Starting phenix.real_space_refine on Wed Feb 21 06:14:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdo_21643/02_2024/6wdo_21643.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdo_21643/02_2024/6wdo_21643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdo_21643/02_2024/6wdo_21643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdo_21643/02_2024/6wdo_21643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdo_21643/02_2024/6wdo_21643.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdo_21643/02_2024/6wdo_21643.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 124 5.16 5 C 19265 2.51 5 N 5081 2.21 5 O 5395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ASP 147": "OD1" <-> "OD2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 322": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 313": "OD1" <-> "OD2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "I ASP 123": "OD1" <-> "OD2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 119": "OD1" <-> "OD2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "K PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 161": "NH1" <-> "NH2" Residue "K ASP 209": "OD1" <-> "OD2" Residue "K TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 288": "OE1" <-> "OE2" Residue "K TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 328": "OE1" <-> "OE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O ASP 147": "OD1" <-> "OD2" Residue "O ASP 209": "OD1" <-> "OD2" Residue "O TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 293": "OE1" <-> "OE2" Residue "O ARG 295": "NH1" <-> "NH2" Residue "O TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 313": "OD1" <-> "OD2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M GLU 212": "OE1" <-> "OE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 313": "OD1" <-> "OD2" Residue "M TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 107": "NH1" <-> "NH2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 129": "NH1" <-> "NH2" Residue "Q PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 154": "NH1" <-> "NH2" Residue "Q TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 235": "OD1" <-> "OD2" Residue "Q PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 316": "OD1" <-> "OD2" Residue "Q ASP 319": "OD1" <-> "OD2" Residue "Q TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 407": "OE1" <-> "OE2" Residue "Q PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 427": "OE1" <-> "OE2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R ASP 134": "OD1" <-> "OD2" Residue "R PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 190": "OE1" <-> "OE2" Residue "R ARG 195": "NH1" <-> "NH2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 265": "OE1" <-> "OE2" Residue "R PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 107": "NH1" <-> "NH2" Residue "S ASP 108": "OD1" <-> "OD2" Residue "S GLU 113": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S ARG 129": "NH1" <-> "NH2" Residue "S PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 154": "NH1" <-> "NH2" Residue "S TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 235": "OD1" <-> "OD2" Residue "S PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 316": "OD1" <-> "OD2" Residue "S ASP 319": "OD1" <-> "OD2" Residue "S TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 407": "OE1" <-> "OE2" Residue "S PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 427": "OE1" <-> "OE2" Residue "T ARG 107": "NH1" <-> "NH2" Residue "T PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 120": "NH1" <-> "NH2" Residue "T ASP 134": "OD1" <-> "OD2" Residue "T PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 190": "OE1" <-> "OE2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T GLU 196": "OE1" <-> "OE2" Residue "T PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 265": "OE1" <-> "OE2" Residue "T PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29867 Number of models: 1 Model: "" Number of chains: 22 Chain: "G" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2102 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 1 Chain: "H" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 389 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "I" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "J" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "K" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "L" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "O" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2102 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 1 Chain: "P" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "M" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "N" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "Q" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2136 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "R" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2395 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Chain: "S" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2136 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "T" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2395 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.22, per 1000 atoms: 0.51 Number of scatterers: 29867 At special positions: 0 Unit cell: (201.3, 108.9, 182.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 124 16.00 O 5395 8.00 N 5081 7.00 C 19265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.32 Conformation dependent library (CDL) restraints added in 5.1 seconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6958 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 23 sheets defined 66.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'G' and resid 107 through 117 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'G' and resid 175 through 248 removed outlier: 3.797A pdb=" N THR G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU G 193 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.673A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP G 237 " --> pdb=" O THR G 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR G 242 " --> pdb=" O GLY G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 286 removed outlier: 3.806A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 309 removed outlier: 3.855A pdb=" N GLN G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 306 " --> pdb=" O PHE G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 334 removed outlier: 3.653A pdb=" N ASP G 330 " --> pdb=" O GLN G 326 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU G 331 " --> pdb=" O ALA G 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 94 removed outlier: 4.174A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.568A pdb=" N THR H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.376A pdb=" N ARG C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 146 removed outlier: 3.543A pdb=" N LEU C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 190 Processing helix chain 'C' and resid 191 through 257 Proline residue: C 216 - end of helix removed outlier: 3.800A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Proline residue: C 265 - end of helix removed outlier: 4.016A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 311 removed outlier: 4.089A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.633A pdb=" N GLN C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 97 removed outlier: 3.554A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.754A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.553A pdb=" N ASP A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 249 removed outlier: 3.727A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.801A pdb=" N LYS A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.584A pdb=" N TRP A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 