0.002 PHE B 234 TYR 0.018 0.002 TYR G 442 ARG 0.007 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 437 time to evaluate : 4.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7116 (ttpp) REVERT: A 498 GLU cc_start: 0.6785 (tp30) cc_final: 0.6533 (tp30) REVERT: B 24 LYS cc_start: 0.7555 (mtmt) cc_final: 0.7316 (tmtt) REVERT: B 118 MET cc_start: 0.7443 (mtp) cc_final: 0.7017 (mtp) REVERT: B 189 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5872 (m-30) REVERT: B 321 TYR cc_start: 0.4605 (t80) cc_final: 0.3551 (t80) REVERT: C 30 MET cc_start: 0.8338 (mmm) cc_final: 0.7953 (mmm) REVERT: D 88 ASN cc_start: 0.7834 (t0) cc_final: 0.7519 (t0) REVERT: D 321 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7075 (t80) REVERT: D 381 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5257 (tt0) REVERT: D 434 GLU cc_start: 0.5704 (pm20) cc_final: 0.5414 (pm20) REVERT: E 1 MET cc_start: 0.4876 (ttt) cc_final: 0.2672 (tpt) REVERT: E 255 ASN cc_start: 0.5542 (OUTLIER) cc_final: 0.5292 (t0) REVERT: E 481 LYS cc_start: 0.7728 (pttp) cc_final: 0.6584 (tptt) REVERT: E 504 ILE cc_start: 0.5529 (mt) cc_final: 0.5234 (mt) REVERT: F 189 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6975 (t70) REVERT: G 295 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.4809 (p90) REVERT: G 321 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: G 481 LYS cc_start: 0.7340 (pttp) cc_final: 0.6323 (tptp) REVERT: H 1 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.2123 (mmm) REVERT: H 295 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5210 (p90) REVERT: H 461 TYR cc_start: 0.8684 (p90) cc_final: 0.8287 (p90) REVERT: I 118 MET cc_start: 0.7218 (mpp) cc_final: 0.6701 (mpp) REVERT: I 216 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7919 (p0) REVERT: I 340 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: I 396 PHE cc_start: 0.8049 (m-10) cc_final: 0.7219 (t80) REVERT: I 490 LYS cc_start: 0.7063 (ptpp) cc_final: 0.6003 (mptt) REVERT: J 1 MET cc_start: 0.3624 (ttt) cc_final: 0.0594 (tpt) REVERT: K 118 MET cc_start: 0.6523 (ptp) cc_final: 0.6000 (mtm) REVERT: K 295 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.5727 (p90) REVERT: K 319 MET cc_start: 0.7698 (ttt) cc_final: 0.7403 (ttt) REVERT: L 148 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7891 (mp) REVERT: L 337 ASN cc_start: 0.6141 (m-40) cc_final: 0.5734 (m110) REVERT: L 422 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8159 (ttmm) REVERT: M 1 MET cc_start: 0.3294 (ttt) cc_final: 0.2632 (ptm) REVERT: M 94 MET cc_start: 0.6978 (mtp) cc_final: 0.6685 (mtp) REVERT: M 137 MET cc_start: 0.4461 (mmp) cc_final: 0.3978 (mmp) REVERT: M 295 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.4239 (p90) REVERT: M 302 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6072 (mt-10) REVERT: M 450 ARG cc_start: 0.6019 (tmm-80) cc_final: 0.5469 (ttp-170) REVERT: M 481 LYS cc_start: 0.7408 (pttp) cc_final: 0.6010 (mmtt) outliers start: 212 outliers final: 175 residues processed: 608 average time/residue: 0.5262 time to fit residues: 546.3195 Evaluate side-chains 609 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 419 time to evaluate : 5.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 321 TYR Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 311 GLU Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 7.9990 chunk 588 optimal weight: 20.0000 chunk 536 optimal weight: 30.0000 chunk 572 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 517 optimal weight: 30.0000 chunk 541 optimal weight: 20.0000 chunk 570 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN K 33 ASN K 99 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 48750 Z= 0.257 Angle : 0.567 8.563 66378 Z= 0.307 Chirality : 0.045 0.223 7878 Planarity : 0.004 0.042 8567 Dihedral : 4.965 22.608 6669 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.07 % Allowed : 17.39 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 6110 helix: 1.51 (0.12), residues: 1989 sheet: 0.12 (0.19), residues: 910 loop : -1.95 (0.10), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 383 PHE 0.018 0.002 PHE B 234 TYR 0.014 0.002 TYR I 67 ARG 0.007 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 427 time to evaluate : 5.