Starting phenix.real_space_refine on Sat Feb 24 02:44:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sja_25160/02_2024/7sja_25160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sja_25160/02_2024/7sja_25160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sja_25160/02_2024/7sja_25160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sja_25160/02_2024/7sja_25160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sja_25160/02_2024/7sja_25160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sja_25160/02_2024/7sja_25160_updated.pdb" } resolution = 3.8 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= 1.394 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 282 5.16 5 C 25698 2.51 5 N 6978 2.21 5 O 7914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 359": "NH1" <-> "NH2" Residue "F TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 160": "OD1" <-> "OD2" Residue "J PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 160": "OD1" <-> "OD2" Residue "K PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 390": "NH1" <-> "NH2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40920 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "K" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "L" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.00, per 1000 atoms: 0.49 Number of scatterers: 40920 At special positions: 0 Unit cell: (167.9, 103.5, 216.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 36 15.00 Mg 12 11.99 O 7914 8.00 N 6978 7.00 C 25698 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.83 Conformation dependent library (CDL) restraints added in 7.5 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 30 sheets defined 47.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.828A pdb=" N ILE A 115 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.642A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.106A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 126 removed outlier: 5.115A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 241 removed outlier: 4.647A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 426 Processing helix chain 'C' and resid 10 through 27 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.828A pdb=" N ILE C 115 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.642A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 383 through 400 removed outlier: 4.107A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 126 removed outlier: 5.114A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.647A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 373 through 390 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 405 through 426 Processing helix chain 'E' and resid 10 through 27 Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.828A pdb=" N ILE E 115 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP E 116 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.642A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.107A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 11 through 27 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 126 removed outlier: 5.115A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 222 through 241 removed outlier: 4.647A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 293 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 373 through 390 Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 405 through 426 Processing helix chain 'G' and resid 11 through 27 Processing helix chain 'G' and resid 41 through 45 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 109 through 126 removed outlier: 5.115A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 158 Processing helix chain 'G' and resid 181 through 195 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 222 through 241 removed outlier: 4.647A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 286 through 293 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 305 through 307 No H-bonds generated for 'chain 'G' and resid 305 through 307' Processing helix chain 'G' and resid 323 through 336 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 373 through 390 Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 405 through 426 Processing helix chain 'H' and resid 11 through 27 Processing helix chain 'H' and resid 41 through 45 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 109 through 126 removed outlier: 5.115A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 158 Processing helix chain 'H' and resid 181 through 195 Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 222 through 241 removed outlier: 4.648A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 293 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 323 through 336 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 373 through 390 Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 405 through 426 Processing helix chain 'I' and resid 11 through 27 Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 126 removed outlier: 5.115A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 158 Processing helix chain 'I' and resid 181 through 195 Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 241 removed outlier: 4.647A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 Processing helix chain 'I' and resid 286 through 293 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 373 through 390 Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 405 through 426 Processing helix chain 'J' and resid 10 through 27 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 103 through 108 Processing helix chain 'J' and resid 111 through 128 removed outlier: 3.828A pdb=" N ILE J 115 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP J 116 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 Processing helix chain 'J' and resid 183 through 194 Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.642A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 278 through 280 No H-bonds generated for 'chain 'J' and resid 278 through 280' Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 383 through 400 removed outlier: 4.107A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'K' and resid 10 through 27 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 72 through 80 Processing helix chain 'K' and resid 103 through 108 Processing helix chain 'K' and resid 111 through 128 removed outlier: 3.828A pdb=" N ILE K 115 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP K 116 " --> pdb=" O GLU K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.642A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 278 through 280 No H-bonds generated for 'chain 'K' and resid 278 through 280' Processing helix chain 'K' and resid 288 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 383 through 400 removed outlier: 4.106A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'L' and resid 10 through 27 Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 72 through 80 Processing helix chain 'L' and resid 103 through 108 Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.829A pdb=" N ILE L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP L 116 " --> pdb=" O GLU L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 Processing helix chain 'L' and resid 183 through 194 Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.643A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 278 through 280 No H-bonds generated for 'chain 'L' and resid 278 through 280' Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 383 through 400 removed outlier: 4.107A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA L 389 " --> pdb=" O ALA L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.146A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 270 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP A 205 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N TYR A 272 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE A 267 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR A 381 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'B' and resid 63 through 65 removed outlier: 8.483A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 51 through 54 Processing sheet with id= E, first strand: chain 'B' and resid 267 through 271 Processing sheet with id= F, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.147A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE C 5 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE C 135 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE C 7 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 137 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 9 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS C 139 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA C 270 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP C 205 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N TYR C 272 " --> pdb=" O ASP C 205 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE C 267 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR C 381 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'D' and resid 63 through 65 removed outlier: 8.483A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL D 5 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE D 133 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE D 7 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU D 135 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 165 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS D 137 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 167 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 51 through 54 Processing sheet with id= J, first strand: chain 'D' and resid 267 through 271 Processing sheet with id= K, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.147A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE E 135 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL E 9 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS E 139 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA E 270 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP E 205 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N TYR E 272 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE E 267 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR E 381 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'F' and resid 63 through 65 removed outlier: 8.484A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL F 5 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE F 133 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE F 7 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 163 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU F 135 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN F 165 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS F 137 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE F 167 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 51 through 54 Processing sheet with id= O, first strand: chain 'F' and resid 267 through 271 Processing sheet with id= P, first strand: chain 'G' and resid 63 through 65 removed outlier: 8.483A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL G 5 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE G 133 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE G 7 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU G 135 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE G 163 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU G 135 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN G 165 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS G 137 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE G 167 " --> pdb=" O HIS G 137 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 51 through 54 Processing sheet with id= R, first strand: chain 'G' and resid 267 through 271 Processing sheet with id= S, first strand: chain 'H' and resid 63 through 65 removed outlier: 8.483A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL H 5 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE H 133 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE H 7 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU H 135 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE H 163 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU H 135 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN H 165 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS H 137 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE H 167 " --> pdb=" O HIS H 137 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 51 through 54 Processing sheet with id= U, first strand: chain 'H' and resid 267 through 271 Processing sheet with id= V, first strand: chain 'I' and resid 63 through 65 removed outlier: 8.483A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL I 5 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE I 133 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE I 7 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU I 135 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE I 163 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU I 135 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN I 165 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS I 137 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE I 167 " --> pdb=" O HIS I 137 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 51 through 54 Processing sheet with id= X, first strand: chain 'I' and resid 267 through 271 Processing sheet with id= Y, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.146A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE J 5 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE J 135 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE J 7 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL J 137 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL J 9 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS J 139 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA J 270 " --> pdb=" O MET J 