285 removed outlier: 4.185A pdb=" N PHE A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.067A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'B' and resid 65 through 94 removed outlier: 3.723A pdb=" N ILE B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.620A pdb=" N VAL B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 4.087A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 169 through 190 removed outlier: 3.564A pdb=" N THR E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 253 removed outlier: 3.588A pdb=" N LEU E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.661A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.583A pdb=" N PHE E 269 " --> pdb=" O PRO E 265 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 273 " --> pdb=" O PHE E 269 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 310 removed outlier: 3.875A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.534A pdb=" N ASP E 322 " --> pdb=" O ASN E 318 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 323 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 93 removed outlier: 3.965A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 4.078A pdb=" N VAL F 80 " --> pdb=" O PRO F 76 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.906A pdb=" N ARG I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 146 Processing helix chain 'I' and resid 171 through 249 removed outlier: 3.520A pdb=" N THR I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU I 193 " --> pdb=" O THR I 189 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU I 205 " --> pdb=" O ARG I 201 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU I 208 " --> pdb=" O ILE I 204 " (cutoff:3.500A) Proline residue: I 216 - end of helix removed outlier: 3.908A pdb=" N LYS I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE I 224 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS I 230 " --> pdb=" O ARG I 226 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP I 237 " --> pdb=" O THR I 233 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU I 240 " --> pdb=" O LEU I 236 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE I 247 " --> pdb=" O MET I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 262 Processing helix chain 'I' and resid 263 through 285 removed outlier: 4.083A pdb=" N PHE I 269 " --> pdb=" O PRO I 265 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 271 " --> pdb=" O THR I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 311 removed outlier: 4.149A pdb=" N ASP I 296 " --> pdb=" O PRO I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 340 removed outlier: 3.745A pdb=" N GLN I 319 " --> pdb=" O GLU I 315 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Proline residue: I 337 - end of helix Processing helix chain 'J' and resid 66 through 80 removed outlier: 4.666A pdb=" N SER J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) Proline residue: J 76 - end of helix Processing helix chain 'J' and resid 80 through 92 removed outlier: 4.167A pdb=" N LYS J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.685A pdb=" N GLU K 95 " --> pdb=" O SER K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.940A pdb=" N ARG K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 146 Processing helix chain 'K' and resid 171 through 190 Processing helix chain 'K' and resid 191 through 257 Proline residue: K 216 - end of helix removed outlier: 3.699A pdb=" N LYS K 219 " --> pdb=" O ALA K 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL K 220 " --> pdb=" O PRO K 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 235 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP K 237 " --> pdb=" O THR K 233 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE K 247 " --> pdb=" O MET K 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY K 248 " --> pdb=" O ALA K 244 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 257 " --> pdb=" O LEU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 Proline residue: K 265 - end of helix removed outlier: 4.131A pdb=" N PHE K 269 " --> pdb=" O PRO K 265 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR K 271 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 309 removed outlier: 3.514A pdb=" N LYS K 309 " --> pdb=" O LYS K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 335 removed outlier: 3.729A pdb=" N TYR K 317 " --> pdb=" O ASP K 313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN K 319 " --> pdb=" O GLU K 315 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU K 331 " --> pdb=" O ALA K 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 71 Processing helix chain 'L' and resid 75 through 94 removed outlier: 3.586A pdb=" N LYS L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 118 removed outlier: 4.293A pdb=" N GLU O 118 " --> pdb=" O GLN O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 146 Processing helix chain 'O' and resid 175 through 248 removed outlier: 3.670A pdb=" N THR O 181 " --> pdb=" O ASN O 177 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 182 " --> pdb=" O ASP O 178 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU O 193 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU O 197 " --> pdb=" O GLU O 193 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 3.537A pdb=" N ARG O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL O 235 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP O 237 " --> pdb=" O THR O 233 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR O 242 " --> pdb=" O GLY O 238 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET O 243 " --> pdb=" O GLY O 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 253 removed outlier: 4.056A pdb=" N ARG O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 248 through 253' Processing helix chain 'O' and resid 265 through 286 removed outlier: 3.512A pdb=" N ILE O 270 " --> pdb=" O VAL O 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR O 279 " --> pdb=" O ALA O 275 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 310 removed outlier: 3.790A pdb=" N GLN O 298 " --> pdb=" O ALA O 294 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU O 301 " --> pdb=" O ARG O 297 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER O 310 " --> pdb=" O GLY O 306 " (cutoff:3.500A) Processing helix chain 'O' and resid 314 through 334 removed outlier: 3.896A pdb=" N GLU O 328 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU O 331 " --> pdb=" O ALA O 327 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 96 removed outlier: 3.650A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.519A pdb=" N THR P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU P 94 " --> pdb=" O ALA P 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 119 removed outlier: 3.913A pdb=" N ARG M 113 " --> pdb=" O GLY M 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 146 removed outlier: 3.614A pdb=" N LEU M 146 " --> pdb=" O ASP M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 190 removed outlier: 3.648A pdb=" N VAL M 179 " --> pdb=" O THR M 175 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 256 removed outlier: 3.716A pdb=" N GLU M 212 " --> pdb=" O GLU M 208 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA M 215 " --> pdb=" O LYS M 211 " (cutoff:3.500A) Proline residue: M 216 - end of helix removed outlier: 3.554A pdb=" N VAL M 220 " --> pdb=" O PRO M 216 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU M 229 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 232 " --> pdb=" O ALA M 228 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU M 234 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU M 250 " --> pdb=" O GLN M 246 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 253 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP M 255 " --> pdb=" O ALA