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7610 (mtmt) cc_final: 0.7113 (ttpp) REVERT: A 498 GLU cc_start: 0.6781 (tp30) cc_final: 0.6528 (tp30) REVERT: B 189 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6034 (m-30) REVERT: B 321 TYR cc_start: 0.4445 (t80) cc_final: 0.3678 (t80) REVERT: C 30 MET cc_start: 0.8308 (mmm) cc_final: 0.7946 (mmm) REVERT: D 30 MET cc_start: 0.7391 (mmm) cc_final: 0.6980 (mmm) REVERT: D 88 ASN cc_start: 0.7839 (t0) cc_final: 0.7513 (t0) REVERT: D 321 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6850 (t80) REVERT: D 381 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5257 (tt0) REVERT: E 1 MET cc_start: 0.4704 (ttt) cc_final: 0.2878 (tpt) REVERT: E 481 LYS cc_start: 0.7655 (pttp) cc_final: 0.6563 (tptt) REVERT: E 504 ILE cc_start: 0.5619 (mt) cc_final: 0.5334 (mt) REVERT: F 189 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6978 (t70) REVERT: G 295 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.4816 (p90) REVERT: G 321 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: G 481 LYS cc_start: 0.7357 (pttp) cc_final: 0.6324 (tptp) REVERT: H 1 MET cc_start: 0.4049 (OUTLIER) cc_final: 0.2075 (mmm) REVERT: H 124 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7217 (tp40) REVERT: H 295 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5074 (p90) REVERT: H 461 TYR cc_start: 0.8687 (p90) cc_final: 0.8278 (p90) REVERT: I 118 MET cc_start: 0.7213 (mpp) cc_final: 0.6715 (mpp) REVERT: I 216 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7989 (p0) REVERT: I 340 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: I 396 PHE cc_start: 0.8032 (m-10) cc_final: 0.7226 (t80) REVERT: I 490 LYS cc_start: 0.7054 (ptpp) cc_final: 0.5997 (mptt) REVERT: J 1 MET cc_start: 0.3482 (ttt) cc_final: 0.0511 (tpt) REVERT: K 118 MET cc_start: 0.6566 (ptp) cc_final: 0.6088 (mtm) REVERT: K 295 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.5732 (p90) REVERT: K 319 MET cc_start: 0.7722 (ttt) cc_final: 0.7432 (ttt) REVERT: L 148 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7871 (mp) REVERT: L 337 ASN cc_start: 0.6094 (m-40) cc_final: 0.5781 (m110) REVERT: M 1 MET cc_start: 0.3214 (ttt) cc_final: 0.2562 (ptm) REVERT: M 94 MET cc_start: 0.6953 (mtp) cc_final: 0.6669 (mtp) REVERT: M 137 MET cc_start: 0.4486 (mmp) cc_final: 0.3990 (mmp) REVERT: M 295 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.4299 (p90) REVERT: M 302 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6166 (mt-10) REVERT: M 341 LYS cc_start: 0.4587 (mmtt) cc_final: 0.4364 (mptt) REVERT: M 450 ARG cc_start: 0.6010 (tmm-80) cc_final: 0.5466 (ttp-170) REVERT: M 481 LYS cc_start: 0.7385 (pttp) cc_final: 0.6018 (mmtt) outliers start: 207 outliers final: 174 residues processed: 596 average time/residue: 0.5478 time to fit residues: 557.4538 Evaluate side-chains 605 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 417 time to evaluate : 5.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 321 TYR Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 311 GLU Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 7.9990 chunk 605 optimal weight: 10.0000 chunk 369 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 420 optimal weight: 2.9990 chunk 634 optimal weight: 3.9990 chunk 584 optimal weight: 20.0000 chunk 505 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 390 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN E 255 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN K 99 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 GLN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 48750 Z= 0.235 Angle : 0.558 8.759 66378 Z= 0.301 Chirality : 0.045 0.218 7878 Planarity : 0.003 0.042 8567 Dihedral : 4.920 24.508 6669 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.93 % Allowed : 17.59 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 6110 helix: 1.61 (0.12), residues: 1963 sheet: 0.14 (0.19), residues: 910 loop : -1.93 (0.10), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 383 PHE 0.017 0.002 PHE B 234 TYR 0.019 0.002 TYR G 442 ARG 0.006 0.001 ARG A 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12220 Ramachandran restraints generated. 6110 Oldfield, 0 Emsley, 6110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 421 time to evaluate : 5.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7108 (ttpp) REVERT: A 498 GLU cc_start: 0.6776 (tp30) cc_final: 0.6523 (tp30) REVERT: B 118 MET cc_start: 0.7435 (mtp) cc_final: 0.7004 (mtp) REVERT: B 189 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6125 (m-30) REVERT: B 321 TYR cc_start: 0.4647 (t80) cc_final: 0.3586 (t80) REVERT: C 30 MET cc_start: 0.8294 (mmm) cc_final: 0.7941 (mmm) REVERT: C 114 VAL cc_start: 0.5394 (OUTLIER) cc_final: 0.5075 (p) REVERT: D 30 MET cc_start: 0.7353 (mmm) cc_final: 0.7008 (mmm) REVERT: D 88 ASN cc_start: 0.7853 (t0) cc_final: 0.7527 (t0) REVERT: D 104 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6152 (mp) REVERT: D 321 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6839 (t80) REVERT: D 381 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5237 (tt0) REVERT: E 1 MET cc_start: 0.4597 (ttt) cc_final: 0.2894 (tpt) REVERT: E 481 LYS cc_start: 0.7686 (pttp) cc_final: 0.6571 (tptt) REVERT: E 504 ILE cc_start: 0.5647 (mt) cc_final: 0.5398 (mt) REVERT: F 189 