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP J 205 " --> pdb=" O ALA J 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N TYR J 272 " --> pdb=" O ASP J 205 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE J 267 " --> pdb=" O THR J 381 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR J 381 " --> pdb=" O PHE J 267 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.146A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE K 5 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE K 135 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE K 7 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL K 137 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL K 9 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS K 139 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA K 270 " --> pdb=" O MET K 203 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP K 205 " --> pdb=" O ALA K 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N TYR K 272 " --> pdb=" O ASP K 205 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE K 267 " --> pdb=" O THR K 381 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR K 381 " --> pdb=" O PHE K 267 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AC, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.147A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE L 5 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE L 135 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE L 7 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL L 137 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL L 9 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS L 139 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA L 270 " --> pdb=" O MET L 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP L 205 " --> pdb=" O ALA L 270 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N TYR L 272 " --> pdb=" O ASP L 205 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE L 267 " --> pdb=" O THR L 381 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR L 381 " --> pdb=" O PHE L 267 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 53 through 55 1800 hydrogen bonds defined for protein. 4842 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: 14.63 Time building geometry restraints manager: 17.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13545 1.34 - 1.46: 7208 1.46 - 1.57: 20587 1.57 - 1.69: 60 1.69 - 1.81: 444 Bond restraints: 41844 Sorted by residual: bond pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.34e-02 5.57e+03 2.18e+00 bond pdb=" N ARG B 359 " pdb=" CA ARG B 359 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.13e+00 bond pdb=" CA PHE L 169 " pdb=" CB PHE L 169 " ideal model delta sigma weight residual 1.539 1.475 0.065 4.88e-02 4.20e+02 1.75e+00 bond pdb=" CA PHE A 169 " pdb=" CB PHE A 169 " ideal model delta sigma weight residual 1.539 1.476 0.064 4.88e-02 4.20e+02 1.70e+00 ... (remaining 41839 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 1363 106.57 - 113.43: 22905 113.43 - 120.29: 15447 120.29 - 127.15: 16663 127.15 - 134.01: 466 Bond angle restraints: 56844 Sorted by residual: angle pdb=" N ARG D 359 " pdb=" CA ARG D 359 " pdb=" C ARG D 359 " ideal model delta sigma weight residual 110.80 126.95 -16.15 2.13e+00 2.20e-01 5.75e+01 angle pdb=" N PRO F 358 " pdb=" CA PRO F 358 " pdb=" C PRO F 358 " ideal model delta sigma weight residual 111.19 102.57 8.62 1.57e+00 4.06e-01 3.02e+01 angle pdb=" N ARG G 359 " pdb=" CA ARG G 359 " pdb=" C ARG G 359 " ideal model delta sigma weight residual 110.10 118.15 -8.05 1.49e+00 4.50e-01 2.92e+01 angle pdb=" N ARG B 359 " pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 110.80 122.25 -11.45 2.13e+00 2.20e-01 2.89e+01 angle pdb=" N GLY G 360 " pdb=" CA GLY G 360 " pdb=" C GLY G 360 " ideal model delta sigma weight residual 114.69 120.96 -6.27 1.19e+00 7.06e-01 2.78e+01 ... (remaining 56839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.04: 24424 33.04 - 66.08: 416 66.08 - 99.12: 24 99.12 - 132.15: 6 132.15 - 165.19: 18 Dihedral angle restraints: 24888 sinusoidal: 9948 harmonic: 14940 Sorted by residual: dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.60 165.19 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP K 501 " pdb=" C1' GTP K 501 " pdb=" N9 GTP K 501 " pdb=" O4' GTP K 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.58 165.17 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.56 165.16 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 24885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5863 0.090 - 0.180: 355 0.180 - 0.270: 2 0.270 - 0.360: 1 0.360 - 0.450: 1 Chirality restraints: 6222 Sorted by residual: chirality pdb=" CA ARG D 359 " pdb=" N ARG D 359 " pdb=" C ARG D 359 " pdb=" CB ARG D 359 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA ARG B 359 " pdb=" N ARG B 359 " pdb=" C ARG B 359 " pdb=" CB ARG B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ARG I 359 " pdb=" N ARG I 359 " pdb=" C ARG I 359 " pdb=" CB ARG I 359 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 6219 not shown) Planarity restraints: 7386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 357 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C PRO F 357 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO F 357 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO F 358 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 357 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C PRO D 357 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO D 357 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO D 358 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 357 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C PRO B 357 " -0.037 2.00e-02 2.50e+03 pdb=" O PRO B 357 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 358 " 0.012 2.00e-02 2.50e+03 ... (remaining 7383 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 565 2.54 - 3.13: 34924 3.13 - 3.72: 66968 3.72 - 4.31: 90339 4.31 - 4.90: 150946 Nonbonded interactions: 343742 Sorted by model distance: nonbonded pdb=" O3B GTP J 501 " pdb="MG MG J 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP K 501 " pdb="MG MG K 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP C 501 " pdb="MG MG C 502 " model vdw 1.951 2.170 nonbonded pdb=" O3B GTP L 501 " pdb="MG MG L 502 " model vdw 1.951 2.170 ... (remaining 343737 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 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 29.650 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 102.210 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.330 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 0.065 41844 Z= 0.293 Angle : 0.604 16.150 56844 Z= 0.347 Chirality : 0.043 0.450 6222 Planarity : 0.004 0.044 7386 Dihedral : 13.621 165.193 15300 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 5.93 % Allowed : 7.27 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.48 (0.12), residues: 5130 helix: 0.74 (0.10), residues: 2496 sheet: -0.17 (0.18), residues: 744 loop : -1.81 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 21 HIS 0.005 0.001 HIS G 396 PHE 0.010 0.001 PHE A 296 TYR 0.008 0.001 TYR L 83 ARG 0.003 0.000 ARG H 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1853 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1592 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.8223 (m) cc_final: 0.7870 (m) REVERT: A 33 ASP cc_start: 0.7798 (m-30) cc_final: 0.7450 (p0) REVERT: A 149 PHE cc_start: 0.8975 (t80) cc_final: 0.8743 (t80) REVERT: A 167 LEU cc_start: 0.8556 (mt) cc_final: 0.8117 (mt) REVERT: A 172 TYR cc_start: 0.7382 (t80) cc_final: 0.7008 (t80) REVERT: A 223 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7100 (p) REVERT: A 283 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6835 (m170) REVERT: A 317 LEU cc_start: 0.8933 (mt) cc_final: 0.8503 (mt) REVERT: A 396 ASP cc_start: 0.8145 (m-30) cc_final: 0.7737 (m-30) REVERT: A 402 ARG cc_start: 0.7966 (mmt-90) cc_final: 0.7616 (tpp80) REVERT: A 413 MET cc_start: 0.7489 (ttm) cc_final: 0.7006 (ttm) REVERT: A 430 LYS cc_start: 0.9304 (ttmt) cc_final: 0.8673 (tppt) REVERT: B 33 SER cc_start: 0.8660 (m) cc_final: 0.8133 (p) REVERT: B 184 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7422 (p0) REVERT: B 279 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: B 281 TYR cc_start: 0.8022 (m-80) cc_final: 0.7820 (m-80) REVERT: B 321 MET cc_start: 0.8275 (ptp) cc_final: 0.8074 (ptp) REVERT: B 324 LYS cc_start: 0.8881 (tmtp) cc_final: 0.8119 (tppt) REVERT: B 363 MET cc_start: 0.7312 (ptp) cc_final: 0.7074 (ptp) REVERT: B 395 LEU cc_start: 0.7994 (tp) cc_final: 0.7747 (tp) REVERT: B 415 MET cc_start: 0.7271 (ttm) cc_final: 0.6574 (ttp) REVERT: C 69 ASP cc_start: 0.7915 (t0) cc_final: 0.7215 (t70) REVERT: C 115 ILE cc_start: 0.9012 (tp) cc_final: 0.8677 (tp) REVERT: C 167 LEU cc_start: 0.8893 (mt) cc_final: 0.8423 (mt) REVERT: C 207 GLU cc_start: 0.8269 (tt0) cc_final: 0.8039 (mt-10) REVERT: C 223 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.7250 (p) REVERT: C 257 THR cc_start: 0.9229 (m) cc_final: 0.9003 (p) REVERT: C 283 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5885 (m170) REVERT: C 301 GLN cc_start: 0.8138 (mt0) cc_final: 0.7574 (mm-40) REVERT: C 302 MET cc_start: 0.8225 (mtt) cc_final: 0.8002 (mtt) REVERT: C 430 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9042 (pttm) REVERT: D 33 SER cc_start: 0.8885 (m) cc_final: 0.8524 (p) REVERT: D 94 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8238 (mm-40) REVERT: D 279 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: D 364 SER cc_start: 0.8499 (p) cc_final: 0.8167 (p) REVERT: D 395 LEU cc_start: 0.8181 (tp) cc_final: 0.7787 (tp) REVERT: E 20 CYS cc_start: 0.8606 (m) cc_final: 0.8254 (m) REVERT: E 49 PHE cc_start: 0.8373 (p90) cc_final: 0.7948 (p90) REVERT: E 69 ASP cc_start: 0.7902 (t0) cc_final: 0.7358 (t0) REVERT: E 84 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.8256 (ttp-110) REVERT: E 223 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7599 (p) REVERT: E 232 SER cc_start: 0.8829 (p) cc_final: 0.8425 (t) REVERT: E 257 THR cc_start: 0.9313 (m) cc_final: 0.8980 (p) REVERT: E 282 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: E 407 TRP cc_start: 0.8490 (m100) cc_final: 0.8195 (m100) REVERT: E 420 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8240 (pp20) REVERT: E 430 LYS cc_start: 0.9413 (ttmt) cc_final: 0.9062 (tppt) REVERT: F 3 GLU cc_start: 0.6393 (mp0) cc_final: 0.5761 (mp0) REVERT: F 33 SER cc_start: 0.8674 (m) cc_final: 0.8215 (p) REVERT: F 81 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6454 (m-10) REVERT: F 257 MET cc_start: 0.8488 (mmp) cc_final: 0.7975 (mmm) REVERT: F 279 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: F 281 TYR cc_start: 0.8075 (m-80) cc_final: 0.7595 (m-80) REVERT: F 297 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8152 (ptpt) REVERT: F 363 MET cc_start: 0.7448 (ptp) cc_final: 0.7190 (ptp) REVERT: G 2 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8523 (mtm180) REVERT: G 6 HIS cc_start: 0.8069 (t70) cc_final: 0.7419 (t70) REVERT: G 11 GLN cc_start: 0.7972 (tt0) cc_final: 0.7767 (pt0) REVERT: G 27 GLU cc_start: 0.8817 (tt0) cc_final: 0.8604 (tt0) REVERT: G 41 ASP cc_start: 0.7579 (p0) cc_final: 0.6985 (p0) REVERT: G 58 LYS cc_start: 0.7175 (tttt) cc_final: 0.6957 (ttpt) REVERT: G 67 ASP cc_start: 0.8531 (t0) cc_final: 0.7311 (p0) REVERT: G 81 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6990 (m-10) REVERT: G 92 PHE cc_start: 0.8309 (p90) cc_final: 0.7135 (p90) REVERT: G 135 LEU cc_start: 0.8607 (tp) cc_final: 0.8401 (mp) REVERT: G 139 LEU cc_start: 0.7992 (mt) cc_final: 0.7779 (mt) REVERT: G 158 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8576 (tt0) REVERT: G 174 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8713 (mmmm) REVERT: G 208 TYR cc_start: 0.8910 (m-10) cc_final: 0.8661 (m-80) REVERT: G 216 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8410 (mmtp) REVERT: G 255 VAL cc_start: 0.8421 (t) cc_final: 0.8089 (p) REVERT: G 267 MET cc_start: 0.7996 (ptp) cc_final: 0.7673 (ptm) REVERT: G 289 LEU cc_start: 0.9204 (mp) cc_final: 0.8970 (mt) REVERT: G 292 GLN cc_start: 0.8034 (tt0) cc_final: 0.7792 (tt0) REVERT: G 322 SER cc_start: 0.8367 (m) cc_final: 0.8050 (p) REVERT: G 323 MET cc_start: 0.8162 (mmm) cc_final: 0.7928 (tpp) REVERT: G 367 PHE cc_start: 0.8581 (t80) cc_final: 0.8223 (t80) REVERT: G 376 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7958 (pt0) REVERT: G 379 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8902 (mttt) REVERT: G 397 TRP cc_start: 0.8634 (m100) cc_final: 0.8354 (m-10) REVERT: H 2 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8024 (ptm160) REVERT: H 6 HIS cc_start: 0.8241 (t70) cc_final: 0.7659 (t70) REVERT: H 41 ASP cc_start: 0.7205 (p0) cc_final: 0.6679 (p0) REVERT: H 118 ASP cc_start: 0.8650 (m-30) cc_final: 0.8284 (t0) REVERT: H 130 LEU cc_start: 0.8418 (tp) cc_final: 0.8158 (tp) REVERT: H 154 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8283 (mmmm) REVERT: H 159 TYR cc_start: 0.7866 (m-80) cc_final: 0.7328 (m-80) REVERT: H 174 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8492 (mmmt) REVERT: H 216 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8468 (mmtp) REVERT: H 255 VAL cc_start: 0.7970 (t) cc_final: 0.7474 (p) REVERT: H 267 MET cc_start: 0.7685 (ptp) cc_final: 0.6824 (ptp) REVERT: H 297 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8255 (mmtm) REVERT: H 321 MET cc_start: 0.8625 (ptp) cc_final: 0.8292 (ptp) REVERT: H 322 SER cc_start: 0.8127 (m) cc_final: 0.7626 (p) REVERT: H 339 SER cc_start: 0.7382 (p) cc_final: 0.7046 (t) REVERT: H 351 VAL cc_start: 0.9422 (t) cc_final: 0.9050 (m) REVERT: H 397 TRP cc_start: 0.8672 (m100) cc_final: 0.8337 (m-10) REVERT: I 2 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8246 (mtm-85) REVERT: I 6 HIS cc_start: 0.8050 (t70) cc_final: 0.7554 (t70) REVERT: I 33 SER cc_start: 0.9137 (m) cc_final: 0.8874 (p) REVERT: I 41 ASP cc_start: 0.8006 (p0) cc_final: 0.7189 (p0) REVERT: I 44 LEU cc_start: 0.9147 (mt) cc_final: 0.8913 (pp) REVERT: I 67 ASP cc_start: 0.8432 (t0) cc_final: 0.7403 (p0) REVERT: I 69 GLU cc_start: 0.7632 (pt0) cc_final: 0.7204 (pm20) REVERT: I 92 PHE cc_start: 0.8203 (p90) cc_final: 0.7420 (p90) REVERT: I 130 LEU cc_start: 0.8587 (tp) cc_final: 0.8264 (tp) REVERT: I 135 LEU cc_start: 0.8873 (tp) cc_final: 0.8590 (mp) REVERT: I 154 LYS cc_start: 0.9013 (mmtp) cc_final: 0.8807 (mmmm) REVERT: I 159 TYR cc_start: 0.7934 (m-80) cc_final: 0.7674 (m-80) REVERT: I 164 MET cc_start: 0.8469 (tpp) cc_final: 0.8248 (mmm) REVERT: I 174 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8530 (mmmm) REVERT: I 184 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8798 (p0) REVERT: I 208 TYR cc_start: 0.9082 (m-10) cc_final: 0.8733 (m-80) REVERT: I 246 LEU cc_start: 0.8286 (tp) cc_final: 0.7964 (tt) REVERT: I 267 MET cc_start: 0.7782 (ptp) cc_final: 0.7235 (ptm) REVERT: I 297 LYS cc_start: 0.8787 (ptpt) cc_final: 0.8348 (mmtm) REVERT: I 321 MET cc_start: 0.8682 (ptp) cc_final: 0.8169 (ptp) REVERT: I 322 SER cc_start: 0.8365 (m) cc_final: 0.8012 (p) REVERT: I 339 SER cc_start: 0.7588 (p) cc_final: 0.7359 (t) REVERT: I 351 VAL cc_start: 0.9584 (t) cc_final: 0.9219 (p) REVERT: I 363 MET cc_start: 0.8092 (ptp) cc_final: 0.7776 (ptp) REVERT: I 367 PHE cc_start: 0.8512 (t80) cc_final: 0.8073 (t80) REVERT: I 423 GLN cc_start: 0.8891 (tp40) cc_final: 0.8690 (tp40) REVERT: J 33 ASP cc_start: 0.8303 (m-30) cc_final: 0.8004 (p0) REVERT: J 110 ILE cc_start: 0.9117 (mm) cc_final: 0.8894 (tp) REVERT: J 138 PHE cc_start: 0.8545 (m-10) cc_final: 0.8252 (m-10) REVERT: J 282 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: J 375 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8580 (p) REVERT: J 377 MET cc_start: 0.8957 (ttp) cc_final: 0.8555 (ttp) REVERT: K 50 ASN cc_start: 0.8262 (t0) cc_final: 0.7963 (t0) REVERT: K 120 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8913 (t0) REVERT: K 160 ASP cc_start: 0.8648 (t70) cc_final: 0.8447 (t0) REVERT: K 172 TYR cc_start: 0.6950 (t80) cc_final: 0.6507 (t80) REVERT: K 219 ILE cc_start: 0.8353 (mt) cc_final: 0.7878 (mt) REVERT: K 282 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: K 345 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7393 (p0) REVERT: K 351 PHE cc_start: 0.8085 (m-80) cc_final: 0.7856 (m-10) REVERT: K 357 TYR cc_start: 0.7797 (m-80) cc_final: 0.7070 (m-80) REVERT: K 377 MET cc_start: 0.8823 (ttp) cc_final: 0.8503 (ttp) REVERT: K 388 TRP cc_start: 0.8557 (m100) cc_final: 0.8345 (m100) REVERT: L 20 CYS cc_start: 0.8136 (m) cc_final: 0.7670 (m) REVERT: L 31 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7857 (mt0) REVERT: L 50 ASN cc_start: 0.8477 (t0) cc_final: 0.8212 (t0) REVERT: L 133 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7964 (mm-40) REVERT: L 149 PHE cc_start: 0.9108 (t80) cc_final: 0.8868 (t80) REVERT: L 176 GLN cc_start: 0.8519 (mt0) cc_final: 0.8265 (mt0) REVERT: L 317 LEU cc_start: 0.9426 (mt) cc_final: 0.9108 (mt) REVERT: L 375 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8127 (p) REVERT: L 377 MET cc_start: 0.8961 (ttp) cc_final: 0.8643 (ttm) outliers start: 261 outliers final: 102 residues processed: 1776 average time/residue: 0.5335 time to fit residues: 1527.5745 Evaluate side-chains 1137 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1015 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 283 HIS Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.9990 chunk 386 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 132 optimal weight: 0.2980 chunk 260 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 463 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 347 ASN B 423 GLN C 11 GLN C 128 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS D 347 ASN E 11 GLN E 88 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 307 HIS ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN H 245 GLN H 247 ASN I 57 HIS I 226 ASN I 247 ASN ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 HIS J 88 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN J 249 ASN J 293 ASN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 226 ASN K 249 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 41844 Z= 0.312 Angle : 0.647 10.204 56844 Z= 0.330 Chirality : 0.045 0.221 6222 Planarity : 0.005 0.058 7386 Dihedral : 12.912 168.142 5966 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.68 % Allowed : 16.92 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.37 (0.12), residues: 5130 helix: 0.69 (0.10), residues: 2526 sheet: -0.14 (0.18), residues: 768 loop : -1.55 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 407 HIS 0.005 0.001 HIS A 406 PHE 0.022 0.002 PHE C 49 TYR 0.025 0.001 TYR E 24 ARG 0.008 0.001 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1090 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8312 (p90) cc_final: 0.8058 (p90) REVERT: A 203 MET cc_start: 0.8391 (mmm) cc_final: 0.8080 (mmm) REVERT: A 223 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7394 (p) REVERT: A 302 MET cc_start: 0.7783 (mtt) cc_final: 0.7552 (mtt) REVERT: A 402 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7904 (tpp80) REVERT: A 430 LYS cc_start: 0.9232 (ttmt) cc_final: 0.8541 (tppt) REVERT: B 33 SER cc_start: 0.8652 (m) cc_final: 0.8227 (p) REVERT: B 86 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6798 (ttm-80) REVERT: B 184 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7716 (p0) REVERT: B 213 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7781 (ttp80) REVERT: B 257 MET cc_start: 0.8651 (mmm) cc_final: 0.8451 (mmt) REVERT: B 279 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: B 370 ASN cc_start: 0.8542 (t0) cc_final: 0.8327 (t0) REVERT: B 390 ARG cc_start: 0.8300 (ttm170) cc_final: 0.8057 (ttt180) REVERT: C 69 ASP cc_start: 0.7997 (t0) cc_final: 0.7496 (t70) REVERT: C 83 TYR cc_start: 0.7772 (m-80) cc_final: 0.7469 (m-80) REVERT: C 223 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7606 (p) REVERT: C 257 THR cc_start: 0.9291 (m) cc_final: 0.9074 (p) REVERT: C 302 MET cc_start: 0.8238 (mtt) cc_final: 0.8028 (mtt) REVERT: C 430 LYS cc_start: 0.9426 (ttmt) cc_final: 0.9020 (pttm) REVERT: D 33 SER cc_start: 0.8894 (m) cc_final: 0.8560 (p) REVERT: D 94 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8208 (tp40) REVERT: D 279 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: D 364 SER cc_start: 0.8615 (p) cc_final: 0.8177 (p) REVERT: D 421 GLU cc_start: 0.8287 (tp30) cc_final: 0.7876 (tp30) REVERT: D 423 GLN cc_start: 0.8948 (tp40) cc_final: 0.8699 (pt0) REVERT: E 49 PHE cc_start: 0.8313 (p90) cc_final: 0.8005 (p90) REVERT: E 69 ASP cc_start: 0.7883 (t0) cc_final: 0.7212 (t70) REVERT: E 88 HIS cc_start: 0.7739 (t70) cc_final: 0.7104 (t70) REVERT: E 223 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7841 (p) REVERT: E 257 THR cc_start: 0.9331 (m) cc_final: 0.9073 (p) REVERT: E 282 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: E 357 TYR cc_start: 0.8036 (m-80) cc_final: 0.7631 (m-80) REVERT: E 388 TRP cc_start: 0.8886 (m100) cc_final: 0.8679 (m100) REVERT: E 398 MET cc_start: 0.8826 (mtt) cc_final: 0.8557 (mmt) REVERT: E 430 LYS cc_start: 0.9416 (ttmt) cc_final: 0.8829 (tppt) REVERT: F 33 SER cc_start: 0.8753 (m) cc_final: 0.8362 (p) REVERT: F 81 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: F 111 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: F 177 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8438 (t0) REVERT: F 257 MET cc_start: 0.8615 (mmp) cc_final: 0.8147 (mmm) REVERT: F 279 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: F 299 MET cc_start: 0.8204 (mmm) cc_final: 0.7969 (mmp) REVERT: F 363 MET cc_start: 0.7494 (ptp) cc_final: 0.7244 (ptp) REVERT: G 6 HIS cc_start: 0.8158 (t70) cc_final: 0.7552 (t70) REVERT: G 7 ILE cc_start: 0.8874 (mt) cc_final: 0.8625 (mp) REVERT: G 12 CYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8744 (p) REVERT: G 41 ASP cc_start: 0.7656 (p0) cc_final: 0.7197 (p0) REVERT: G 92 PHE cc_start: 0.8349 (p90) cc_final: 0.8022 (p90) REVERT: G 101 TRP cc_start: 0.8357 (t60) cc_final: 0.7842 (t60) REVERT: G 136 THR cc_start: 0.8065 (m) cc_final: 0.7385 (p) REVERT: G 154 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8294 (mmmm) REVERT: G 164 MET cc_start: 0.8396 (mmm) cc_final: 0.8175 (mmm) REVERT: G 174 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8679 (mmmm) REVERT: G 216 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8427 (mmtp) REVERT: G 267 MET cc_start: 0.7951 (ptp) cc_final: 0.7595 (ptm) REVERT: G 397 TRP cc_start: 0.8665 (m100) cc_final: 0.8344 (m-10) REVERT: G 422 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6144 (t80) REVERT: H 6 HIS cc_start: 0.8268 (t70) cc_final: 0.7620 (t70) REVERT: H 11 GLN cc_start: 0.8038 (tt0) cc_final: 0.7833 (pt0) REVERT: H 12 CYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8718 (p) REVERT: H 41 ASP cc_start: 0.7321 (p0) cc_final: 0.7013 (p0) REVERT: H 73 MET cc_start: 0.8981 (mpp) cc_final: 0.8751 (mpp) REVERT: H 130 LEU cc_start: 0.8436 (tp) cc_final: 0.8112 (tp) REVERT: H 174 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8485 (mmmt) REVERT: H 216 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8445 (mmtp) REVERT: H 267 MET cc_start: 0.7624 (ptp) cc_final: 0.7312 (ptm) REVERT: H 299 MET cc_start: 0.6845 (mmp) cc_final: 0.5827 (mmp) REVERT: H 300 MET cc_start: 0.7967 (mtt) cc_final: 0.7629 (mtt) REVERT: H 322 SER cc_start: 0.7906 (m) cc_final: 0.7566 (p) REVERT: H 397 TRP cc_start: 0.8618 (m100) cc_final: 0.8347 (m-10) REVERT: I 6 HIS cc_start: 0.8103 (t70) cc_final: 0.7379 (t70) REVERT: I 33 SER cc_start: 0.9109 (m) cc_final: 0.8850 (p) REVERT: I 41 ASP cc_start: 0.7941 (p0) cc_final: 0.7072 (p0) REVERT: I 44 LEU cc_start: 0.9140 (mt) cc_final: 0.8933 (pp) REVERT: I 58 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6883 (ttpt) REVERT: I 92 PHE cc_start: 0.8327 (p90) cc_final: 0.8083 (p90) REVERT: I 130 LEU cc_start: 0.8367 (tp) cc_final: 0.8094 (tp) REVERT: I 134 GLN cc_start: 0.8329 (pt0) cc_final: 0.7963 (pp30) REVERT: I 135 LEU cc_start: 0.8903 (tp) cc_final: 0.8637 (tp) REVERT: I 136 THR cc_start: 0.8053 (m) cc_final: 0.7588 (p) REVERT: I 139 LEU cc_start: 0.7978 (mt) cc_final: 0.7676 (mm) REVERT: I 174 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8648 (mmmm) REVERT: I 184 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8675 (p0) REVERT: I 246 LEU cc_start: 0.8343 (tp) cc_final: 0.8030 (tt) REVERT: I 267 MET cc_start: 0.7938 (ptp) cc_final: 0.7449 (ptm) REVERT: I 322 SER cc_start: 0.8094 (m) cc_final: 0.7793 (p) REVERT: I 351 VAL cc_start: 0.9520 (t) cc_final: 0.9172 (m) REVERT: I 363 MET cc_start: 0.8232 (ptp) cc_final: 0.7939 (ptp) REVERT: I 367 PHE cc_start: 0.8542 (t80) cc_final: 0.8224 (t80) REVERT: I 388 MET cc_start: 0.6928 (mmt) cc_final: 0.6702 (mmt) REVERT: I 423 GLN cc_start: 0.8865 (tp40) cc_final: 0.8663 (tp40) REVERT: J 110 ILE cc_start: 0.9205 (mm) cc_final: 0.8943 (tp) REVERT: J 138 PHE cc_start: 0.8614 (m-10) cc_final: 0.8332 (m-10) REVERT: J 229 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8099 (mmm160) REVERT: J 282 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: J 358 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8631 (tp40) REVERT: J 388 TRP cc_start: 0.8659 (m100) cc_final: 0.8296 (m100) REVERT: K 31 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8094 (mt0) REVERT: K 49 PHE cc_start: 0.8485 (p90) cc_final: 0.8257 (p90) REVERT: K 50 ASN cc_start: 0.8330 (t0) cc_final: 0.7961 (t0) REVERT: K 282 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: K 345 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7437 (p0) REVERT: L 84 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7288 (ttm-80) outliers start: 294 outliers final: 195 residues processed: 1290 average time/residue: 0.5489 time to fit residues: 1174.1148 Evaluate side-chains 1122 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 908 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 320 ARG Chi-restraints excluded: chain H residue 367 PHE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 318 LEU Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 385 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 463 optimal weight: 10.0000 chunk 501 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 460 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 372 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN L 249 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 41844 Z= 0.337 Angle : 0.654 10.208 56844 Z= 0.333 Chirality : 0.045 0.299 6222 Planarity : 0.005 0.060 7386 Dihedral : 12.854 169.140 5932 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.88 % Allowed : 18.85 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.39 (0.12), residues: 5130 helix: 0.63 (0.10), residues: 2490 sheet: -0.04 (0.18), residues: 756 loop : -1.51 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 407 HIS 0.008 0.001 HIS K 88 PHE 0.022 0.002 PHE C 49 TYR 0.024 0.002 TYR K 161 ARG 0.008 0.001 ARG F 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 968 time to evaluate : 4.