M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 268 Processing helix chain 'M' and resid 270 through 285 removed outlier: 4.172A pdb=" N MET M 276 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR M 279 " --> pdb=" O ALA M 275 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE M 282 " --> pdb=" O MET M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 310 removed outlier: 3.893A pdb=" N ASP M 296 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU M 301 " --> pdb=" O ARG M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 335 removed outlier: 3.645A pdb=" N TYR M 317 " --> pdb=" O ASP M 313 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET M 329 " --> pdb=" O ALA M 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 79 removed outlier: 4.599A pdb=" N ILE N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Proline residue: N 76 - end of helix Processing helix chain 'N' and resid 79 through 93 removed outlier: 4.231A pdb=" N SER N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE N 88 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 121 removed outlier: 3.566A pdb=" N ASN Q 116 " --> pdb=" O MET Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 130 removed outlier: 3.903A pdb=" N ILE Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 130 " --> pdb=" O LYS Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 156 Processing helix chain 'Q' and resid 193 through 198 Processing helix chain 'Q' and resid 206 through 218 Processing helix chain 'Q' and resid 219 through 231 removed outlier: 4.134A pdb=" N GLU Q 224 " --> pdb=" O GLN Q 220 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE Q 225 " --> pdb=" O ARG Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.507A pdb=" N GLN Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 292 through 294 No H-bonds generated for 'chain 'Q' and resid 292 through 294' Processing helix chain 'Q' and resid 295 through 315 Processing helix chain 'Q' and resid 317 through 319 No H-bonds generated for 'chain 'Q' and resid 317 through 319' Processing helix chain 'Q' and resid 323 through 336 removed outlier: 3.743A pdb=" N LEU Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 339 through 353 removed outlier: 5.132A pdb=" N LYS Q 350 " --> pdb=" O GLN Q 346 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS Q 351 " --> pdb=" O ARG Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 373 removed outlier: 4.318A pdb=" N PHE Q 367 " --> pdb=" O GLU Q 363 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 381 removed outlier: 3.566A pdb=" N VAL Q 377 " --> pdb=" O ASN Q 373 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR Q 379 " --> pdb=" O ASN Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 386 Processing helix chain 'Q' and resid 394 through 405 Processing helix chain 'Q' and resid 410 through 420 removed outlier: 3.987A pdb=" N VAL Q 416 " --> pdb=" O VAL Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 441 removed outlier: 3.875A pdb=" N LEU Q 441 " --> pdb=" O MET Q 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'R' and resid 105 through 115 Processing helix chain 'R' and resid 124 through 129 removed outlier: 3.540A pdb=" N LEU R 127 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR R 128 " --> pdb=" O LYS R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 140 removed outlier: 4.901A pdb=" N LEU R 136 " --> pdb=" O ILE R 132 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 171 removed outlier: 3.761A pdb=" N THR R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 184 removed outlier: 4.121A pdb=" N HIS R 178 " --> pdb=" O HIS R 174 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL R 179 " --> pdb=" O SER R 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 207 removed outlier: 5.310A pdb=" N LYS R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG R 195 " --> pdb=" O MET R 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE R 203 " --> pdb=" O LYS R 199 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 204 " --> pdb=" O LEU R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 248 through 273 removed outlier: 3.519A pdb=" N LEU R 259 " --> pdb=" O PHE R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 292 removed outlier: 3.960A pdb=" N GLU R 285 " --> pdb=" O GLU R 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP R 286 " --> pdb=" O ASP R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 307 removed outlier: 3.962A pdb=" N TRP R 300 " --> pdb=" O LYS R 296 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU R 305 " --> pdb=" O LYS R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 327 Processing helix chain 'R' and resid 327 through 335 Processing helix chain 'R' and resid 335 through 342 Processing helix chain 'R' and resid 346 through 359 Processing helix chain 'R' and resid 363 through 375 removed outlier: 4.195A pdb=" N THR R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 392 removed outlier: 3.907A pdb=" N VAL R 390 " --> pdb=" O GLU R 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 110 through 121 removed outlier: 3.566A pdb=" N ASN S 116 " --> pdb=" O MET S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 130 removed outlier: 3.903A pdb=" N ILE S 127 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR S 130 " --> pdb=" O LYS S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 156 Processing helix chain 'S' and resid 193 through 198 Processing helix chain 'S' and resid 206 through 218 Processing helix chain 'S' and resid 219 through 231 removed outlier: 4.134A pdb=" N GLU S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 249 removed outlier: 3.506A pdb=" N GLN S 245 " --> pdb=" O GLU S 241 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 283 Processing helix chain 'S' and resid 292 through 294 No H-bonds generated for 'chain 'S' and resid 292 through 294' Processing helix chain 'S' and resid 295 through 315 Processing helix chain 'S' and resid 317 through 319 No H-bonds generated for 'chain 'S' and resid 317 through 319' Processing helix chain 'S' and resid 323 through 336 removed outlier: 3.744A pdb=" N LEU S 331 " --> pdb=" O PHE S 327 " (cutoff:3.500A) Processing helix chain 'S' and resid 339 through 353 removed outlier: 5.131A pdb=" N LYS S 350 " --> pdb=" O GLN S 346 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS S 351 " --> pdb=" O ARG S 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 361 through 373 removed outlier: 4.319A pdb=" N PHE S 367 " --> pdb=" O GLU S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 381 removed outlier: 3.565A pdb=" N VAL S 377 " --> pdb=" O ASN S 373 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR S 379 " --> pdb=" O ASN S 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 386 Processing helix chain 'S' and resid 394 through 405 Processing helix chain 'S' and resid 410 through 420 removed outlier: 3.987A pdb=" N VAL S 416 " --> pdb=" O VAL S 412 " (cutoff:3.500A) Processing helix chain 'S' and resid 433 through 441 removed outlier: 3.875A pdb=" N LEU S 441 " --> pdb=" O MET S 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 94 Processing helix chain 'T' and resid 105 through 115 Processing helix chain 'T' and resid 124 through 129 removed outlier: 3.540A pdb=" N LEU T 127 " --> pdb=" O VAL T 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR T 128 " --> pdb=" O LYS T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 140 removed outlier: 4.902A pdb=" N LEU T 136 " --> pdb=" O ILE T 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN T 140 " --> pdb=" O LEU T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 removed outlier: 3.761A pdb=" N THR T 171 " --> pdb=" O LEU T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 173 through 184 removed outlier: 4.120A pdb=" N HIS T 178 " --> pdb=" O HIS T 174 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL T 179 " --> pdb=" O SER T 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU T 184 " --> pdb=" O ALA T 180 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 207 removed outlier: 5.309A pdb=" N LYS T 194 " --> pdb=" O GLU T 190 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG T 195 " --> pdb=" O MET T 191 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU T 196 " --> pdb=" O ILE T 192 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE T 197 " --> pdb=" O GLU T 193 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE T 203 " --> pdb=" O LYS T 199 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE T 204 " --> pdb=" O LEU T 200 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 240 Processing helix chain 'T' and resid 248 through 273 removed outlier: 3.519A pdb=" N LEU T 259 " --> pdb=" O PHE T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 292 removed outlier: 3.960A pdb=" N GLU T 285 " --> pdb=" O GLU T 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP T 286 " --> pdb=" O ASP T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 307 removed outlier: 3.962A pdb=" N TRP T 300 " --> pdb=" O LYS T 296 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU T 305 " --> pdb=" O LYS T 301 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 327 Processing helix chain 'T' and resid 327 through 335 Processing helix chain 'T' and resid 335 through 342 Processing helix chain 'T' and resid 346 through 359 Processing helix chain 'T' and resid 363 through 375 removed outlier: 4.194A pdb=" N THR T 369 " --> pdb=" O ASN T 365 " (cutoff:3.500A) Processing helix chain 'T' and resid 383 through 392 removed outlier: 3.909A pdb=" N VAL T 390 " --> pdb=" O GLU T 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AA2, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.698A pdb=" N ALA G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE G 149 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 151 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 134 through 135 removed outlier: 6.941A pdb=" N ARG G 134 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR E 100 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 76 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 80 Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.721A pdb=" N PHE C 149 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.681A pdb=" N VAL A 78 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 128 removed outlier: 3.676A pdb=" N PHE A 149 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 126 through 128 removed outlier: 3.594A pdb=" N VAL E 152 " --> pdb=" O ALA E 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 76 through 80 removed outlier: 3.714A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'K' and resid 77 through 80 Processing sheet with id=AB4, first strand: chain 'K' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'O' and resid 88 through 89 Processing sheet with id=AB6, first strand: chain 'O' and resid 126 through 128 removed outlier: 3.760A pdb=" N ALA O 126 " --> pdb=" O VAL O 152 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE O 149 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL O 160 " --> pdb=" O PHE O 149 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU O 151 " --> pdb=" O TYR O 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 76 through 80 Processing sheet with id=AB8, first strand: chain 'M' and resid 149 through 152 Processing sheet with id=AB9, first strand: chain 'Q' and resid 321 through 322 Processing sheet with id=AC1, first strand: chain 'R' and resid 103 through 104 Processing sheet with id=AC2, first strand: chain 'R' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'S' and resid 321 through 322 Processing sheet with id=AC4, first strand: chain 'T' and resid 103 through 104 Processing sheet with id=AC5, first strand: chain 'T' and resid 278 through 279 1644 hydrogen bonds defined for protein. 4785 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: 8.19 Time building geometry restraints manager: 13.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6441 1.33 - 1.45: 6693 1.45 - 1.57: 17118 1.57 - 1.69: 0 1.69 - 1.82: 220 Bond restraints: 30472 Sorted by residual: bond pdb=" N ILE C 153 " pdb=" CA ILE C 153 " ideal model delta sigma weight residual 1.459 1.532 -0.073 1.25e-02 6.40e+03 3.39e+01 bond pdb=" N ILE P 97 " pdb=" CA ILE P 97 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL M 152 " pdb=" CA VAL M 152 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.97e+00 bond pdb=" N LEU E 156 " pdb=" CA LEU E 156 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" N ASN C 154 " pdb=" CA ASN C 154 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.23e-02 6.61e+03 8.54e+00 ... (remaining 30467 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.21: 621 106.21 - 113.73: 17215 113.73 - 121.26: 16726 121.26 - 128.79: 6358 128.79 - 136.31: 194 Bond angle restraints: 41114 Sorted by residual: angle pdb=" C ASP P 96 " pdb=" N ILE P 97 " pdb=" CA ILE P 97 " ideal model delta sigma weight residual 120.49 131.85 -11.36 1.38e+00 5.25e-01 6.78e+01 angle pdb=" N ASP P 96 " pdb=" CA ASP P 96 " pdb=" C ASP P 96 " ideal model delta sigma weight residual 108.19 118.04 -9.85 1.29e+00 6.01e-01 5.83e+01 angle pdb=" N GLU P 93 " pdb=" CA GLU P 93 " pdb=" C GLU P 93 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.23e+00 6.61e-01 5.55e+01 angle pdb=" N ILE B 73 " pdb=" CA ILE B 73 " pdb=" C ILE B 73 " ideal model delta sigma weight residual 113.53 106.56 6.97 9.80e-01 1.04e+00 5.05e+01 angle pdb=" C LYS O 180 " pdb=" N THR O 181 " pdb=" CA THR O 181 " ideal model delta sigma weight residual 120.38 111.44 8.94 1.37e+00 5.33e-01 4.26e+01 ... (remaining 41109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 16229 17.79 - 35.59: 1729 35.59 - 53.38: 368 53.38 - 71.18: 68 71.18 - 88.97: 33 Dihedral angle restraints: 18427 sinusoidal: 7706 harmonic: 10721 Sorted by residual: dihedral pdb=" CA GLU A 257 " pdb=" C GLU A 257 " pdb=" N TYR A 258 " pdb=" CA TYR A 258 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" C ASP P 96 " pdb=" N ASP P 96 " pdb=" CA ASP P 96 " pdb=" CB ASP P 96 " ideal model delta harmonic sigma weight residual -122.60 -135.83 13.23 0 2.50e+00 1.60e-01 2.80e+01 dihedral pdb=" N ASP P 96 " pdb=" C ASP P 96 " pdb=" CA ASP P 96 " pdb=" CB ASP P 96 " ideal model delta harmonic sigma weight residual 122.80 135.89 -13.09 0 2.50e+00 1.60e-01 2.74e+01 ... (remaining 18424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4510 0.109 - 0.217: 90 0.217 - 0.326: 4 0.326 - 0.434: 1 0.434 - 0.543: 2 Chirality restraints: 4607 Sorted by residual: chirality pdb=" CA ASP P 96 " pdb=" N ASP P 96 " pdb=" C ASP P 96 " pdb=" CB ASP P 96 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA ILE C 153 " pdb=" N ILE C 153 " pdb=" C ILE C 153 " pdb=" CB ILE C 153 " both_signs ideal model delta sigma weight residual False 2.43 2.90 -0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA ILE E 153 " pdb=" N ILE E 153 " pdb=" C ILE E 153 " pdb=" CB ILE E 153 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 4604 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR O 175 " 0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C THR O 175 " -0.061 2.00e-02 2.50e+03 pdb=" O THR O 175 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU O 176 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 94 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C GLU P 94 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU P 94 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS P 95 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS O 180 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS O 180 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS O 180 " -0.021 2.00e-02 2.50e+03 pdb=" N