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6960 (t70) REVERT: G 295 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.4798 (p90) REVERT: G 481 LYS cc_start: 0.7365 (pttp) cc_final: 0.6315 (tptp) REVERT: H 1 MET cc_start: 0.3983 (OUTLIER) cc_final: 0.1964 (mmm) REVERT: H 124 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7212 (tp40) REVERT: H 295 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.5092 (p90) REVERT: H 461 TYR cc_start: 0.8684 (p90) cc_final: 0.8272 (p90) REVERT: I 118 MET cc_start: 0.7273 (mpp) cc_final: 0.6770 (mpp) REVERT: I 216 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8022 (p0) REVERT: I 340 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: I 396 PHE cc_start: 0.8046 (m-10) cc_final: 0.7228 (t80) REVERT: I 413 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8746 (tt) REVERT: I 490 LYS cc_start: 0.7047 (ptpp) cc_final: 0.5992 (mptt) REVERT: J 1 MET cc_start: 0.3459 (ttt) cc_final: 0.0506 (tpt) REVERT: K 101 PRO cc_start: 0.7857 (Cg_exo) cc_final: 0.7629 (Cg_endo) REVERT: K 118 MET cc_start: 0.6553 (ptp) cc_final: 0.6080 (mtm) REVERT: K 295 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.5723 (p90) REVERT: K 319 MET cc_start: 0.7721 (ttt) cc_final: 0.7418 (ttt) REVERT: L 148 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7842 (mp) REVERT: L 337 ASN cc_start: 0.6133 (m-40) cc_final: 0.5722 (m110) REVERT: M 1 MET cc_start: 0.3273 (ttt) cc_final: 0.2581 (ptm) REVERT: M 69 LYS cc_start: 0.7853 (pttt) cc_final: 0.7652 (mmtp) REVERT: M 94 MET cc_start: 0.6904 (mtp) cc_final: 0.6626 (mtp) REVERT: M 137 MET cc_start: 0.4477 (mmp) cc_final: 0.3979 (mmp) REVERT: M 295 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.4281 (p90) REVERT: M 302 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6093 (mt-10) REVERT: M 341 LYS cc_start: 0.4594 (mmtt) cc_final: 0.4296 (mptt) REVERT: M 450 ARG cc_start: 0.6010 (tmm-80) cc_final: 0.5470 (ttp-170) REVERT: M 481 LYS cc_start: 0.7318 (pttp) cc_final: 0.5995 (mmtt) outliers start: 200 outliers final: 175 residues processed: 586 average time/residue: 0.5482 time to fit residues: 547.9000 Evaluate side-chains 607 residues out of total 5083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 416 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 295 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 125 ASN Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain H residue 374 ASP Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 295 PHE Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 340 ASP Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 ASN Chi-restraints excluded: chain J residue 242 ASP Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 396 PHE Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 467 PHE Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 407 THR Chi-restraints excluded: chain K residue 415 VAL Chi-restraints excluded: chain K residue 440 GLN Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 295 PHE Chi-restraints excluded: chain L residue 311 GLU Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 233 LEU Chi-restraints excluded: chain M residue 295 PHE Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 366 CYS Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 374 ASP Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 471 THR Chi-restraints excluded: chain M residue 500 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 9.9990 chunk 538 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 465 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 506 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 519 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 overall best weight: 8.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 99 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** H 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 99 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 417 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096729 restraints weight = 133805.863| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.48 r_work: 0.3413 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 48750 Z= 0.282 Angle : 0.593 9.042 66378 Z= 0.322 Chirality : 0.046 0.198 7878 Planarity : 0.004 0.043 8567 Dihedral : 5.101 26.807 6669 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.95 % Allowed : 17.78 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 6110 helix: 1.51 (0.12), residues: 1963 sheet: 0.13 (0.17), residues: 1040 loop : -2.04 (0.10), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 383 PHE 0.021 0.002 PHE B 234 TYR 0.015 0.002 TYR I 67 ARG 0.006 0.001 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12636.07 seconds wall clock time: 227 minutes 10.71 seconds (13630.71 seconds total)