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8260 (p90) cc_final: 0.8043 (p90) REVERT: A 149 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8714 (t80) REVERT: A 203 MET cc_start: 0.8420 (mmm) cc_final: 0.8188 (mmm) REVERT: A 223 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 398 MET cc_start: 0.9047 (mmt) cc_final: 0.8399 (mmt) REVERT: A 402 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7773 (tpp80) REVERT: A 430 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8741 (tppt) REVERT: B 33 SER cc_start: 0.8699 (m) cc_final: 0.8427 (p) REVERT: B 111 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: B 279 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: B 390 ARG cc_start: 0.8347 (ttm170) cc_final: 0.8143 (ttt-90) REVERT: B 403 MET cc_start: 0.8294 (mmm) cc_final: 0.7921 (mmm) REVERT: C 69 ASP cc_start: 0.8023 (t0) cc_final: 0.7494 (t70) REVERT: C 156 ARG cc_start: 0.8973 (mtp180) cc_final: 0.8676 (mmm-85) REVERT: C 223 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7705 (p) REVERT: C 252 LEU cc_start: 0.8612 (mt) cc_final: 0.6875 (mp) REVERT: C 257 THR cc_start: 0.9264 (m) cc_final: 0.9011 (p) REVERT: C 370 LYS cc_start: 0.8177 (tttp) cc_final: 0.7536 (tptp) REVERT: C 430 LYS cc_start: 0.9502 (ttmt) cc_final: 0.9196 (pttm) REVERT: D 33 SER cc_start: 0.9033 (m) cc_final: 0.8647 (p) REVERT: D 94 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8191 (tp40) REVERT: D 279 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: D 297 LYS cc_start: 0.8864 (tttt) cc_final: 0.8307 (tttp) REVERT: D 364 SER cc_start: 0.8556 (p) cc_final: 0.8094 (p) REVERT: D 421 GLU cc_start: 0.8368 (tp30) cc_final: 0.8077 (tp30) REVERT: E 49 PHE cc_start: 0.8325 (p90) cc_final: 0.7916 (p90) REVERT: E 69 ASP cc_start: 0.7942 (t0) cc_final: 0.7325 (t70) REVERT: E 150 THR cc_start: 0.9118 (m) cc_final: 0.8900 (m) REVERT: E 256 GLN cc_start: 0.8553 (mp10) cc_final: 0.8208 (mp-120) REVERT: E 257 THR cc_start: 0.9445 (m) cc_final: 0.9244 (p) REVERT: E 388 TRP cc_start: 0.8978 (m100) cc_final: 0.8715 (m100) REVERT: E 430 LYS cc_start: 0.9505 (ttmt) cc_final: 0.8977 (tppt) REVERT: F 33 SER cc_start: 0.8784 (m) cc_final: 0.8461 (p) REVERT: F 81 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.5917 (m-10) REVERT: F 86 ARG cc_start: 0.5515 (tpt170) cc_final: 0.4836 (tpm170) REVERT: F 111 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: F 177 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8379 (t0) REVERT: F 279 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: F 363 MET cc_start: 0.7497 (ptp) cc_final: 0.7205 (ptp) REVERT: G 6 HIS cc_start: 0.8150 (t70) cc_final: 0.7592 (t70) REVERT: G 7 ILE cc_start: 0.8920 (mt) cc_final: 0.8685 (mp) REVERT: G 12 CYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8741 (p) REVERT: G 41 ASP cc_start: 0.7790 (p0) cc_final: 0.7383 (p0) REVERT: G 101 TRP cc_start: 0.8522 (t60) cc_final: 0.7966 (t60) REVERT: G 136 THR cc_start: 0.8188 (m) cc_final: 0.7637 (p) REVERT: G 174 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8632 (mmmm) REVERT: G 216 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8417 (mmtp) REVERT: G 267 MET cc_start: 0.8008 (ptp) cc_final: 0.7604 (ptm) REVERT: G 292 GLN cc_start: 0.8046 (tt0) cc_final: 0.7797 (tt0) REVERT: G 351 VAL cc_start: 0.9348 (t) cc_final: 0.8931 (p) REVERT: G 362 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8823 (mtmm) REVERT: G 397 TRP cc_start: 0.8696 (m100) cc_final: 0.8360 (m-10) REVERT: G 422 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.6235 (t80) REVERT: G 423 GLN cc_start: 0.8667 (tp40) cc_final: 0.8456 (tm-30) REVERT: H 6 HIS cc_start: 0.8136 (t70) cc_final: 0.7527 (t70) REVERT: H 11 GLN cc_start: 0.8063 (tt0) cc_final: 0.7805 (pt0) REVERT: H 12 CYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8754 (p) REVERT: H 27 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8826 (tm-30) REVERT: H 33 SER cc_start: 0.8970 (m) cc_final: 0.8535 (p) REVERT: H 41 ASP cc_start: 0.7413 (p0) cc_final: 0.7054 (p0) REVERT: H 73 MET cc_start: 0.9035 (mpp) cc_final: 0.8661 (mpp) REVERT: H 101 TRP cc_start: 0.8172 (t60) cc_final: 0.7792 (t60) REVERT: H 130 LEU cc_start: 0.8537 (tp) cc_final: 0.8126 (tp) REVERT: H 174 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8507 (mmmt) REVERT: H 184 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8600 (p0) REVERT: H 216 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8439 (mmtp) REVERT: H 267 MET cc_start: 0.7800 (ptp) cc_final: 0.7444 (ptp) REVERT: H 299 MET cc_start: 0.7000 (mmp) cc_final: 0.6210 (mmp) REVERT: H 300 MET cc_start: 0.8147 (mtt) cc_final: 0.7940 (mtt) REVERT: H 322 SER cc_start: 0.8003 (m) cc_final: 0.7758 (p) REVERT: H 362 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8319 (mtmm) REVERT: H 397 TRP cc_start: 0.8632 (m100) cc_final: 0.8348 (m-10) REVERT: I 6 HIS cc_start: 0.8065 (t70) cc_final: 0.7533 (t70) REVERT: I 33 SER cc_start: 0.9128 (m) cc_final: 0.8889 (p) REVERT: I 41 ASP cc_start: 0.8005 (p0) cc_final: 0.7641 (p0) REVERT: I 50 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8180 (m-10) REVERT: I 58 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7046 (ttpt) REVERT: I 67 ASP cc_start: 0.8295 (t0) cc_final: 0.7810 (t70) REVERT: I 92 PHE cc_start: 0.8350 (p90) cc_final: 0.8124 (p90) REVERT: I 101 TRP cc_start: 0.8454 (t60) cc_final: 0.7802 (t60) REVERT: I 130 LEU cc_start: 0.8384 (tp) cc_final: 0.8120 (tp) REVERT: I 134 GLN cc_start: 0.8351 (pt0) cc_final: 0.7970 (pp30) REVERT: I 135 LEU cc_start: 0.8914 (tp) cc_final: 0.8627 (tp) REVERT: I 139 LEU cc_start: 0.7966 (mt) cc_final: 0.7582 (mm) REVERT: I 174 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8652 (mmmm) REVERT: I 184 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8522 (p0) REVERT: I 205 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7778 (pp20) REVERT: I 246 LEU cc_start: 0.8383 (tp) cc_final: 0.8023 (tt) REVERT: I 257 MET cc_start: 0.8683 (mmm) cc_final: 0.8302 (mmm) REVERT: I 267 MET cc_start: 0.8006 (ptp) cc_final: 0.7499 (ptm) REVERT: I 351 VAL cc_start: 0.9503 (t) cc_final: 0.9014 (p) REVERT: I 362 LYS cc_start: 0.8636 (pttt) cc_final: 0.8414 (pttp) REVERT: I 363 MET cc_start: 0.8124 (ptp) cc_final: 0.7850 (ptp) REVERT: I 379 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8746 (ptpt) REVERT: I 388 MET cc_start: 0.6974 (mmt) cc_final: 0.6764 (mmt) REVERT: J 138 PHE cc_start: 0.8662 (m-10) cc_final: 0.8322 (m-10) REVERT: J 230 LEU cc_start: 0.9249 (mp) cc_final: 0.8891 (tt) REVERT: J 282 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: J 388 TRP cc_start: 0.8686 (m100) cc_final: 0.8459 (m100) REVERT: K 33 ASP cc_start: 0.8017 (p0) cc_final: 0.7790 (p0) REVERT: K 49 PHE cc_start: 0.8520 (p90) cc_final: 0.8275 (p90) REVERT: K 110 ILE cc_start: 0.8961 (mm) cc_final: 0.8698 (tp) REVERT: K 127 ASP cc_start: 0.7753 (p0) cc_final: 0.7457 (p0) REVERT: K 157 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9087 (mm) REVERT: K 203 MET cc_start: 0.8141 (mmp) cc_final: 0.7218 (mmt) REVERT: K 282 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: K 434 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: L 84 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7328 (ttm-80) REVERT: L 149 PHE cc_start: 0.9166 (t80) cc_final: 0.8880 (t80) REVERT: L 203 MET cc_start: 0.8671 (mmp) cc_final: 0.8294 (mmp) outliers start: 303 outliers final: 219 residues processed: 1179 average time/residue: 0.5261 time to fit residues: 1017.8848 Evaluate side-chains 1137 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 894 time to evaluate : 4.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 354 CYS Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 184 ASN Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 354 CYS Chi-restraints excluded: chain H residue 367 PHE Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 428 LEU Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 465 optimal weight: 0.9980 chunk 492 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 441 optimal weight: 0.9990 chunk 132 optimal weight: 0.0020 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 423 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 89 ASN D 131 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 ASN F 337 ASN G 89 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41844 Z= 0.169 Angle : 0.587 9.492 56844 Z= 0.294 Chirality : 0.043 0.205 6222 Planarity : 0.004 0.049 7386 Dihedral : 12.577 168.255 5920 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.36 % Allowed : 20.55 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.02 (0.12), residues: 5130 helix: 0.85 (0.10), residues: 2478 sheet: 0.39 (0.19), residues: 744 loop : -1.28 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 407 HIS 0.007 0.001 HIS L 393 PHE 0.027 0.001 PHE G 20 TYR 0.026 0.001 TYR C 24 ARG 0.009 0.000 ARG E 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1065 time to evaluate : 5.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8201 (p90) cc_final: 0.7850 (p90) REVERT: A 77 GLU cc_start: 0.8967 (pt0) cc_final: 0.8714 (pt0) REVERT: A 149 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8616 (t80) REVERT: A 166 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7834 (mttt) REVERT: A 370 LYS cc_start: 0.7932 (tttp) cc_final: 0.7183 (tmtt) REVERT: A 377 MET cc_start: 0.8607 (tmm) cc_final: 0.8392 (tmm) REVERT: A 379 SER cc_start: 0.8815 (t) cc_final: 0.8530 (t) REVERT: A 411 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8106 (tm-30) REVERT: A 430 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8806 (tppt) REVERT: B 33 SER cc_start: 0.8654 (m) cc_final: 0.8398 (p) REVERT: B 111 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: B 125 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 147 MET cc_start: 0.8720 (mmm) cc_final: 0.8369 (ttm) REVERT: B 213 ARG cc_start: 0.8556 (tmm-80) cc_final: 0.7986 (ttp80) REVERT: B 390 ARG cc_start: 0.8413 (ttm170) cc_final: 0.8092 (ttt180) REVERT: B 403 MET cc_start: 0.8298 (mmm) cc_final: 0.7891 (mmm) REVERT: B 421 GLU cc_start: 0.7883 (tp30) cc_final: 0.7538 (tp30) REVERT: C 69 ASP cc_start: 0.7867 (t0) cc_final: 0.7379 (t70) REVERT: C 98 ASP cc_start: 0.7696 (p0) cc_final: 0.7447 (p0) REVERT: C 156 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8638 (mmm-85) REVERT: C 223 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (p) REVERT: C 257 THR cc_start: 0.9307 (m) cc_final: 0.9099 (p) REVERT: C 282 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: C 370 LYS cc_start: 0.8145 (tttp) cc_final: 0.7610 (tptp) REVERT: C 430 LYS cc_start: 0.9510 (ttmt) cc_final: 0.9202 (pttm) REVERT: D 33 SER cc_start: 0.8956 (m) cc_final: 0.8564 (p) REVERT: D 291 GLN cc_start: 0.8396 (pt0) cc_final: 0.7946 (pt0) REVERT: D 297 LYS cc_start: 0.8794 (tttt) cc_final: 0.8456 (tttp) REVERT: D 347 ASN cc_start: 0.8429 (p0) cc_final: 0.8206 (p0) REVERT: D 350 LYS cc_start: 0.9058 (tppt) cc_final: 0.8406 (tppt) REVERT: D 364 SER cc_start: 0.8383 (p) cc_final: 0.8024 (p) REVERT: D 370 ASN cc_start: 0.8354 (t0) cc_final: 0.7952 (t0) REVERT: D 421 GLU cc_start: 0.8293 (tp30) cc_final: 0.8020 (tp30) REVERT: D 423 GLN cc_start: 0.8897 (tp40) cc_final: 0.8632 (pt0) REVERT: E 49 PHE cc_start: 0.8233 (p90) cc_final: 0.7844 (p90) REVERT: E 69 ASP cc_start: 0.7772 (t0) cc_final: 0.7163 (t70) REVERT: E 370 LYS cc_start: 0.8191 (tttp) cc_final: 0.7612 (tptp) REVERT: E 388 TRP cc_start: 0.8915 (m100) cc_final: 0.8657 (m100) REVERT: E 398 MET cc_start: 0.9093 (mmm) cc_final: 0.8567 (mmt) REVERT: E 407 TRP cc_start: 0.8635 (m100) cc_final: 0.8360 (m100) REVERT: E 430 LYS cc_start: 0.9456 (ttmt) cc_final: 0.8968 (tppt) REVERT: F 33 SER cc_start: 0.8754 (m) cc_final: 0.8392 (p) REVERT: F 177 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8359 (t0) REVERT: F 200 TYR cc_start: 0.8711 (m-10) cc_final: 0.8443 (m-10) REVERT: F 257 MET cc_start: 0.8489 (mmp) cc_final: 0.8036 (mmm) REVERT: F 279 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: F 363 MET cc_start: 0.7440 (ptp) cc_final: 0.7215 (ptp) REVERT: G 6 HIS cc_start: 0.8166 (t70) cc_final: 0.7563 (t70) REVERT: G 7 ILE cc_start: 0.8945 (mt) cc_final: 0.8553 (mp) REVERT: G 12 CYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8733 (p) REVERT: G 27 GLU cc_start: 0.8944 (tt0) cc_final: 0.8686 (tm-30) REVERT: G 41 ASP cc_start: 0.7792 (p0) cc_final: 0.7444 (p0) REVERT: G 101 TRP cc_start: 0.8562 (t60) cc_final: 0.8025 (t60) REVERT: G 125 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9038 (mt-10) REVERT: G 136 THR cc_start: 0.8300 (m) cc_final: 0.7946 (p) REVERT: G 174 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8565 (mmmm) REVERT: G 216 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8392 (mmtp) REVERT: G 267 MET cc_start: 0.7943 (ptp) cc_final: 0.7707 (ptm) REVERT: G 293 MET cc_start: 0.8056 (mtp) cc_final: 0.7850 (mtt) REVERT: G 300 MET cc_start: 0.7922 (mtt) cc_final: 0.7436 (mtt) REVERT: G 351 VAL cc_start: 0.9253 (t) cc_final: 0.8830 (p) REVERT: G 362 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8718 (mtmm) REVERT: G 367 PHE cc_start: 0.8480 (t80) cc_final: 0.8149 (t80) REVERT: G 397 TRP cc_start: 0.8643 (m100) cc_final: 0.8204 (m-10) REVERT: G 422 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.6283 (t80) REVERT: H 6 HIS cc_start: 0.7911 (t70) cc_final: 0.7519 (t70) REVERT: H 12 CYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8660 (p) REVERT: H 27 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8723 (tm-30) REVERT: H 33 SER cc_start: 0.8871 (m) cc_final: 0.8378 (p) REVERT: H 41 ASP cc_start: 0.7319 (p0) cc_final: 0.6957 (p0) REVERT: H 73 MET cc_start: 0.9064 (mpp) cc_final: 0.7953 (mpp) REVERT: H 81 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5198 (m-10) REVERT: H 130 LEU cc_start: 0.8519 (tp) cc_final: 0.8174 (tp) REVERT: H 134 GLN cc_start: 0.8354 (pp30) cc_final: 0.8142 (pp30) REVERT: H 136 THR cc_start: 0.8585 (m) cc_final: 0.8062 (p) REVERT: H 174 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8444 (mmmt) REVERT: H 216 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8378 (mmtp) REVERT: H 255 VAL cc_start: 0.8247 (t) cc_final: 0.7905 (t) REVERT: H 267 MET cc_start: 0.7709 (ptp) cc_final: 0.7398 (ptm) REVERT: H 299 MET cc_start: 0.6922 (mmp) cc_final: 0.6024 (mmp) REVERT: H 300 MET cc_start: 0.8128 (mtt) cc_final: 0.7779 (mtt) REVERT: H 307 HIS cc_start: 0.9002 (m-70) cc_final: 0.8647 (m-70) REVERT: H 322 SER cc_start: 0.7787 (m) cc_final: 0.7091 (p) REVERT: H 362 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8312 (mtmm) REVERT: H 397 TRP cc_start: 0.8600 (m100) cc_final: 0.8334 (m-10) REVERT: I 6 HIS cc_start: 0.8051 (t70) cc_final: 0.7511 (t70) REVERT: I 7 ILE cc_start: 0.9123 (mt) cc_final: 0.8901 (mp) REVERT: I 33 SER cc_start: 0.9208 (m) cc_final: 0.8957 (p) REVERT: I 41 ASP cc_start: 0.7944 (p0) cc_final: 0.7114 (p0) REVERT: I 50 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: I 67 ASP cc_start: 0.8173 (t0) cc_final: 0.7624 (t0) REVERT: I 92 PHE cc_start: 0.8367 (p90) cc_final: 0.8145 (p90) REVERT: I 101 TRP cc_start: 0.8588 (t60) cc_final: 0.7907 (t60) REVERT: I 125 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8994 (mt-10) REVERT: I 130 LEU cc_start: 0.8318 (tp) cc_final: 0.8018 (tp) REVERT: I 134 GLN cc_start: 0.8339 (pt0) cc_final: 0.8078 (pp30) REVERT: I 135 LEU cc_start: 0.8821 (tp) cc_final: 0.8436 (tp) REVERT: I 136 THR cc_start: 0.8309 (m) cc_final: 0.7808 (p) REVERT: I 174 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8596 (mmmm) REVERT: I 184 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8526 (p0) REVERT: I 246 LEU cc_start: 0.8343 (tp) cc_final: 0.7912 (tt) REVERT: I 267 MET cc_start: 0.7851 (ptp) cc_final: 0.7453 (ptm) REVERT: I 343 GLU cc_start: 0.8810 (tp30) cc_final: 0.8561 (tp30) REVERT: I 351 VAL cc_start: 0.9439 (t) cc_final: 0.9009 (m) REVERT: I 363 MET cc_start: 0.8010 (ptp) cc_final: 0.7788 (ptp) REVERT: I 379 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8815 (ptpp) REVERT: J 138 PHE cc_start: 0.8697 (m-10) cc_final: 0.8385 (m-10) REVERT: J 230 LEU cc_start: 0.9202 (mp) cc_final: 0.8849 (tt) REVERT: J 282 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: J 332 ILE cc_start: 0.9518 (mm) cc_final: 0.9067 (tp) REVERT: J 388 TRP cc_start: 0.8699 (m100) cc_final: 0.8415 (m100) REVERT: K 33 ASP cc_start: 0.8024 (p0) cc_final: 0.7728 (p0) REVERT: K 127 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7501 (p0) REVERT: K 149 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8051 (t80) REVERT: K 203 MET cc_start: 0.8093 (mmp) cc_final: 0.7292 (mmm) REVERT: K 282 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: K 388 TRP cc_start: 0.8611 (m100) cc_final: 0.7989 (m100) REVERT: K 417 GLU cc_start: 0.8482 (tt0) cc_final: 0.8231 (tt0) REVERT: K 434 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8318 (pp20) REVERT: L 149 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8862 (t80) REVERT: L 322 ASP cc_start: 0.7565 (p0) cc_final: 0.7317 (p0) outliers start: 236 outliers final: 153 residues processed: 1225 average time/residue: 0.5380 time to fit residues: 1089.1418 Evaluate side-chains 1087 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 914 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 0.0770 chunk 279 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 420 optimal weight: 0.0870 chunk 340 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 442 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 3.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 301 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 41844 Z= 0.251 Angle : 0.628 11.420 56844 Z= 0.314 Chirality : 0.044 0.214 6222 Planarity : 0.005 0.067 7386 Dihedral : 12.454 169.387 5890 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 6.38 % Allowed : 20.78 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.07 (0.12), residues: 5130 helix: 0.82 (0.10), residues: 2478 sheet: 0.35 (0.19), residues: 756 loop : -1.33 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 407 HIS 0.011 0.001 HIS G 307 PHE 0.028 0.001 PHE K 49 TYR 0.029 0.001 TYR H 159 ARG 0.013 0.001 ARG L 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 939 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8194 (p90) cc_final: 0.7833 (p90) REVERT: A 149 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8686 (t80) REVERT: A 152 LEU cc_start: 0.8510 (tp) cc_final: 0.8304 (tp) REVERT: A 377 MET cc_start: 0.8658 (tmm) cc_final: 0.8393 (tmm) REVERT: A 411 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8114 (tm-30) REVERT: A 430 LYS cc_start: 0.9329 (ttmt) cc_final: 0.8779 (tppt) REVERT: B 33 SER cc_start: 0.8674 (m) cc_final: 0.8410 (p) REVERT: B 111 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: B 125 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7976 (tm-30) REVERT: B 136 THR cc_start: 0.8369 (m) cc_final: 0.6944 (t) REVERT: B 213 ARG cc_start: 0.8614 (tmm-80) cc_final: 0.8033 (ttp80) REVERT: B 403 MET cc_start: 0.8333 (mmm) cc_final: 0.7923 (mmm) REVERT: C 69 ASP cc_start: 0.7943 (t0) cc_final: 0.7404 (t70) REVERT: C 98 ASP cc_start: 0.8131 (p0) cc_final: 0.7826 (p0) REVERT: C 156 ARG cc_start: 0.8927 (mtp180) cc_final: 0.8588 (mmm-85) REVERT: C 257 THR cc_start: 0.9299 (m) cc_final: 0.9094 (p) REVERT: C 282 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: C 370 LYS cc_start: 0.8109 (tttp) cc_final: 0.7570 (tptp) REVERT: C 398 MET cc_start: 0.8987 (mmt) cc_final: 0.8556 (mmt) REVERT: C 430 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9206 (pttm) REVERT: D 33 SER cc_start: 0.8880 (m) cc_final: 0.8540 (p) REVERT: D 88 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8311 (p0) REVERT: D 209 ASP cc_start: 0.8640 (m-30) cc_final: 0.8415 (m-30) REVERT: D 257 MET cc_start: 0.7875 (mmm) cc_final: 0.7506 (mmt) REVERT: D 291 GLN cc_start: 0.8321 (pt0) cc_final: 0.7902 (pt0) REVERT: D 350 LYS cc_start: 0.9137 (tppt) cc_final: 0.8301 (tppt) REVERT: D 364 SER cc_start: 0.8430 (p) cc_final: 0.8093 (p) REVERT: D 370 ASN cc_start: 0.8414 (t0) cc_final: 0.7998 (t0) REVERT: D 423 GLN cc_start: 0.8873 (tp40) cc_final: 0.8635 (pt0) REVERT: E 49 PHE cc_start: 0.8233 (p90) cc_final: 0.7851 (p90) REVERT: E 69 ASP cc_start: 0.7939 (t0) cc_final: 0.7436 (t70) REVERT: E 370 LYS cc_start: 0.8238 (tttp) cc_final: 0.7681 (tptp) REVERT: E 388 TRP cc_start: 0.8913 (m100) cc_final: 0.8713 (m100) REVERT: E 398 MET cc_start: 0.9094 (mmm) cc_final: 0.8448 (mmt) REVERT: E 430 LYS cc_start: 0.9465 (ttmt) cc_final: 0.8988 (tppt) REVERT: F 33 SER cc_start: 0.8730 (m) cc_final: 0.8457 (p) REVERT: F 200 TYR cc_start: 0.8721 (m-10) cc_final: 0.8401 (m-10) REVERT: F 279 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: G 7 ILE cc_start: 0.9030 (mt) cc_final: 0.8701 (mp) REVERT: G 12 CYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8652 (p) REVERT: G 22 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8559 (tp30) REVERT: G 27 GLU cc_start: 0.9028 (tt0) cc_final: 0.8639 (tm-30) REVERT: G 41 ASP cc_start: 0.7887 (p0) cc_final: 0.7531 (p0) REVERT: G 67 ASP cc_start: 0.8047 (t70) cc_final: 0.7679 (t70) REVERT: G 81 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5581 (m-10) REVERT: G 101 TRP cc_start: 0.8409 (t60) cc_final: 0.7981 (t60) REVERT: G 125 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9042 (mt-10) REVERT: G 136 THR cc_start: 0.8412 (m) cc_final: 0.8104 (p) REVERT: G 174 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8615 (mmmm) REVERT: G 216 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8399 (mmtp) REVERT: G 300 MET cc_start: 0.7975 (mtt) cc_final: 0.7518 (mtt) REVERT: G 351 VAL cc_start: 0.9273 (t) cc_final: 0.8892 (p) REVERT: G 362 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8662 (mtmm) REVERT: G 367 PHE cc_start: 0.8588 (t80) cc_final: 0.8234 (t80) REVERT: G 397 TRP cc_start: 0.8756 (m100) cc_final: 0.8347 (m-10) REVERT: G 422 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6343 (t80) REVERT: H 6 HIS cc_start: 0.7933 (t70) cc_final: 0.7523 (t70) REVERT: H 12 CYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8691 (p) REVERT: H 27 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8859 (tm-30) REVERT: H 33 SER cc_start: 0.8838 (m) cc_final: 0.8322 (p) REVERT: H 41 ASP cc_start: 0.7486 (p0) cc_final: 0.7140 (p0) REVERT: H 73 MET cc_start: 0.9061 (mpp) cc_final: 0.7986 (mpp) REVERT: H 101 TRP cc_start: 0.8274 (t60) cc_final: 0.7715 (t60) REVERT: H 130 LEU cc_start: 0.8543 (tp) cc_final: 0.8185 (tp) REVERT: H 136 THR cc_start: 0.8604 (m) cc_final: 0.8110 (p) REVERT: H 174 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8426 (mmmt) REVERT: H 300 MET cc_start: 0.8201 (mtt) cc_final: 0.7921 (mtt) REVERT: H 322 SER cc_start: 0.7835 (m) cc_final: 0.7562 (p) REVERT: H 330 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8156 (tmm) REVERT: H 362 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8297 (mtmm) REVERT: H 397 TRP cc_start: 0.8587 (m100) cc_final: 0.8303 (m-10) REVERT: I 6 HIS cc_start: 0.8076 (t70) cc_final: 0.7591 (t70) REVERT: I 7 ILE cc_start: 0.9132 (mt) cc_final: 0.8902 (mp) REVERT: I 33 SER cc_start: 0.9116 (m) cc_final: 0.8822 (p) REVERT: I 41 ASP cc_start: 0.7867 (p0) cc_final: 0.7464 (p0) REVERT: I 50 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8277 (m-10) REVERT: I 67 ASP cc_start: 0.8181 (t0) cc_final: 0.7749 (t70) REVERT: I 92 PHE cc_start: 0.8512 (p90) cc_final: 0.8243 (p90) REVERT: I 101 TRP cc_start: 0.8547 (t60) cc_final: 0.7900 (t60) REVERT: I 125 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8977 (mt-10) REVERT: I 130 LEU cc_start: 0.8506 (tp) cc_final: 0.8076 (tp) REVERT: I 134 GLN cc_start: 0.8433 (pt0) cc_final: 0.8076 (pp30) REVERT: I 135 LEU cc_start: 0.8880 (tp) cc_final: 0.8559 (tp) REVERT: I 136 THR cc_start: 0.8596 (m) cc_final: 0.7979 (p) REVERT: I 174 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8619 (mmmm) REVERT: I 184 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8452 (p0) REVERT: I 246 LEU cc_start: 0.8364 (tp) cc_final: 0.7998 (tt) REVERT: I 267 MET cc_start: 0.7936 (ptp) cc_final: 0.7510 (ptm) REVERT: I 307 HIS cc_start: 0.8984 (m-70) cc_final: 0.8740 (m-70) REVERT: I 343 GLU cc_start: 0.8821 (tp30) cc_final: 0.8574 (tp30) REVERT: I 351 VAL cc_start: 0.9448 (t) cc_final: 0.9049 (m) REVERT: I 363 MET cc_start: 0.7909 (ptp) cc_final: 0.7618 (ptp) REVERT: I 379 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8832 (ptpp) REVERT: J 138 PHE cc_start: 0.8769 (m-80) cc_final: 0.8435 (m-10) REVERT: J 230 LEU cc_start: 0.9239 (mp) cc_final: 0.8864 (tt) REVERT: J 282 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: J 332 ILE cc_start: 0.9527 (mm) cc_final: 0.9174 (tp) REVERT: J 388 TRP cc_start: 0.8640 (m100) cc_final: 0.8333 (m100) REVERT: K 33 ASP cc_start: 0.8121 (p0) cc_final: 0.7772 (p0) REVERT: K 127 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7679 (p0) REVERT: K 388 TRP cc_start: 0.8680 (m100) cc_final: 0.8397 (m100) REVERT: K 434 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8148 (pp20) REVERT: L 110 ILE cc_start: 0.9256 (mm) cc_final: 0.8857 (tp) REVERT: L 149 PHE cc_start: 0.9126 (t80) cc_final: 0.8886 (t80) REVERT: L 203 MET cc_start: 0.8586 (mmp) cc_final: 0.8186 (mmp) REVERT: L 269 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8785 (pp) outliers start: 281 outliers final: 205 residues processed: 1131 average time/residue: 0.5035 time to fit residues: 943.1672 Evaluate side-chains 1091 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 868 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 425 TYR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 0.8980 chunk 443 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 493 optimal weight: 4.9990 chunk 409 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 347 ASN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41844 Z= 0.173 Angle : 0.612 10.069 56844 Z= 0.302 Chirality : 0.043 0.226 6222 Planarity : 0.004 0.066 7386 Dihedral : 12.310 168.899 5886 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.88 % Allowed : 22.77 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 5130 helix: 0.87 (0.11), residues: 2448 sheet: 0.57 (0.19), residues: 744 loop : -1.18 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 407 HIS 0.011 0.001 HIS G 307 PHE 0.032 0.001 PHE G 20 TYR 0.031 0.001 TYR C 24 ARG 0.008 0.000 ARG L 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 971 time to evaluate : 5.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8084 (p90) cc_final: 0.7659 (p90) REVERT: A 116 ASP cc_start: 0.8586 (p0) cc_final: 0.8075 (m-30) REVERT: A 149 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8663 (t80) REVERT: A 252 LEU cc_start: 0.8004 (mp) cc_final: 0.6538 (mm) REVERT: A 377 MET cc_start: 0.8594 (tmm) cc_final: 0.8324 (tmm) REVERT: A 391 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 411 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8228 (tm-30) REVERT: A 413 MET cc_start: 0.8194 (ttm) cc_final: 0.7621 (mtt) REVERT: A 430 LYS cc_start: 0.9322 (ttmt) cc_final: 0.8798 (tppt) REVERT: B 33 SER cc_start: 0.8634 (m) cc_final: 0.8392 (p) REVERT: B 111 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: B 125 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 136 THR cc_start: 0.8224 (m) cc_final: 0.6744 (t) REVERT: B 159 TYR cc_start: 0.8783 (m-80) cc_final: 0.8484 (m-80) REVERT: C 69 ASP cc_start: 0.7848 (t0) cc_final: 0.7397 (t70) REVERT: C 98 ASP cc_start: 0.8041 (p0) cc_final: 0.7723 (p0) REVERT: C 156 ARG cc_start: 0.8903 (mtp180) cc_final: 0.8582 (mmm-85) REVERT: C 203 MET cc_start: 0.8376 (mmm) cc_final: 0.8029 (mmm) REVERT: C 232 SER cc_start: 0.8813 (t) cc_final: 0.8532 (t) REVERT: C 257 THR cc_start: 0.9323 (m) cc_final: 0.9109 (p) REVERT: C 282 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: C 351 PHE cc_start: 0.7469 (m-80) cc_final: 0.6406 (m-80) REVERT: C 370 LYS cc_start: 0.8071 (tttp) cc_final: 0.7460 (tptp) REVERT: C 430 LYS cc_start: 0.9514 (ttmt) cc_final: 0.9207 (pttm) REVERT: C 432 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7351 (t80) REVERT: D 33 SER cc_start: 0.8855 (m) cc_final: 0.8502 (p) REVERT: D 88 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7986 (p0) REVERT: D 136 THR cc_start: 0.8381 (m) cc_final: 0.6945 (t) REVERT: D 257 MET cc_start: 0.7536 (mmm) cc_final: 0.7124 (mmt) REVERT: D 287 PRO cc_start: 0.9244 (Cg_exo) cc_final: 0.8961 (Cg_endo) REVERT: D 297 LYS cc_start: 0.8955 (tttt) cc_final: 0.8724 (tttm) REVERT: D 324 LYS cc_start: 0.8878 (tttt) cc_final: 0.8064 (tptt) REVERT: D 350 LYS cc_start: 0.8977 (tppt) cc_final: 0.8347 (tppt) REVERT: D 364 SER cc_start: 0.8471 (p) cc_final: 0.8126 (p) REVERT: D 370 ASN cc_start: 0.8439 (t0) cc_final: 0.7999 (t0) REVERT: E 49 PHE cc_start: 0.8147 (p90) cc_final: 0.7784 (p90) REVERT: E 69 ASP cc_start: 0.7927 (t0) cc_final: 0.7544 (t0) REVERT: E 154 MET cc_start: 0.9014 (mmm) cc_final: 0.8720 (mmm) REVERT: E 156 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8396 (mmm-85) REVERT: E 370 LYS cc_start: 0.8124 (tttp) cc_final: 0.7637 (tptp) REVERT: E 398 MET cc_start: 0.9118 (mmm) cc_final: 0.8528 (mmt) REVERT: E 407 TRP cc_start: 0.8638 (m100) cc_final: 0.8347 (m100) REVERT: E 430 LYS cc_start: 0.9464 (ttmt) cc_final: 0.8971 (tppt) REVERT: F 33 SER cc_start: 0.8706 (m) cc_final: 0.8390 (p) REVERT: F 330 MET cc_start: 0.8676 (mmm) cc_final: 0.8420 (mmm) REVERT: G 12 CYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8643 (p) REVERT: G 22 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8769 (tp30) REVERT: G 27 GLU cc_start: 0.9042 (tt0) cc_final: 0.8706 (tm-30) REVERT: G 41 ASP cc_start: 0.7862 (p0) cc_final: 0.7523 (p0) REVERT: G 67 ASP cc_start: 0.7846 (t70) cc_final: 0.7431 (t70) REVERT: G 101 TRP cc_start: 0.8417 (t60) cc_final: 0.7992 (t60) REVERT: G 125 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9063 (mt-10) REVERT: G 136 THR cc_start: 0.8311 (m) cc_final: 0.7862 (p) REVERT: G 174 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8565 (mmmm) REVERT: G 216 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8416 (mmtp) REVERT: G 298 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8188 (t0) REVERT: G 351 VAL cc_start: 0.9223 (t) cc_final: 0.8819 (p) REVERT: G 362 LYS cc_start: 0.9027 (mtmm) cc_final: 0.8699 (mtmm) REVERT: G 367 PHE cc_start: 0.8597 (t80) cc_final: 0.8276 (t80) REVERT: G 397 TRP cc_start: 0.8736 (m100) cc_final: 0.8267 (m-10) REVERT: G 422 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.6237 (t80) REVERT: H 6 HIS cc_start: 0.7886 (t70) cc_final: 0.7529 (t70) REVERT: H 12 CYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8712 (p) REVERT: H 27 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8876 (tm-30) REVERT: H 33 SER cc_start: 0.8688 (m) cc_final: 0.8176 (p) REVERT: H 41 ASP cc_start: 0.7371 (p0) cc_final: 0.7017 (p0) REVERT: H 73 MET cc_start: 0.9055 (mpp) cc_final: 0.7981 (mpp) REVERT: H 101 TRP cc_start: 0.8356 (t60) cc_final: 0.7766 (t60) REVERT: H 122 LYS cc_start: 0.9188 (tttm) cc_final: 0.8705 (pttt) REVERT: H 136 THR cc_start: 0.8689 (m) cc_final: 0.8234 (p) REVERT: H 157 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: H 174 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8379 (mmmt) REVERT: H 216 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7714 (pptt) REVERT: H 300 MET cc_start: 0.8216 (mtt) cc_final: 0.8007 (mtt) REVERT: H 307 HIS cc_start: 0.8947 (m-70) cc_final: 0.8631 (m-70) REVERT: H 322 SER cc_start: 0.7769 (m) cc_final: 0.7407 (p) REVERT: H 362 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8284 (mtmm) REVERT: H 397 TRP cc_start: 0.8584 (m100) cc_final: 0.8275 (m-10) REVERT: I 6 HIS cc_start: 0.8048 (t70) cc_final: 0.7551 (t70) REVERT: I 7 ILE cc_start: 0.9148 (mt) cc_final: 0.8937 (mp) REVERT: I 33 SER cc_start: 0.9149 (m) cc_final: 0.8864 (p) REVERT: I 41 ASP cc_start: 0.7831 (p0) cc_final: 0.7477 (p0) REVERT: I 50 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8212 (m-10) REVERT: I 67 ASP cc_start: 0.8071 (t0) cc_final: 0.7662 (t70) REVERT: I 92 PHE cc_start: 0.8529 (p90) cc_final: 0.8244 (p90) REVERT: I 101 TRP cc_start: 0.8573 (t60) cc_final: 0.7928 (t60) REVERT: I 125 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8984 (mt-10) REVERT: I 130 LEU cc_start: 0.8448 (tp) cc_final: 0.8139 (tp) REVERT: I 134 GLN cc_start: 0.8404 (pt0) cc_final: 0.8069 (pp30) REVERT: I 135 LEU cc_start: 0.8858 (tp) cc_final: 0.8565 (tp) REVERT: I 136 THR cc_start: 0.8534 (m) cc_final: 0.7991 (p) REVERT: I 174 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8582 (mmmm) REVERT: I 184 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8318 (p0) REVERT: I 246 LEU cc_start: 0.8349 (tp) cc_final: 0.7901 (tt) REVERT: I 257 MET cc_start: 0.8393 (mmt) cc_final: 0.8156 (mmm) REVERT: I 267 MET cc_start: 0.7877 (ptp) cc_final: 0.7479 (ptm) REVERT: I 343 GLU cc_start: 0.8788 (tp30) cc_final: 0.8545 (tp30) REVERT: I 351 VAL cc_start: 0.9395 (t) cc_final: 0.8974 (m) REVERT: I 363 MET cc_start: 0.7816 (ptp) cc_final: 0.7316 (ptp) REVERT: J 138 PHE cc_start: 0.8767 (m-80) cc_final: 0.8450 (m-10) REVERT: J 172 TYR cc_start: 0.7578 (t80) cc_final: 0.6979 (t80) REVERT: J 203 MET cc_start: 0.8298 (mmp) cc_final: 0.7548 (mmm) REVERT: J 230 LEU cc_start: 0.9192 (mp) cc_final: 0.8869 (tt) REVERT: J 282 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: J 332 ILE cc_start: 0.9506 (mm) cc_final: 0.9115 (tp) REVERT: J 339 ARG cc_start: 0.7939 (tpm170) cc_final: 0.7726 (tpt90) REVERT: J 432 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7150 (t80) REVERT: K 33 ASP cc_start: 0.8165 (p0) cc_final: 0.7900 (p0) REVERT: K 84 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.6913 (ttm-80) REVERT: K 127 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (p0) REVERT: K 149 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.7965 (t80) REVERT: K 157 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9063 (mm) REVERT: K 203 MET cc_start: 0.8018 (mmp) cc_final: 0.7109 (mmt) REVERT: K 434 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: L 110 ILE cc_start: 0.9233 (mm) cc_final: 0.8837 (tp) REVERT: L 149 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8835 (t80) REVERT: L 203 MET cc_start: 0.8520 (mmp) cc_final: 0.8144 (mmp) REVERT: L 269 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8744 (pp) outliers start: 215 outliers final: 152 residues processed: 1118 average time/residue: 0.5167 time to fit residues: 957.2617 Evaluate side-chains 1078 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 904 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 349 VAL Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 chunk 415 optimal weight: 0.0870 chunk 275 optimal weight: 2.9990 chunk 491 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 28 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN J 293 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN L 393 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 41844 Z= 0.233 Angle : 0.625 11.817 56844 Z= 0.311 Chirality : 0.044 0.214 6222 Planarity : 0.005 0.060 7386 Dihedral : 12.281 169.771 5874 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.45 % Allowed : 23.61 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.03 (0.12), residues: 5130 helix: 0.83 (0.11), residues: 2436 sheet: 0.43 (0.19), residues: 768 loop : -1.15 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 407 HIS 0.008 0.001 HIS A 406 PHE 0.030 0.001 PHE K 49 TYR 0.031 0.001 TYR H 159 ARG 0.009 0.001 ARG K 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 914 time to evaluate : 4.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8082 (p90) cc_final: 0.7642 (p90) REVERT: A 109 THR cc_start: 0.8701 (m) cc_final: 0.8324 (m) REVERT: A 116 ASP cc_start: 0.8582 (p0) cc_final: 0.8126 (m-30) REVERT: A 149 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (t80) REVERT: A 370 LYS cc_start: 0.7844 (tttp) cc_final: 0.7095 (tmtt) REVERT: A 377 MET cc_start: 0.8623 (tmm) cc_final: 0.8345 (tmm) REVERT: A 411 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8302 (tp30) REVERT: A 430 LYS cc_start: 0.9338 (ttmt) cc_final: 0.8805 (tppt) REVERT: B 111 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: B 125 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 136 THR cc_start: 0.8391 (m) cc_final: 0.6887 (t) REVERT: B 279 GLN cc_start: 0.8142 (pt0) cc_final: 0.7867 (mt0) REVERT: C 69 ASP cc_start: 0.7979 (t0) cc_final: 0.7634 (t70) REVERT: C 98 ASP cc_start: 0.8152 (p0) cc_final: 0.7900 (p0) REVERT: C 156 ARG cc_start: 0.8899 (mtp180) cc_final: 0.8587 (mmm-85) REVERT: C 203 MET cc_start: 0.8410 (mmm) cc_final: 0.8110 (mmm) REVERT: C 232 SER cc_start: 0.8841 (t) cc_final: 0.8577 (t) REVERT: C 257 THR cc_start: 0.9379 (m) cc_final: 0.9161 (p) REVERT: C 282 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8666 (m-80) REVERT: C 351 PHE cc_start: 0.7607 (m-80) cc_final: 0.6597 (m-80) REVERT: C 370 LYS cc_start: 0.8061 (tttp) cc_final: 0.7438 (tptp) REVERT: C 398 MET cc_start: 0.8940 (mmt) cc_final: 0.8535 (mmp) REVERT: C 430 LYS cc_start: 0.9516 (ttmt) cc_final: 0.9199 (pttm) REVERT: C 432 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7337 (t80) REVERT: D 33 SER cc_start: 0.8904 (m) cc_final: 0.8592 (p) REVERT: D 88 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8020 (p0) REVERT: D 125 GLU cc_start: 0.8444 (tp30) cc_final: 0.8218 (tp30) REVERT: D 136 THR cc_start: 0.8366 (m) cc_final: 0.6943 (t) REVERT: D 257 MET cc_start: 0.7708 (mmm) cc_final: 0.7258 (mmt) REVERT: D 291 GLN cc_start: 0.8136 (pt0) cc_final: 0.7760 (pt0) REVERT: D 297 LYS cc_start: 0.8894 (tttt) cc_final: 0.8650 (tttm) REVERT: D 350 LYS cc_start: 0.8962 (tppt) cc_final: 0.8305 (tppt) REVERT: D 364 SER cc_start: 0.8455 (p) cc_final: 0.8122 (p) REVERT: D 370 ASN cc_start: 0.8472 (t0) cc_final: 0.8241 (t0) REVERT: E 49 PHE cc_start: 0.8166 (p90) cc_final: 0.7765 (p90) REVERT: E 69 ASP cc_start: 0.8002 (t0) cc_final: 0.7635 (t0) REVERT: E 88 HIS cc_start: 0.4851 (OUTLIER) cc_final: 0.3762 (t70) REVERT: E 97 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7150 (mm-30) REVERT: E 370 LYS cc_start: 0.8093 (tttp) cc_final: 0.7580 (tptp) REVERT: E 398 MET cc_start: 0.9139 (mmm) cc_final: 0.8525 (mmt) REVERT: E 407 TRP cc_start: 0.8631 (m100) cc_final: 0.8355 (m100) REVERT: E 430 LYS cc_start: 0.9469 (ttmt) cc_final: 0.9005 (tppt) REVERT: F 33 SER cc_start: 0.8696 (m) cc_final: 0.8440 (p) REVERT: F 330 MET cc_start: 0.8761 (mmm) cc_final: 0.8542 (mmm) REVERT: F 350 LYS cc_start: 0.9376 (tptm) cc_final: 0.8502 (tptp) REVERT: G 12 CYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8648 (p) REVERT: G 41 ASP cc_start: 0.7874 (p0) cc_final: 0.7561 (p0) REVERT: G 67 ASP cc_start: 0.7858 (t70) cc_final: 0.7473 (t70) REVERT: G 101 TRP cc_start: 0.8370 (t60) cc_final: 0.7939 (t60) REVERT: G 125 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9070 (mt-10) REVERT: G 136 THR cc_start: 0.8259 (m) cc_final: 0.7901 (p) REVERT: G 174 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8667 (mmmm) REVERT: G 216 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8440 (mmtp) REVERT: G 257 MET cc_start: 0.8703 (mmm) cc_final: 0.8484 (mtt) REVERT: G 266 PHE cc_start: 0.8771 (m-10) cc_final: 0.8394 (m-10) REVERT: G 298 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8358 (t0) REVERT: G 351 VAL cc_start: 0.9217 (t) cc_final: 0.8815 (p) REVERT: G 367 PHE cc_start: 0.8606 (t80) cc_final: 0.8306 (t80) REVERT: G 397 TRP cc_start: 0.8767 (m100) cc_final: 0.8282 (m-10) REVERT: G 422 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6292 (t80) REVERT: H 6 HIS cc_start: 0.7794 (t70) cc_final: 0.7387 (t70) REVERT: H 12 CYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8714 (p) REVERT: H 27 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8902 (tm-30) REVERT: H 41 ASP cc_start: 0.7547 (p0) cc_final: 0.7209 (p0) REVERT: H 73 MET cc_start: 0.9062 (mpp) cc_final: 0.8738 (mpp) REVERT: H 136 THR cc_start: 0.8603 (m) cc_final: 0.8164 (p) REVERT: H 174 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8461 (mmmt) REVERT: H 293 MET cc_start: 0.7675 (mtt) cc_final: 0.7432 (mtt) REVERT: H 300 MET cc_start: 0.8254 (mtt) cc_final: 0.8006 (mtt) REVERT: H 307 HIS cc_start: 0.8965 (m-70) cc_final: 0.8612 (m-70) REVERT: H 322 SER cc_start: 0.7772 (m) cc_final: 0.7425 (p) REVERT: H 362 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8530 (ptmm) REVERT: H 397 TRP cc_start: 0.8618 (m100) cc_final: 0.8288 (m-10) REVERT: I 6 HIS cc_start: 0.8058 (t70) cc_final: 0.7551 (t70) REVERT: I 7 ILE cc_start: 0.9141 (mt) cc_final: 0.8919 (mp) REVERT: I 33 SER cc_start: 0.9035 (m) cc_final: 0.8688 (p) REVERT: I 41 ASP cc_start: 0.7861 (p0) cc_final: 0.7504 (p0) REVERT: I 50 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8307 (m-10) REVERT: I 67 ASP cc_start: 0.8024 (t0) cc_final: 0.7625 (t70) REVERT: I 92 PHE cc_start: 0.8601 (p90) cc_final: 0.8296 (p90) REVERT: I 125 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8950 (mt-10) REVERT: I 130 LEU cc_start: 0.8512 (tp) cc_final: 0.8133 (tp) REVERT: I 134 GLN cc_start: 0.8438 (pt0) cc_final: 0.8088 (pp30) REVERT: I 135 LEU cc_start: 0.8906 (tp) cc_final: 0.8617 (tp) REVERT: I 136 THR cc_start: 0.8595 (m) cc_final: 0.7984 (p) REVERT: I 174 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8635 (mmmm) REVERT: I 246 LEU cc_start: 0.8396 (tp) cc_final: 0.8010 (tt) REVERT: I 267 MET cc_start: 0.7902 (ptp) cc_final: 0.7437 (ptm) REVERT: I 343 GLU cc_start: 0.8818 (tp30) cc_final: 0.8573 (tp30) REVERT: I 351 VAL cc_start: 0.9359 (t) cc_final: 0.8920 (m) REVERT: I 363 MET cc_start: 0.7695 (ptp) cc_final: 0.7461 (ptp) REVERT: J 138 PHE cc_start: 0.8757 (m-80) cc_final: 0.8421 (m-10) REVERT: J 230 LEU cc_start: 0.9212 (mp) cc_final: 0.8840 (tt) REVERT: J 332 ILE cc_start: 0.9543 (mm) cc_final: 0.9183 (tp) REVERT: J 432 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7246 (t80) REVERT: K 33 ASP cc_start: 0.8455 (p0) cc_final: 0.8226 (p0) REVERT: K 127 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7888 (p0) REVERT: K 157 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9106 (mm) REVERT: K 417 GLU cc_start: 0.8235 (tt0) cc_final: 0.7977 (tt0) REVERT: K 432 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7520 (t80) REVERT: K 434 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: L 110 ILE cc_start: 0.9272 (mm) cc_final: 0.8865 (tp) REVERT: L 149 PHE cc_start: 0.9083 (t80) cc_final: 0.8825 (t80) REVERT: L 269 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (pp) outliers start: 240 outliers final: 177 residues processed: 1084 average time/residue: 0.5148 time to fit residues: 922.4426 Evaluate side-chains 1063 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 868 time to evaluate : 4.