THR O 181 " -0.020 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2081 2.72 - 3.27: 36189 3.27 - 3.81: 50684 3.81 - 4.36: 61366 4.36 - 4.90: 94647 Nonbonded interactions: 244967 Sorted by model distance: nonbonded pdb=" O GLN I 184 " pdb=" OG1 THR I 188 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR A 76 " pdb=" OG SER A 87 " model vdw 2.185 2.440 nonbonded pdb=" O GLN O 185 " pdb=" OG1 THR O 189 " model vdw 2.185 2.440 nonbonded pdb=" O LEU R 184 " pdb=" OG1 THR R 186 " model vdw 2.186 2.440 nonbonded pdb=" O LEU T 184 " pdb=" OG1 THR T 186 " model vdw 2.186 2.440 ... (remaining 244962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 172 through 336)) selection = chain 'G' selection = (chain 'I' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'K' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'M' and (resid 75 through 164 or resid 172 through 336)) selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 48 through 97) selection = (chain 'D' and resid 48 through 97) selection = chain 'F' selection = (chain 'H' and resid 48 through 97) selection = (chain 'J' and resid 48 through 97) selection = (chain 'L' and resid 48 through 97) selection = (chain 'N' and resid 48 through 97) selection = (chain 'P' and resid 48 through 97) } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'T' } 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.560 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 73.620 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.160 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.005 0.073 30472 Z= 0.323 Angle : 0.729 12.504 41114 Z= 0.423 Chirality : 0.046 0.543 4607 Planarity : 0.004 0.066 5208 Dihedral : 15.464 88.973 11469 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.77 % Allowed : 8.13 % Favored : 91.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.11), residues: 3585 helix: -3.55 (0.07), residues: 2179 sheet: -3.43 (0.29), residues: 224 loop : -2.60 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 256 HIS 0.005 0.001 HIS A 170 PHE 0.017 0.001 PHE Q 223 TYR 0.014 0.002 TYR O 79 ARG 0.031 0.001 ARG Q 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 532 time to evaluate : 3.290 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: G 84 PRO cc_start: 0.8620 (Cg_exo) cc_final: 0.8296 (Cg_endo) REVERT: G 236 LEU cc_start: 0.9022 (tp) cc_final: 0.8727 (tp) REVERT: H 59 LYS cc_start: 0.9315 (tmmt) cc_final: 0.9072 (tttt) REVERT: H 96 ASP cc_start: 0.8188 (p0) cc_final: 0.7979 (p0) REVERT: A 205 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 212 GLU cc_start: 0.8856 (tp30) cc_final: 0.8581 (tp30) REVERT: A 267 THR cc_start: 0.8732 (m) cc_final: 0.8517 (p) REVERT: B 73 ILE cc_start: 0.8368 (mm) cc_final: 0.8053 (mm) REVERT: B 79 TYR cc_start: 0.7363 (t80) cc_final: 0.6961 (t80) REVERT: E 154 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7755 (m110) REVERT: E 289 TYR cc_start: 0.8590 (t80) cc_final: 0.7861 (t80) REVERT: E 329 MET cc_start: 0.7957 (tpt) cc_final: 0.7703 (tmm) REVERT: F 79 TYR cc_start: 0.7656 (t80) cc_final: 0.6775 (m-10) REVERT: I 236 LEU cc_start: 0.8938 (mt) cc_final: 0.8639 (tp) REVERT: I 267 THR cc_start: 0.8760 (m) cc_final: 0.8556 (p) REVERT: J 57 LEU cc_start: 0.8943 (mp) cc_final: 0.8704 (mp) REVERT: J 94 GLU cc_start: 0.8893 (pp20) cc_final: 0.8457 (pp20) REVERT: J 98 PHE cc_start: 0.8577 (t80) cc_final: 0.7756 (t80) REVERT: K 172 ASN cc_start: 0.8477 (m110) cc_final: 0.8048 (m-40) REVERT: O 84 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: M 113 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8216 (tmm-80) REVERT: M 276 MET cc_start: 0.8160 (ttt) cc_final: 0.7653 (ttt) REVERT: N 79 TYR cc_start: 0.7682 (t80) cc_final: 0.6972 (m-10) REVERT: Q 345 MET cc_start: 0.8782 (mmm) cc_final: 0.8262 (mmm) REVERT: Q 386 MET cc_start: 0.8846 (mmt) cc_final: 0.8519 (mmt) REVERT: Q 396 MET cc_start: 0.9419 (tmm) cc_final: 0.9188 (tmm) REVERT: R 91 MET cc_start: 0.8109 (mmm) cc_final: 0.7796 (mmt) REVERT: R 254 ARG cc_start: 0.9073 (mtt90) cc_final: 0.8732 (mpp80) REVERT: S 209 TYR cc_start: 0.9128 (t80) cc_final: 0.8865 (t80) REVERT: S 345 MET cc_start: 0.8970 (mmm) cc_final: 0.8561 (mmm) REVERT: S 366 ASN cc_start: 0.9046 (p0) cc_final: 0.8839 (p0) REVERT: S 396 MET cc_start: 0.9357 (tmm) cc_final: 0.8629 (tmm) REVERT: T 91 MET cc_start: 0.8293 (mmm) cc_final: 0.8039 (tpp) REVERT: T 278 MET cc_start: 0.8199 (ttm) cc_final: 0.7697 (ttp) outliers start: 25 outliers final: 15 residues processed: 555 average time/residue: 0.4460 time to fit residues: 377.0938 Evaluate side-chains 402 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 386 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 179 VAL Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain Q residue 213 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 239 PHE Chi-restraints excluded: chain T residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN C 159 HIS C 194 GLN C 341 HIS A 80 GLN A 81 ASN A 116 GLN A 177 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 185 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 339 GLN I 80 GLN I 81 ASN I 116 GLN I 159 HIS ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN K 116 GLN K 172 ASN K 194 GLN K 341 HIS ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 GLN ** O 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN Q 326 GLN Q 373 ASN R 88 GLN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN R 393 ASN S 247 GLN S 326 GLN S 373 ASN ** S 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 ASN T 393 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 30472 Z= 0.260 Angle : 0.715 12.035 41114 Z= 0.369 Chirality : 0.044 0.246 4607 Planarity : 0.005 0.060 5208 Dihedral : 5.889 53.175 4046 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.79 % Allowed : 16.85 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3585 helix: -1.21 (0.10), residues: 2271 sheet: -2.62 (0.33), residues: 190 loop : -2.08 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 256 HIS 0.009 0.001 HIS R 178 PHE 0.022 0.002 PHE S 223 TYR 0.025 0.002 TYR P 79 ARG 0.009 0.001 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 455 time to evaluate : 3.537 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: G 84 PRO cc_start: 0.8591 (Cg_exo) cc_final: 0.8287 (Cg_endo) REVERT: G 249 ILE cc_start: 0.8852 (tt) cc_final: 0.8439 (tt) REVERT: G 276 MET cc_start: 0.8362 (ttp) cc_final: 0.7700 (ttp) REVERT: H 85 SER cc_start: 0.8503 (t) cc_final: 0.8149 (p) REVERT: H 96 ASP cc_start: 0.8206 (p0) cc_final: 0.7984 (p0) REVERT: A 187 TYR cc_start: 0.8710 (t80) cc_final: 0.8348 (t80) REVERT: A 267 THR cc_start: 0.9008 (m) cc_final: 0.8756 (p) REVERT: B 57 LEU cc_start: 0.9063 (mm) cc_final: 0.8814 (mp) REVERT: B 79 TYR cc_start: 0.6850 (t80) cc_final: 0.6379 (m-10) REVERT: E 243 MET cc_start: 0.8493 (ttt) cc_final: 0.8215 (ttt) REVERT: E 260 TRP cc_start: 0.8346 (t-100) cc_final: 0.8034 (t-100) REVERT: E 289 TYR cc_start: 0.8575 (t80) cc_final: 0.7869 (t80) REVERT: E 329 MET cc_start: 0.7779 (tpt) cc_final: 0.7436 (tmm) REVERT: F 79 TYR cc_start: 0.7433 (t80) cc_final: 0.6768 (m-10) REVERT: I 200 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8796 (tm-30) REVERT: I 212 GLU cc_start: 0.8674 (tp30) cc_final: 0.8348 (tp30) REVERT: I 236 LEU cc_start: 0.8859 (mt) cc_final: 0.8585 (tt) REVERT: I 246 GLN cc_start: 0.8610 (tp40) cc_final: 0.8342 (tp40) REVERT: I 265 PRO cc_start: 0.8789 (Cg_exo) cc_final: 0.8545 (Cg_endo) REVERT: I 267 THR cc_start: 0.8977 (m) cc_final: 0.8727 (p) REVERT: J 94 GLU cc_start: 0.8813 (pp20) cc_final: 0.8436 (pp20) REVERT: K 172 ASN cc_start: 0.8408 (m-40) cc_final: 0.8179 (m-40) REVERT: K 209 ASP cc_start: 0.8899 (t0) cc_final: 0.8502 (t0) REVERT: K 243 MET cc_start: 0.8031 (ttm) cc_final: 0.7683 (ttm) REVERT: O 84 PRO cc_start: 0.8588 (Cg_exo) cc_final: 0.8264 (Cg_endo) REVERT: O 276 MET cc_start: 0.8286 (ttp) cc_final: 0.7716 (ttp) REVERT: M 154 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8487 (m-40) REVERT: M 276 MET cc_start: 0.8558 (ttt) cc_final: 0.8174 (ttt) REVERT: M 329 MET cc_start: 0.8148 (tmm) cc_final: 0.7897 (tmm) REVERT: N 79 TYR cc_start: 0.7410 (t80) cc_final: 0.6685 (m-10) REVERT: Q 240 MET cc_start: 0.9431 (ppp) cc_final: 0.9121 (tmm) REVERT: Q 345 MET cc_start: 0.8735 (mmm) cc_final: 0.8327 (mmm) REVERT: Q 381 LEU cc_start: 0.9398 (tp) cc_final: 0.9184 (tp) REVERT: Q 396 MET cc_start: 0.9408 (tmm) cc_final: 0.9200 (tmm) REVERT: R 91 MET cc_start: 0.8052 (mmm) cc_final: 0.7543 (tpp) REVERT: R 102 TYR cc_start: 0.8932 (m-80) cc_final: 0.8668 (m-80) REVERT: R 183 MET cc_start: 0.9243 (tmm) cc_final: 0.8874 (tmm) REVERT: R 256 MET cc_start: 0.8831 (mmm) cc_final: 0.8584 (mtm) REVERT: S 209 TYR cc_start: 0.8923 (t80) cc_final: 0.8584 (t80) REVERT: S 345 MET cc_start: 0.8896 (mmm) cc_final: 0.8539 (mmm) REVERT: S 366 ASN cc_start: 0.9030 (p0) cc_final: 0.8824 (p0) REVERT: S 381 LEU cc_start: 0.9459 (tp) cc_final: 0.9203 (tp) REVERT: S 396 MET cc_start: 0.9350 (tmm) cc_final: 0.9026 (tmm) REVERT: T 91 MET cc_start: 0.8208 (mmm) cc_final: 0.7921 (tpp) REVERT: T 109 PHE cc_start: 0.8587 (t80) cc_final: 0.8340 (t80) REVERT: T 183 MET cc_start: 0.9188 (tmm) cc_final: 0.8803 (tmm) REVERT: T 256 MET cc_start: 0.8901 (mmm) cc_final: 0.8556 (mtm) REVERT: T 278 MET cc_start: 0.8004 (ttm) cc_final: 0.7597 (ttp) outliers start: 91 outliers final: 57 residues processed: 517 average time/residue: 0.3999 time to fit residues: 327.9350 Evaluate side-chains 448 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 390 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 324 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 270 optimal weight: 0.0970 chunk 221 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 351 optimal weight: 0.0870 chunk 290 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 261 optimal weight: 0.0070 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN E 114 GLN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 287 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** M 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN Q 385 HIS ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN S 222 ASN S 385 HIS ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30472 Z= 0.176 Angle : 0.647 12.708 41114 Z= 0.326 Chirality : 0.042 0.177 4607 Planarity : 0.004 0.057 5208 Dihedral : 5.140 43.630 4026 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.82 % Allowed : 19.98 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3585 helix: -0.27 (0.11), residues: 2268 sheet: -2.14 (0.35), residues: 190 loop : -1.70 (0.20), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 260 HIS 0.006 0.001 HIS T 384 PHE 0.027 0.001 PHE P 88 TYR 0.027 0.001 TYR H 79 ARG 0.009 0.000 ARG K 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 463 time to evaluate : 3.743 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: G 84 PRO cc_start: 0.8635 (Cg_exo) cc_final: 0.8317 (Cg_endo) REVERT: G 249 ILE cc_start: 0.8649 (tt) cc_final: 0.8254 (tt) REVERT: G 276 MET cc_start: 0.8099 (ttp) cc_final: 0.7708 (ttp) REVERT: G 283 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9076 (p) REVERT: G 296 ASP cc_start: 0.8393 (m-30) cc_final: 0.8005 (p0) REVERT: H 85 SER cc_start: 0.8370 (t) cc_final: 0.8079 (p) REVERT: H 93 GLU cc_start: 0.8756 (pp20) cc_final: 0.8555 (pp20) REVERT: H 96 ASP cc_start: 0.8265 (p0) cc_final: 0.8063 (p0) REVERT: C 209 ASP cc_start: 0.9116 (t0) cc_final: 0.8827 (t0) REVERT: A 187 TYR cc_start: 0.8626 (t80) cc_final: 0.8205 (t80) REVERT: B 57 LEU cc_start: 0.9043 (mm) cc_final: 0.8824 (mp) REVERT: B 93 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8255 (tp30) REVERT: E 289 TYR cc_start: 0.8478 (t80) cc_final: 0.7668 (t80) REVERT: E 329 MET cc_start: 0.7735 (tpt) cc_final: 0.7361 (tmm) REVERT: F 79 TYR cc_start: 0.7154 (t80) cc_final: 0.6666 (m-10) REVERT: I 161 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7792 (mmt-90) REVERT: I 187 TYR cc_start: 0.8709 (t80) cc_final: 0.8357 (t80) REVERT: I 200 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8835 (tm-30) REVERT: I 212 GLU cc_start: 0.8550 (tp30) cc_final: 0.8188 (tp30) REVERT: I 236 LEU cc_start: 0.8632 (mt) cc_final: 0.8368 (tt) REVERT: I 253 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8621 (tt) REVERT: I 267 THR cc_start: 0.8896 (m) cc_final: 0.8634 (p) REVERT: J 94 GLU cc_start: 0.8710 (pp20) cc_final: 0.8360 (pp20) REVERT: K 209 ASP cc_start: 0.8927 (t0) cc_final: 0.8535 (t0) REVERT: K 243 MET cc_start: 0.7951 (ttm) cc_final: 0.7538 (ttm) REVERT: O 84 PRO cc_start: 0.8502 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: O 263 MET cc_start: 0.8172 (tpp) cc_final: 0.7930 (tpp) REVERT: O 276 MET cc_start: 0.8220 (ttp) cc_final: 0.7764 (ttp) REVERT: O 296 ASP cc_start: 0.8363 (m-30) cc_final: 0.8128 (p0) REVERT: P 88 PHE cc_start: 0.8848 (t80) cc_final: 0.8584 (t80) REVERT: P 98 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6972 (t80) REVERT: M 260 TRP cc_start: 0.8087 (t-100) cc_final: 0.7755 (t-100) REVERT: M 276 MET cc_start: 0.8404 (ttt) cc_final: 0.7922 (ttt) REVERT: M 329 MET cc_start: 0.8227 (tmm) cc_final: 0.7893 (tmm) REVERT: N 79 TYR cc_start: 0.7323 (t80) cc_final: 0.6699 (m-10) REVERT: Q 240 MET cc_start: 0.9428 (ppp) cc_final: 0.9094 (tmm) REVERT: Q 345 MET cc_start: 0.8614 (mmm) cc_final: 0.8248 (mmm) REVERT: Q 381 LEU cc_start: 0.9353 (tp) cc_final: 0.9059 (tp) REVERT: Q 396 MET cc_start: 0.9419 (tmm) cc_final: 0.8992 (tmm) REVERT: Q 406 VAL cc_start: 0.8431 (p) cc_final: 0.8086 (m) REVERT: R 114 MET cc_start: 0.8858 (ttm) cc_final: 0.8486 (mtp) REVERT: R 183 MET cc_start: 0.9150 (tmm) cc_final: 0.8764 (tmm) REVERT: R 256 MET cc_start: 0.8817 (mmm) cc_final: 0.8587 (mtm) REVERT: R 286 TRP cc_start: 0.8735 (t-100) cc_final: 0.8408 (t-100) REVERT: S 209 TYR cc_start: 0.8772 (t80) cc_final: 0.8562 (t80) REVERT: S 345 MET cc_start: 0.8919 (mmm) cc_final: 0.8618 (mmm) REVERT: S 366 ASN cc_start: 0.8977 (p0) cc_final: 0.8712 (p0) REVERT: S 381 LEU cc_start: 0.9441 (tp) cc_final: 0.9183 (tp) REVERT: S 396 MET cc_start: 0.9359 (tmm) cc_final: 0.8772 (tmm) REVERT: S 406 VAL cc_start: 0.8298 (p) cc_final: 0.8001 (m) REVERT: T 91 MET cc_start: 0.8205 (mmm) cc_final: 0.7915 (tpp) REVERT: T 102 TYR cc_start: 0.8784 (m-80) cc_final: 0.8298 (m-80) REVERT: T 114 MET cc_start: 0.8759 (ttm) cc_final: 0.8283 (mtp) REVERT: T 182 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7680 (mmtm) REVERT: T 183 MET cc_start: 0.9067 (tmm) cc_final: 0.8760 (tmm) REVERT: T 278 MET cc_start: 0.7937 (ttm) cc_final: 0.7544 (ttp) REVERT: T 335 MET cc_start: 0.8688 (mmm) cc_final: 0.8125 (mmp) outliers start: 92 outliers final: 48 residues processed: 527 average time/residue: 0.3835 time to fit residues: 325.6053 Evaluate side-chains 446 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 394 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 324 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 266 MET Chi-restraints excluded: chain T residue 363 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN A 177 ASN K 81 ASN O 246 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 GLN Q 222 ASN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 ASN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 30472 Z= 0.382 Angle : 0.731 12.047 41114 Z= 0.366 Chirality : 0.045 0.162 4607 Planarity : 0.004 0.059 5208 Dihedral : 5.254 42.012 4023 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.79 % Allowed : 21.26 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3585 helix: -0.24 (0.11), residues: 2281 sheet: -2.05 (0.36), residues: 190 loop : -1.64 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 260 HIS 0.011 0.001 