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 TYR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 354 CYS Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 9.9990 chunk 196 optimal weight: 0.0020 chunk 293 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 386 optimal weight: 5.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN I 292 GLN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41844 Z= 0.235 Angle : 0.641 12.744 56844 Z= 0.316 Chirality : 0.045 0.273 6222 Planarity : 0.005 0.057 7386 Dihedral : 12.288 170.230 5870 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.11 % Allowed : 24.21 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.00 (0.12), residues: 5130 helix: 0.77 (0.10), residues: 2448 sheet: 0.52 (0.19), residues: 756 loop : -1.18 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 407 HIS 0.019 0.001 HIS A 88 PHE 0.033 0.001 PHE H 20 TYR 0.028 0.001 TYR C 24 ARG 0.010 0.000 ARG K 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 906 time to evaluate : 4.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8106 (p90) cc_final: 0.7649 (p90) REVERT: A 109 THR cc_start: 0.8570 (m) cc_final: 0.8224 (m) REVERT: A 116 ASP cc_start: 0.8601 (p0) cc_final: 0.8141 (m-30) REVERT: A 149 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8743 (t80) REVERT: A 377 MET cc_start: 0.8650 (tmm) cc_final: 0.8308 (tmm) REVERT: A 411 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8306 (tp30) REVERT: A 430 LYS cc_start: 0.9341 (ttmt) cc_final: 0.8808 (tppt) REVERT: B 125 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 136 THR cc_start: 0.8421 (m) cc_final: 0.6917 (t) REVERT: B 190 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8062 (t70) REVERT: B 279 GLN cc_start: 0.8138 (pt0) cc_final: 0.7892 (mt0) REVERT: B 288 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6598 (tm-30) REVERT: B 350 LYS cc_start: 0.8947 (tppt) cc_final: 0.8536 (tppt) REVERT: B 425 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: C 69 ASP cc_start: 0.7976 (t0) cc_final: 0.7625 (t70) REVERT: C 98 ASP cc_start: 0.8163 (p0) cc_final: 0.7791 (p0) REVERT: C 156 ARG cc_start: 0.8905 (mtp180) cc_final: 0.8581 (mmm-85) REVERT: C 203 MET cc_start: 0.8416 (mmm) cc_final: 0.8138 (mmm) REVERT: C 232 SER cc_start: 0.8862 (t) cc_final: 0.8591 (t) REVERT: C 257 THR cc_start: 0.9333 (m) cc_final: 0.9094 (p) REVERT: C 282 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: C 370 LYS cc_start: 0.8056 (tttp) cc_final: 0.7446 (tptp) REVERT: C 430 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9205 (pttm) REVERT: C 432 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7360 (t80) REVERT: D 33 SER cc_start: 0.8905 (m) cc_final: 0.8567 (p) REVERT: D 88 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7764 (p0) REVERT: D 125 GLU cc_start: 0.8465 (tp30) cc_final: 0.8228 (tp30) REVERT: D 257 MET cc_start: 0.7646 (mmm) cc_final: 0.7321 (mmt) REVERT: D 297 LYS cc_start: 0.8875 (tttt) cc_final: 0.8665 (tttm) REVERT: D 350 LYS cc_start: 0.8940 (tppt) cc_final: 0.8406 (tppt) REVERT: D 364 SER cc_start: 0.8514 (p) cc_final: 0.8163 (p) REVERT: D 370 ASN cc_start: 0.8410 (t0) cc_final: 0.8198 (t0) REVERT: E 49 PHE cc_start: 0.8165 (p90) cc_final: 0.7768 (p90) REVERT: E 69 ASP cc_start: 0.7997 (t0) cc_final: 0.7629 (t0) REVERT: E 88 HIS cc_start: 0.4852 (OUTLIER) cc_final: 0.3727 (t70) REVERT: E 370 LYS cc_start: 0.8077 (tttp) cc_final: 0.7540 (tptp) REVERT: E 398 MET cc_start: 0.9148 (mmm) cc_final: 0.8526 (mmt) REVERT: E 407 TRP cc_start: 0.8657 (m100) cc_final: 0.8370 (m100) REVERT: E 430 LYS cc_start: 0.9471 (ttmt) cc_final: 0.9006 (tppt) REVERT: F 33 SER cc_start: 0.8746 (m) cc_final: 0.8504 (p) REVERT: F 69 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: F 350 LYS cc_start: 0.9376 (tptm) cc_final: 0.8492 (tptp) REVERT: G 12 CYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8661 (p) REVERT: G 27 GLU cc_start: 0.9028 (tt0) cc_final: 0.8637 (tm-30) REVERT: G 41 ASP cc_start: 0.7837 (p0) cc_final: 0.7525 (p0) REVERT: G 67 ASP cc_start: 0.7975 (t70) cc_final: 0.7516 (t70) REVERT: G 101 TRP cc_start: 0.8347 (t60) cc_final: 0.7903 (t60) REVERT: G 125 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9123 (mt-10) REVERT: G 136 THR cc_start: 0.8222 (m) cc_final: 0.7893 (p) REVERT: G 174 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8677 (mmmm) REVERT: G 216 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8433 (mmtp) REVERT: G 266 PHE cc_start: 0.8616 (m-10) cc_final: 0.8276 (m-10) REVERT: G 267 MET cc_start: 0.8336 (ttm) cc_final: 0.7665 (tmm) REVERT: G 298 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8532 (m-40) REVERT: G 351 VAL cc_start: 0.9222 (t) cc_final: 0.8808 (p) REVERT: G 367 PHE cc_start: 0.8574 (t80) cc_final: 0.8297 (t80) REVERT: G 397 TRP cc_start: 0.8776 (m100) cc_final: 0.8317 (m-10) REVERT: G 422 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6166 (t80) REVERT: H 6 HIS cc_start: 0.7837 (t70) cc_final: 0.7349 (t70) REVERT: H 27 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8923 (tm-30) REVERT: H 41 ASP cc_start: 0.7561 (p0) cc_final: 0.7235 (p0) REVERT: H 73 MET cc_start: 0.9067 (mpp) cc_final: 0.8754 (mpp) REVERT: H 101 TRP cc_start: 0.8295 (t60) cc_final: 0.7741 (t60) REVERT: H 136 THR cc_start: 0.8599 (m) cc_final: 0.8150 (p) REVERT: H 157 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: H 174 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8449 (mmmt) REVERT: H 307 HIS cc_start: 0.8993 (m-70) cc_final: 0.8646 (m-70) REVERT: H 322 SER cc_start: 0.7815 (m) cc_final: 0.7560 (p) REVERT: H 362 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8614 (ptmm) REVERT: H 379 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8668 (ptpp) REVERT: H 397 TRP cc_start: 0.8625 (m100) cc_final: 0.8304 (m-10) REVERT: I 6 HIS cc_start: 0.8064 (t70) cc_final: 0.7505 (t70) REVERT: I 7 ILE cc_start: 0.9155 (mt) cc_final: 0.8931 (mp) REVERT: I 33 SER cc_start: 0.9041 (m) cc_final: 0.8712 (p) REVERT: I 41 ASP cc_start: 0.7867 (p0) cc_final: 0.7505 (p0) REVERT: I 50 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8260 (m-10) REVERT: I 67 ASP cc_start: 0.8028 (t0) cc_final: 0.7647 (t70) REVERT: I 92 PHE cc_start: 0.8643 (p90) cc_final: 0.8333 (p90) REVERT: I 101 TRP cc_start: 0.8514 (t60) cc_final: 0.7831 (t60) REVERT: I 125 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8953 (mt-10) REVERT: I 130 LEU cc_start: 0.8421 (tp) cc_final: 0.8087 (tp) REVERT: I 134 GLN cc_start: 0.8450 (pt0) cc_final: 0.8095 (pp30) REVERT: I 135 LEU cc_start: 0.8901 (tp) cc_final: 0.8617 (tp) REVERT: I 136 THR cc_start: 0.8543 (m) cc_final: 0.7944 (p) REVERT: I 174 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8665 (mmmm) REVERT: I 233 MET cc_start: 0.9304 (mmm) cc_final: 0.8910 (mmm) REVERT: I 246 LEU cc_start: 0.8391 (tp) cc_final: 0.8003 (tt) REVERT: I 267 MET cc_start: 0.7876 (ptp) cc_final: 0.7438 (ptm) REVERT: I 284 LEU cc_start: 0.8175 (tp) cc_final: 0.7934 (tp) REVERT: I 343 GLU cc_start: 0.8827 (tp30) cc_final: 0.8589 (tp30) REVERT: I 351 VAL cc_start: 0.9330 (t) cc_final: 0.8917 (m) REVERT: I 363 MET cc_start: 0.7643 (ptp) cc_final: 0.7276 (ptp) REVERT: J 33 ASP cc_start: 0.8614 (p0) cc_final: 0.8236 (p0) REVERT: J 138 PHE cc_start: 0.8794 (m-80) cc_final: 0.8463 (m-10) REVERT: J 203 MET cc_start: 0.8334 (mmp) cc_final: 0.8110 (mmm) REVERT: J 230 LEU cc_start: 0.9209 (mp) cc_final: 0.8844 (tt) REVERT: J 432 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7308 (t80) REVERT: K 84 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.6942 (ttm-80) REVERT: K 127 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7945 (p0) REVERT: K 149 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7950 (t80) REVERT: K 157 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9033 (mm) REVERT: K 172 TYR cc_start: 0.7005 (t80) cc_final: 0.6212 (t80) REVERT: K 203 MET cc_start: 0.8174 (mmp) cc_final: 0.7094 (mmt) REVERT: K 432 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7471 (t80) REVERT: K 434 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8110 (pp20) REVERT: L 110 ILE cc_start: 0.9268 (mm) cc_final: 0.8857 (tp) REVERT: L 149 PHE cc_start: 0.9075 (t80) cc_final: 0.8821 (t80) REVERT: L 203 MET cc_start: 0.8531 (mmp) cc_final: 0.8171 (mmp) REVERT: L 269 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8829 (pp) outliers start: 225 outliers final: 187 residues processed: 1061 average time/residue: 0.5038 time to fit residues: 885.1927 Evaluate side-chains 1074 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 865 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 TYR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 354 CYS Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 379 LYS Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 7.9990 chunk 470 optimal weight: 5.9990 chunk 429 optimal weight: 3.9990 chunk 458 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 chunk 140 optimal weight: 0.0770 chunk 413 optimal weight: 7.9990 chunk 433 optimal weight: 9.9990 chunk 456 optimal weight: 0.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 245 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN I 292 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 293 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41844 Z= 0.232 Angle : 0.654 13.988 56844 Z= 0.322 Chirality : 0.045 0.238 6222 Planarity : 0.005 0.060 7386 Dihedral : 12.266 170.419 5868 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.95 % Allowed : 24.93 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.01 (0.12), residues: 5130 helix: 0.76 (0.10), residues: 2442 sheet: 0.49 (0.19), residues: 756 loop : -1.10 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 407 HIS 0.029 0.001 HIS B 190 PHE 0.030 0.001 PHE K 49 TYR 0.031 0.001 TYR C 24 ARG 0.012 0.000 ARG J 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 888 time to evaluate : 4.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8081 (p90) cc_final: 0.7653 (p90) REVERT: A 109 THR cc_start: 0.8583 (m) cc_final: 0.8259 (m) REVERT: A 116 ASP cc_start: 0.8567 (p0) cc_final: 0.8112 (m-30) REVERT: A 149 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8744 (t80) REVERT: A 377 MET cc_start: 0.8683 (tmm) cc_final: 0.8336 (tmm) REVERT: A 411 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8305 (tp30) REVERT: A 430 LYS cc_start: 0.9386 (ttmt) cc_final: 0.8805 (tppt) REVERT: B 72 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8891 (p) REVERT: B 125 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 136 THR cc_start: 0.8301 (m) cc_final: 0.6818 (t) REVERT: B 190 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8079 (t70) REVERT: B 288 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6554 (tm-30) REVERT: B 350 LYS cc_start: 0.8861 (tppt) cc_final: 0.8513 (tppt) REVERT: B 425 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: C 69 ASP cc_start: 0.7962 (t0) cc_final: 0.7606 (t70) REVERT: C 98 ASP cc_start: 0.8151 (p0) cc_final: 0.7857 (p0) REVERT: C 113 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8736 (pt0) REVERT: C 156 ARG cc_start: 0.8900 (mtp180) cc_final: 0.8574 (mmm-85) REVERT: C 203 MET cc_start: 0.8410 (mmm) cc_final: 0.8157 (mmm) REVERT: C 232 SER cc_start: 0.8851 (t) cc_final: 0.8590 (t) REVERT: C 257 THR cc_start: 0.9344 (m) cc_final: 0.9106 (p) REVERT: C 282 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: C 326 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8388 (ttpt) REVERT: C 370 LYS cc_start: 0.7983 (tttp) cc_final: 0.7362 (tptp) REVERT: C 430 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9201 (pttm) REVERT: C 432 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7365 (t80) REVERT: D 33 SER cc_start: 0.8932 (m) cc_final: 0.8633 (p) REVERT: D 88 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7754 (p0) REVERT: D 125 GLU cc_start: 0.8463 (tp30) cc_final: 0.8218 (tp30) REVERT: D 257 MET cc_start: 0.7597 (mmm) cc_final: 0.7225 (mmt) REVERT: D 291 GLN cc_start: 0.8193 (pt0) cc_final: 0.7777 (pt0) REVERT: D 350 LYS cc_start: 0.8941 (tppt) cc_final: 0.8393 (tppt) REVERT: D 364 SER cc_start: 0.8521 (p) cc_final: 0.8160 (p) REVERT: D 370 ASN cc_start: 0.8390 (t0) cc_final: 0.8180 (t0) REVERT: E 49 PHE cc_start: 0.8153 (p90) cc_final: 0.7754 (p90) REVERT: E 69 ASP cc_start: 0.7981 (t0) cc_final: 0.7627 (t0) REVERT: E 88 HIS cc_start: 0.4284 (OUTLIER) cc_final: 0.3195 (t70) REVERT: E 98 ASP cc_start: 0.8241 (p0) cc_final: 0.7966 (p0) REVERT: E 358 GLN cc_start: 0.9032 (mm110) cc_final: 0.8728 (mm-40) REVERT: E 370 LYS cc_start: 0.8030 (tttp) cc_final: 0.7502 (tptp) REVERT: E 398 MET cc_start: 0.9157 (mmm) cc_final: 0.8530 (mmt) REVERT: E 407 TRP cc_start: 0.8609 (m100) cc_final: 0.8296 (m100) REVERT: E 430 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9008 (tppt) REVERT: F 33 SER cc_start: 0.8752 (m) cc_final: 0.8508 (p) REVERT: F 69 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: G 12 CYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8659 (p) REVERT: G 27 GLU cc_start: 0.9065 (tt0) cc_final: 0.8655 (tm-30) REVERT: G 41 ASP cc_start: 0.7845 (p0) cc_final: 0.7536 (p0) REVERT: G 67 ASP cc_start: 0.7841 (t70) cc_final: 0.7467 (t70) REVERT: G 101 TRP cc_start: 0.8342 (t60) cc_final: 0.7893 (t60) REVERT: G 125 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9104 (mt-10) REVERT: G 136 THR cc_start: 0.8207 (m) cc_final: 0.7904 (p) REVERT: G 174 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8700 (mmmm) REVERT: G 216 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8436 (mmtp) REVERT: G 267 MET cc_start: 0.8287 (ttm) cc_final: 0.7696 (tmm) REVERT: G 297 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8135 (mmtm) REVERT: G 298 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8391 (t0) REVERT: G 351 VAL cc_start: 0.9155 (t) cc_final: 0.8806 (m) REVERT: G 367 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8211 (t80) REVERT: G 397 TRP cc_start: 0.8827 (m100) cc_final: 0.8317 (m-10) REVERT: G 422 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6140 (t80) REVERT: H 6 HIS cc_start: 0.7748 (t70) cc_final: 0.7380 (t70) REVERT: H 22 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8726 (tp30) REVERT: H 41 ASP cc_start: 0.7563 (p0) cc_final: 0.7246 (p0) REVERT: H 73 MET cc_start: 0.9047 (mpp) cc_final: 0.8748 (mpp) REVERT: H 101 TRP cc_start: 0.8299 (t60) cc_final: 0.7730 (t60) REVERT: H 136 THR cc_start: 0.8657 (m) cc_final: 0.8226 (p) REVERT: H 157 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8000 (pt0) REVERT: H 174 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8484 (mmmt) REVERT: H 322 SER cc_start: 0.7674 (m) cc_final: 0.7327 (p) REVERT: H 397 TRP cc_start: 0.8641 (m100) cc_final: 0.8320 (m-10) REVERT: I 6 HIS cc_start: 0.8026 (t70) cc_final: 0.7450 (t70) REVERT: I 7 ILE cc_start: 0.9142 (mt) cc_final: 0.8931 (mp) REVERT: I 33 SER cc_start: 0.8994 (m) cc_final: 0.8653 (p) REVERT: I 41 ASP cc_start: 0.7872 (p0) cc_final: 0.7518 (p0) REVERT: I 67 ASP cc_start: 0.8042 (t0) cc_final: 0.7667 (t70) REVERT: I 92 PHE cc_start: 0.8677 (p90) cc_final: 0.8370 (p90) REVERT: I 101 TRP cc_start: 0.8504 (t60) cc_final: 0.7795 (t60) REVERT: I 125 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8951 (mt-10) REVERT: I 130 LEU cc_start: 0.8485 (tp) cc_final: 0.8111 (tp) REVERT: I 134 GLN cc_start: 0.8453 (pt0) cc_final: 0.8133 (pp30) REVERT: I 135 LEU cc_start: 0.8879 (tp) cc_final: 0.8571 (tp) REVERT: I 136 THR cc_start: 0.8549 (m) cc_final: 0.7931 (p) REVERT: I 174 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8668 (mmmm) REVERT: I 233 MET cc_start: 0.9325 (mmm) cc_final: 0.8833 (mmt) REVERT: I 237 THR cc_start: 0.8763 (m) cc_final: 0.8458 (t) REVERT: I 246 LEU cc_start: 0.8404 (tp) cc_final: 0.8010 (tt) REVERT: I 267 MET cc_start: 0.7892 (ptp) cc_final: 0.7469 (ptm) REVERT: I 343 GLU cc_start: 0.8826 (tp30) cc_final: 0.8582 (tp30) REVERT: I 351 VAL cc_start: 0.9334 (t) cc_final: 0.8897 (m) REVERT: J 33 ASP cc_start: 0.8521 (p0) cc_final: 0.8240 (p0) REVERT: J 138 PHE cc_start: 0.8792 (m-80) cc_final: 0.8477 (m-10) REVERT: J 230 LEU cc_start: 0.9206 (mp) cc_final: 0.8837 (tt) REVERT: J 432 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7312 (t80) REVERT: K 127 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7967 (p0) REVERT: K 149 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7962 (t80) REVERT: K 157 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9097 (mm) REVERT: K 172 TYR cc_start: 0.7064 (t80) cc_final: 0.6266 (t80) REVERT: K 203 MET cc_start: 0.8172 (mmp) cc_final: 0.7056 (mmt) REVERT: K 392 ASP cc_start: 0.7275 (m-30) cc_final: 0.6833 (m-30) REVERT: K 432 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7489 (t80) REVERT: K 434 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8313 (pp20) REVERT: L 110 ILE cc_start: 0.9271 (mm) cc_final: 0.8866 (tp) REVERT: L 149 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8821 (t80) REVERT: L 203 MET cc_start: 0.8578 (mmp) cc_final: 0.8252 (mmp) REVERT: L 269 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8769 (pp) outliers start: 218 outliers final: 180 residues processed: 1042 average time/residue: 0.5047 time to fit residues: 874.2516 Evaluate side-chains 1056 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 853 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 425 TYR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 354 CYS Chi-restraints excluded: chain G residue 367 PHE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 149 PHE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 3.9990 chunk 484 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 336 optimal weight: 0.0570 chunk 508 optimal weight: 10.0000 chunk 467 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 279 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 293 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 41844 Z= 0.263 Angle : 0.675 14.092 56844 Z= 0.334 Chirality : 0.045 0.244 6222 Planarity : 0.005 0.062 7386 Dihedral : 12.303 170.824 5867 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.81 % Allowed : 24.95 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 5130 helix: 0.69 (0.10), residues: 2448 sheet: 0.43 (0.19), residues: 756 loop : -1.15 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 407 HIS 0.029 0.001 HIS B 190 PHE 0.031 0.002 PHE H 367 TYR 0.029 0.001 TYR C 24 ARG 0.013 0.001 ARG K 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 870 time to evaluate : 4.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8088 (p90) cc_final: 0.7664 (p90) REVERT: A 109 THR cc_start: 0.8606 (m) cc_final: 0.8229 (m) REVERT: A 114 ILE cc_start: 0.9404 (mt) cc_final: 0.9096 (tp) REVERT: A 116 ASP cc_start: 0.8584 (p0) cc_final: 0.8004 (m-30) REVERT: A 149 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8804 (t80) REVERT: A 377 MET cc_start: 0.8715 (tmm) cc_final: 0.8306 (tmm) REVERT: A 411 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8271 (tp30) REVERT: A 430 LYS cc_start: 0.9387 (ttmt) cc_final: 0.8802 (tppt) REVERT: B 72 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8898 (p) REVERT: B 125 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 136 THR cc_start: 0.8491 (m) cc_final: 0.6994 (t) REVERT: B 279 GLN cc_start: 0.8052 (pt0) cc_final: 0.7748 (mt0) REVERT: B 288 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6469 (tm-30) REVERT: B 350 LYS cc_start: 0.8838 (tppt) cc_final: 0.8474 (tppt) REVERT: B 425 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: C 69 ASP cc_start: 0.7992 (t0) cc_final: 0.7617 (t70) REVERT: C 98 ASP cc_start: 0.8214 (p0) cc_final: 0.7920 (p0) REVERT: C 113 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8700 (pt0) REVERT: C 156 ARG cc_start: 0.8925 (mtp180) cc_final: 0.8604 (mmm-85) REVERT: C 203 MET cc_start: 0.8446 (mmm) cc_final: 0.8227 (mmm) REVERT: C 232 SER cc_start: 0.8878 (t) cc_final: 0.8607 (t) REVERT: C 257 THR cc_start: 0.9362 (m) cc_final: 0.9124 (p) REVERT: C 282 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: C 326 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8405 (ttpt) REVERT: C 370 LYS cc_start: 0.8005 (tttp) cc_final: 0.7373 (tptp) REVERT: C 430 LYS cc_start: 0.9521 (ttmt) cc_final: 0.9205 (pttm) REVERT: C 432 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7364 (t80) REVERT: D 33 SER cc_start: 0.8948 (m) cc_final: 0.8649 (p) REVERT: D 88 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7812 (p0) REVERT: D 125 GLU cc_start: 0.8488 (tp30) cc_final: 0.8235 (tp30) REVERT: D 257 MET cc_start: 0.7665 (mmm) cc_final: 0.7322 (mmt) REVERT: D 291 GLN cc_start: 0.8205 (pt0) cc_final: 0.7825 (pt0) REVERT: D 350 LYS cc_start: 0.8928 (tppt) cc_final: 0.8398 (tppt) REVERT: D 364 SER cc_start: 0.8533 (p) cc_final: 0.8177 (p) REVERT: D 370 ASN cc_start: 0.8375 (t0) cc_final: 0.8170 (t0) REVERT: E 69 ASP cc_start: 0.8002 (t0) cc_final: 0.7647 (t0) REVERT: E 83 TYR cc_start: 0.7737 (m-80) cc_final: 0.7474 (m-80) REVERT: E 88 HIS cc_start: 0.4368 (OUTLIER) cc_final: 0.3320 (t70) REVERT: E 98 ASP cc_start: 0.8274 (p0) cc_final: 0.7991 (p0) REVERT: E 358 GLN cc_start: 0.9024 (mm110) cc_final: 0.8723 (mm-40) REVERT: E 370 LYS cc_start: 0.8036 (tttp) cc_final: 0.7502 (tptp) REVERT: E 398 MET cc_start: 0.9171 (mmm) cc_final: 0.8538 (mmt) REVERT: E 407 TRP cc_start: 0.8664 (m100) cc_final: 0.8348 (m100) REVERT: E 430 LYS cc_start: 0.9473 (ttmt) cc_final: 0.9008 (tppt) REVERT: F 33 SER cc_start: 0.8786 (m) cc_final: 0.8549 (p) REVERT: G 12 CYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8671 (p) REVERT: G 27 GLU cc_start: 0.9093 (tt0) cc_final: 0.8643 (tm-30) REVERT: G 41 ASP cc_start: 0.7901 (p0) cc_final: 0.7613 (p0) REVERT: G 67 ASP cc_start: 0.7989 (t70) cc_final: 0.7551 (t70) REVERT: G 101 TRP cc_start: 0.8313 (t60) cc_final: 0.7856 (t60) REVERT: G 125 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9101 (mt-10) REVERT: G 136 THR cc_start: 0.8216 (m) cc_final: 0.7926 (p) REVERT: G 147 MET cc_start: 0.9127 (ttm) cc_final: 0.8807 (ttt) REVERT: G 174 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8707 (mmmm) REVERT: G 216 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8439 (mmtp) REVERT: G 267 MET cc_start: 0.8243 (ttm) cc_final: 0.7747 (tmm) REVERT: G 297 LYS cc_start: 0.8463 (mmtm) cc_final: 0.8153 (mmtm) REVERT: G 298 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8377 (t0) REVERT: G 300 MET cc_start: 0.8413 (tpp) cc_final: 0.8124 (mmt) REVERT: G 351 VAL cc_start: 0.9117 (t) cc_final: 0.8743 (m) REVERT: G 362 LYS cc_start: 0.9038 (ptpp) cc_final: 0.8673 (pttp) REVERT: G 363 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7991 (ptp) REVERT: G 367 PHE cc_start: 0.8560 (t80) cc_final: 0.8210 (t80) REVERT: G 397 TRP cc_start: 0.8826 (m100) cc_final: 0.8311 (m-10) REVERT: G 422 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6125 (t80) REVERT: H 6 HIS cc_start: 0.7688 (t70) cc_final: 0.7362 (t70) REVERT: H 22 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8742 (tp30) REVERT: H 41 ASP cc_start: 0.7589 (p0) cc_final: 0.7274 (p0) REVERT: H 73 MET cc_start: 0.9056 (mpp) cc_final: 0.8757 (mpp) REVERT: H 101 TRP cc_start: 0.8255 (t60) cc_final: 0.7689 (t60) REVERT: H 136 THR cc_start: 0.8669 (m) cc_final: 0.8225 (p) REVERT: H 174 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8501 (mmmt) REVERT: H 267 MET cc_start: 0.8604 (ptm) cc_final: 0.8176 (ppp) REVERT: H 322 SER cc_start: 0.7752 (m) cc_final: 0.7430 (p) REVERT: H 362 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8639 (mtmm) REVERT: H 397 TRP cc_start: 0.8652 (m100) cc_final: 0.8321 (m-10) REVERT: I 6 HIS cc_start: 0.8011 (t70) cc_final: 0.7462 (t70) REVERT: I 7 ILE cc_start: 0.9140 (mt) cc_final: 0.8921 (mp) REVERT: I 33 SER cc_start: 0.8979 (m) cc_final: 0.8628 (p) REVERT: I 41 ASP cc_start: 0.7939 (p0) cc_final: 0.7558 (p0) REVERT: I 67 ASP cc_start: 0.8057 (t0) cc_final: 0.7705 (t70) REVERT: I 92 PHE cc_start: 0.8762 (p90) cc_final: 0.8477 (p90) REVERT: I 101 TRP cc_start: 0.8492 (t60) cc_final: 0.7746 (t60) REVERT: I 125 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8927 (mt-10) REVERT: I 130 LEU cc_start: 0.8504 (tp) cc_final: 0.8172 (tp) REVERT: I 134 GLN cc_start: 0.8573 (pt0) cc_final: 0.8170 (pp30) REVERT: I 135 LEU cc_start: 0.8889 (tp) cc_final: 0.8598 (tp) REVERT: I 136 THR cc_start: 0.8582 (m) cc_final: 0.7950 (p) REVERT: I 174 LYS cc_start: 0.9297 (mtpt) cc_final: 0.8679 (mmmm) REVERT: I 184 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8353 (p0) REVERT: I 233 MET cc_start: 0.9339 (mmm) cc_final: 0.8944 (mmm) REVERT: I 246 LEU cc_start: 0.8400 (tp) cc_final: 0.8008 (tt) REVERT: I 257 MET cc_start: 0.8845 (mmt) cc_final: 0.8411 (mmt) REVERT: I 267 MET cc_start: 0.8042 (ptp) cc_final: 0.7595 (ptm) REVERT: I 343 GLU cc_start: 0.8835 (tp30) cc_final: 0.8594 (tp30) REVERT: I 351 VAL cc_start: 0.9330 (t) cc_final: 0.8869 (m) REVERT: J 33 ASP cc_start: 0.8542 (p0) cc_final: 0.8263 (p0) REVERT: J 138 PHE cc_start: 0.8803 (m-80) cc_final: 0.8479 (m-10) REVERT: J 230 LEU cc_start: 0.9212 (mp) cc_final: 0.8816 (tt) REVERT: J 377 MET cc_start: 0.8268 (ttp) cc_final: 0.7984 (ttp) REVERT: J 432 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7343 (t80) REVERT: K 84 ARG cc_start: 0.7777 (ttp-110) cc_final: 0.7055 (ttm-80) REVERT: K 127 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7992 (p0) REVERT: K 157 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9140 (mm) REVERT: K 172 TYR cc_start: 0.7061 (t80) cc_final: 0.6723 (t80) REVERT: K 392 ASP cc_start: 0.7255 (m-30) cc_final: 0.6787 (m-30) REVERT: K 432 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7469 (t80) REVERT: K 434 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8095 (pp20) REVERT: L 149 PHE cc_start: 0.9085 (t80) cc_final: 0.8837 (t80) REVERT: L 203 MET cc_start: 0.8620 (mmp) cc_final: 0.8301 (mmp) REVERT: L 269 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8784 (pp) outliers start: 212 outliers final: 183 residues processed: 1020 average time/residue: 0.5075 time to fit residues: 866.2051 Evaluate side-chains 1044 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 842 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 TYR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 354 CYS Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain G residue 425 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 425 TYR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 354 CYS Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 425 TYR Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 322 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 319 TYR Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 8.9990 chunk 430 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 373 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 405 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 416 optimal weight: 0.0270 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN F 226 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 293 ASN K 11 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.119127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.102287 restraints weight = 89612.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.105535 restraints weight = 46683.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.107741 restraints weight = 29204.310| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 41844 Z= 0.188 Angle : 0.666 14.285 56844 Z= 0.327 Chirality : 0.044 0.245 6222 Planarity : 0.004 0.063 7386 Dihedral : 12.216 170.124 5865 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.84 % Allowed : 26.34 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.03 (0.12), residues: 5130 helix: 0.76 (0.11), residues: 2424 sheet: 0.53 (0.19), residues: 756 loop : -1.06 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 407 HIS 0.016 0.001 HIS G 6 PHE 0.033 0.001 PHE H 367 TYR 0.042 0.001 TYR C 24 ARG 0.009 0.000 ARG J 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14207.08 seconds wall clock time: 255 minutes 24.36 seconds (15324.36 seconds total)