HIS H 95 PHE 0.028 0.002 PHE T 283 TYR 0.031 0.002 TYR R 103 ARG 0.008 0.001 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 383 time to evaluate : 3.531 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: G 84 PRO cc_start: 0.8826 (Cg_exo) cc_final: 0.8604 (Cg_endo) REVERT: G 276 MET cc_start: 0.8292 (ttp) cc_final: 0.7730 (ttp) REVERT: G 283 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9124 (p) REVERT: G 296 ASP cc_start: 0.8471 (m-30) cc_final: 0.8187 (p0) REVERT: H 85 SER cc_start: 0.8465 (t) cc_final: 0.8096 (p) REVERT: H 93 GLU cc_start: 0.8763 (pp20) cc_final: 0.8529 (pp20) REVERT: C 161 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7790 (ptt-90) REVERT: C 209 ASP cc_start: 0.9123 (t0) cc_final: 0.8827 (t0) REVERT: D 80 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 187 TYR cc_start: 0.8750 (t80) cc_final: 0.8360 (t80) REVERT: A 263 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7819 (tpp) REVERT: B 79 TYR cc_start: 0.6876 (t80) cc_final: 0.6384 (m-10) REVERT: B 98 PHE cc_start: 0.8338 (t80) cc_final: 0.7967 (t80) REVERT: E 289 TYR cc_start: 0.8498 (t80) cc_final: 0.7625 (t80) REVERT: E 329 MET cc_start: 0.7774 (tpt) cc_final: 0.7501 (tmm) REVERT: F 79 TYR cc_start: 0.7404 (t80) cc_final: 0.6675 (m-10) REVERT: I 187 TYR cc_start: 0.8862 (t80) cc_final: 0.8541 (t80) REVERT: I 212 GLU cc_start: 0.8563 (tp30) cc_final: 0.8255 (tp30) REVERT: I 236 LEU cc_start: 0.8853 (mt) cc_final: 0.8533 (tt) REVERT: I 267 THR cc_start: 0.8962 (m) cc_final: 0.8725 (p) REVERT: J 94 GLU cc_start: 0.8733 (pp20) cc_final: 0.8324 (pp20) REVERT: K 209 ASP cc_start: 0.8970 (t0) cc_final: 0.8586 (t0) REVERT: K 243 MET cc_start: 0.8008 (ttm) cc_final: 0.7637 (ttm) REVERT: O 84 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8346 (Cg_endo) REVERT: O 276 MET cc_start: 0.8335 (ttp) cc_final: 0.7831 (ttp) REVERT: P 98 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6611 (t80) REVERT: M 260 TRP cc_start: 0.8275 (t-100) cc_final: 0.7694 (t-100) REVERT: M 276 MET cc_start: 0.8534 (ttt) cc_final: 0.8022 (ttt) REVERT: M 329 MET cc_start: 0.8209 (tmm) cc_final: 0.7509 (tmm) REVERT: N 79 TYR cc_start: 0.7581 (t80) cc_final: 0.6926 (m-10) REVERT: Q 216 LEU cc_start: 0.9005 (tp) cc_final: 0.8787 (mt) REVERT: Q 240 MET cc_start: 0.9433 (ppp) cc_final: 0.9083 (tmm) REVERT: Q 345 MET cc_start: 0.8693 (mmm) cc_final: 0.8299 (mmm) REVERT: Q 381 LEU cc_start: 0.9387 (tp) cc_final: 0.9149 (tp) REVERT: Q 396 MET cc_start: 0.9450 (tmm) cc_final: 0.8892 (tmm) REVERT: R 114 MET cc_start: 0.8962 (ttm) cc_final: 0.8536 (mtp) REVERT: R 183 MET cc_start: 0.9182 (tmm) cc_final: 0.8860 (tmm) REVERT: R 271 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: R 335 MET cc_start: 0.8674 (mmm) cc_final: 0.8316 (mmp) REVERT: S 209 TYR cc_start: 0.8795 (t80) cc_final: 0.8472 (t80) REVERT: S 345 MET cc_start: 0.8852 (mmm) cc_final: 0.8646 (mmm) REVERT: S 366 ASN cc_start: 0.8968 (p0) cc_final: 0.8692 (p0) REVERT: S 381 LEU cc_start: 0.9476 (tp) cc_final: 0.9256 (tp) REVERT: S 396 MET cc_start: 0.9398 (tmm) cc_final: 0.8800 (tmm) REVERT: S 406 VAL cc_start: 0.8293 (p) cc_final: 0.7978 (m) REVERT: T 91 MET cc_start: 0.8176 (mmm) cc_final: 0.7821 (tpp) REVERT: T 182 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (mmtm) REVERT: T 183 MET cc_start: 0.9140 (tmm) cc_final: 0.8828 (tmm) REVERT: T 335 MET cc_start: 0.8732 (mmm) cc_final: 0.8402 (mmm) outliers start: 156 outliers final: 110 residues processed: 501 average time/residue: 0.3891 time to fit residues: 314.9721 Evaluate side-chains 476 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 359 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 276 MET Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 71 PHE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 323 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 324 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 408 LEU Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 266 MET Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 5 optimal weight: 0.4980 chunk 257 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 295 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 172 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 30472 Z= 0.223 Angle : 0.659 11.274 41114 Z= 0.327 Chirality : 0.042 0.165 4607 Planarity : 0.004 0.057 5208 Dihedral : 5.078 38.010 4023 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.27 % Allowed : 23.14 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3585 helix: 0.05 (0.11), residues: 2276 sheet: -1.83 (0.36), residues: 190 loop : -1.54 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 256 HIS 0.007 0.001 HIS T 384 PHE 0.027 0.001 PHE T 252 TYR 0.032 0.002 TYR Q 334 ARG 0.009 0.000 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 412 time to evaluate : 3.475 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: G 84 PRO cc_start: 0.8750 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: G 172 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7970 (p0) REVERT: G 276 MET cc_start: 0.8172 (ttp) cc_final: 0.7693 (ttp) REVERT: G 296 ASP cc_start: 0.8421 (m-30) cc_final: 0.8156 (p0) REVERT: H 85 SER cc_start: 0.8384 (t) cc_final: 0.8015 (p) REVERT: C 161 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7800 (ptt-90) REVERT: C 209 ASP cc_start: 0.9129 (t0) cc_final: 0.8825 (t0) REVERT: C 263 MET cc_start: 0.8190 (tpt) cc_final: 0.7949 (ttm) REVERT: D 80 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 187 TYR cc_start: 0.8716 (t80) cc_final: 0.8323 (t80) REVERT: B 57 LEU cc_start: 0.9030 (mm) cc_final: 0.8758 (mp) REVERT: B 79 TYR cc_start: 0.6830 (t80) cc_final: 0.6423 (m-10) REVERT: B 98 PHE cc_start: 0.8325 (t80) cc_final: 0.7922 (t80) REVERT: E 289 TYR cc_start: 0.8478 (t80) cc_final: 0.7692 (t80) REVERT: E 329 MET cc_start: 0.7597 (tpt) cc_final: 0.7345 (tmm) REVERT: F 79 TYR cc_start: 0.7245 (t80) cc_final: 0.6590 (m-10) REVERT: I 187 TYR cc_start: 0.8789 (t80) cc_final: 0.8515 (t80) REVERT: I 197 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8806 (tt) REVERT: I 212 GLU cc_start: 0.8517 (tp30) cc_final: 0.8191 (tp30) REVERT: I 236 LEU cc_start: 0.8760 (mt) cc_final: 0.8428 (tt) REVERT: I 267 THR cc_start: 0.8934 (m) cc_final: 0.8685 (p) REVERT: J 94 GLU cc_start: 0.8666 (pp20) cc_final: 0.8236 (pp20) REVERT: K 209 ASP cc_start: 0.8961 (t0) cc_final: 0.8570 (t0) REVERT: K 243 MET cc_start: 0.7955 (ttm) cc_final: 0.7535 (ttm) REVERT: L 96 ASP cc_start: 0.7516 (m-30) cc_final: 0.7059 (m-30) REVERT: O 84 PRO cc_start: 0.8517 (Cg_exo) cc_final: 0.8222 (Cg_endo) REVERT: O 263 MET cc_start: 0.8321 (tpp) cc_final: 0.7949 (tpp) REVERT: O 276 MET cc_start: 0.8261 (ttp) cc_final: 0.7792 (ttp) REVERT: P 98 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6821 (t80) REVERT: M 260 TRP cc_start: 0.8112 (t-100) cc_final: 0.7767 (t-100) REVERT: M 276 MET cc_start: 0.8487 (ttt) cc_final: 0.7783 (ttt) REVERT: N 79 TYR cc_start: 0.7510 (t80) cc_final: 0.6880 (m-10) REVERT: Q 240 MET cc_start: 0.9445 (ppp) cc_final: 0.9098 (tmm) REVERT: Q 330 MET cc_start: 0.8827 (ptt) cc_final: 0.8537 (ptm) REVERT: Q 345 MET cc_start: 0.8732 (mmm) cc_final: 0.8388 (mmm) REVERT: Q 381 LEU cc_start: 0.9414 (tp) cc_final: 0.9189 (tp) REVERT: Q 396 MET cc_start: 0.9429 (tmm) cc_final: 0.9026 (tmm) REVERT: R 91 MET cc_start: 0.7914 (tpp) cc_final: 0.7652 (tpp) REVERT: R 114 MET cc_start: 0.8927 (ttm) cc_final: 0.8492 (mtp) REVERT: R 183 MET cc_start: 0.9141 (tmm) cc_final: 0.8843 (tmm) REVERT: R 256 MET cc_start: 0.8939 (mtm) cc_final: 0.8522 (mtp) REVERT: R 271 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: R 278 MET cc_start: 0.8292 (tmm) cc_final: 0.8078 (tmm) REVERT: S 209 TYR cc_start: 0.8756 (t80) cc_final: 0.8500 (t80) REVERT: S 216 LEU cc_start: 0.9182 (tp) cc_final: 0.8924 (mt) REVERT: S 366 ASN cc_start: 0.8971 (p0) cc_final: 0.8698 (p0) REVERT: S 381 LEU cc_start: 0.9437 (tp) cc_final: 0.9213 (tp) REVERT: S 396 MET cc_start: 0.9398 (tmm) cc_final: 0.8843 (tmm) REVERT: S 406 VAL cc_start: 0.8287 (p) cc_final: 0.7979 (m) REVERT: T 91 MET cc_start: 0.8142 (mmm) cc_final: 0.7768 (tpp) REVERT: T 102 TYR cc_start: 0.8807 (m-80) cc_final: 0.8395 (m-80) REVERT: T 183 MET cc_start: 0.9070 (tmm) cc_final: 0.8777 (tmm) REVERT: T 305 GLU cc_start: 0.8698 (mp0) cc_final: 0.8472 (mp0) REVERT: T 391 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9119 (mm) outliers start: 139 outliers final: 96 residues processed: 510 average time/residue: 0.3765 time to fit residues: 308.9039 Evaluate side-chains 489 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 386 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 65 PHE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain S residue 408 LEU Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 266 MET Chi-restraints excluded: chain T residue 282 ASP Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 2.9990 chunk 311 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 346 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 HIS ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 ASN T 178 HIS ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 30472 Z= 0.194 Angle : 0.651 11.970 41114 Z= 0.321 Chirality : 0.041 0.239 4607 Planarity : 0.004 0.061 5208 Dihedral : 4.944 36.458 4023 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.11 % Allowed : 24.42 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3585 helix: 0.27 (0.11), residues: 2280 sheet: -1.66 (0.37), residues: 190 loop : -1.53 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 256 HIS 0.008 0.001 HIS R 384 PHE 0.026 0.001 PHE P 88 TYR 0.026 0.001 TYR R 249 ARG 0.012 0.000 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 418 time to evaluate : 3.576 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: G 84 PRO cc_start: 0.8786 (Cg_exo) cc_final: 0.8552 (Cg_endo) REVERT: G 263 MET cc_start: 0.8199 (tpp) cc_final: 0.7985 (tpp) REVERT: G 276 MET cc_start: 0.8057 (ttp) cc_final: 0.7736 (ttp) REVERT: G 283 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9055 (p) REVERT: G 296 ASP cc_start: 0.8341 (m-30) cc_final: 0.8110 (p0) REVERT: H 85 SER cc_start: 0.8371 (t) cc_final: 0.8097 (p) REVERT: C 161 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7770 (ptt-90) REVERT: C 209 ASP cc_start: 0.9134 (t0) cc_final: 0.8815 (t0) REVERT: A 187 TYR cc_start: 0.8675 (t80) cc_final: 0.8297 (t80) REVERT: B 57 LEU cc_start: 0.9007 (mm) cc_final: 0.8728 (mp) REVERT: B 71 PHE cc_start: 0.8418 (m-80) cc_final: 0.7997 (m-80) REVERT: B 98 PHE cc_start: 0.8148 (t80) cc_final: 0.7721 (t80) REVERT: E 289 TYR cc_start: 0.8486 (t80) cc_final: 0.7667 (t80) REVERT: E 329 MET cc_start: 0.7521 (tpt) cc_final: 0.7289 (tmm) REVERT: F 79 TYR cc_start: 0.7153 (t80) cc_final: 0.6793 (m-10) REVERT: I 187 TYR cc_start: 0.8756 (t80) cc_final: 0.8444 (t80) REVERT: I 200 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8917 (tm-30) REVERT: I 212 GLU cc_start: 0.8503 (tp30) cc_final: 0.8166 (tp30) REVERT: I 236 LEU cc_start: 0.8717 (mt) cc_final: 0.8401 (tt) REVERT: K 209 ASP cc_start: 0.8978 (t0) cc_final: 0.8579 (t0) REVERT: K 243 MET cc_start: 0.7902 (ttm) cc_final: 0.7462 (ttm) REVERT: K 326 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8363 (tp-100) REVERT: L 96 ASP cc_start: 0.7447 (m-30) cc_final: 0.7004 (m-30) REVERT: O 84 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8180 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8656 (tt) REVERT: O 263 MET cc_start: 0.8343 (tpp) cc_final: 0.8077 (tpp) REVERT: O 276 MET cc_start: 0.8250 (ttp) cc_final: 0.7793 (ttp) REVERT: P 98 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6837 (t80) REVERT: M 190 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8062 (pp) REVERT: M 260 TRP cc_start: 0.8155 (t-100) cc_final: 0.7648 (t-100) REVERT: M 276 MET cc_start: 0.8454 (ttt) cc_final: 0.8006 (ttt) REVERT: N 79 TYR cc_start: 0.7450 (t80) cc_final: 0.6825 (m-10) REVERT: Q 240 MET cc_start: 0.9449 (ppp) cc_final: 0.9101 (tmm) REVERT: Q 345 MET cc_start: 0.8733 (mmm) cc_final: 0.8369 (mmm) REVERT: Q 396 MET cc_start: 0.9368 (tmm) cc_final: 0.9108 (tmm) REVERT: R 91 MET cc_start: 0.7873 (tpp) cc_final: 0.7649 (tpp) REVERT: R 114 MET cc_start: 0.8981 (ttm) cc_final: 0.8558 (mtp) REVERT: R 161 THR cc_start: 0.9118 (m) cc_final: 0.8830 (t) REVERT: R 183 MET cc_start: 0.9117 (tmm) cc_final: 0.8848 (tmm) REVERT: R 256 MET cc_start: 0.8918 (mtm) cc_final: 0.8483 (mtp) REVERT: R 271 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: S 209 TYR cc_start: 0.8705 (t80) cc_final: 0.8468 (t80) REVERT: S 216 LEU cc_start: 0.9162 (tp) cc_final: 0.8956 (mt) REVERT: S 305 HIS cc_start: 0.9454 (t-90) cc_final: 0.8963 (t-90) REVERT: S 345 MET cc_start: 0.8629 (mmm) cc_final: 0.8228 (mmm) REVERT: S 366 ASN cc_start: 0.8943 (p0) cc_final: 0.8669 (p0) REVERT: S 381 LEU cc_start: 0.9422 (tp) cc_final: 0.9204 (tp) REVERT: S 396 MET cc_start: 0.9338 (tmm) cc_final: 0.8822 (tmm) REVERT: S 406 VAL cc_start: 0.8306 (p) cc_final: 0.8012 (m) REVERT: T 91 MET cc_start: 0.8138 (mmm) cc_final: 0.7767 (tpp) REVERT: T 102 TYR cc_start: 0.8768 (m-80) cc_final: 0.8326 (m-80) REVERT: T 114 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (tpp) REVERT: T 278 MET cc_start: 0.8011 (tmm) cc_final: 0.7773 (tmm) REVERT: T 301 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8538 (tptp) REVERT: T 335 MET cc_start: 0.8589 (mmm) cc_final: 0.8152 (mmm) REVERT: T 391 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9110 (mm) outliers start: 134 outliers final: 106 residues processed: 514 average time/residue: 0.3800 time to fit residues: 316.7764 Evaluate side-chains 505 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 390 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 323 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain S residue 408 LEU Chi-restraints excluded: chain T residue 114 MET Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 282 ASP Chi-restraints excluded: chain T residue 301 LYS Chi-restraints excluded: chain T residue 365 ASN Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 197 optimal weight: 8.9990 chunk 252 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 172 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 HIS ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 30472 Z= 0.196 Angle : 0.650 12.038 41114 Z= 0.319 Chirality : 0.041 0.222 4607 Planarity : 0.004 0.054 5208 Dihedral : 4.873 34.742 4023 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.79 % Allowed : 24.76 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3585 helix: 0.42 (0.11), residues: 2275 sheet: -1.53 (0.38), residues: 190 loop : -1.53 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 256 HIS 0.008 0.001 HIS T 384 PHE 0.041 0.001 PHE T 252 TYR 0.025 0.001 TYR R 249 ARG 0.013 0.000 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 406 time to evaluate : 3.387 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: G 84 PRO cc_start: 0.8790 (Cg_exo) cc_final: 0.8540 (Cg_endo) REVERT: G 283 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9070 (p) REVERT: G 296 ASP cc_start: 0.8326 (m-30) cc_final: 0.8112 (p0) REVERT: C 161 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7789 (ptt-90) REVERT: C 209 ASP cc_start: 0.9142 (t0) cc_final: 0.8836 (t0) REVERT: A 187 TYR cc_start: 0.8662 (t80) cc_final: 0.8241 (t80) REVERT: B 57 LEU cc_start: 0.9017 (mm) cc_final: 0.8711 (mp) REVERT: B 71 PHE cc_start: 0.8332 (m-80) cc_final: 0.8042 (m-80) REVERT: B 98 PHE cc_start: 0.8096 (t80) cc_final: 0.7632 (t80) REVERT: E 289 TYR cc_start: 0.8508 (t80) cc_final: 0.7724 (t80) REVERT: E 329 MET cc_start: 0.7514 (tpt) cc_final: 0.7264 (tmm) REVERT: F 79 TYR cc_start: 0.7117 (t80) cc_final: 0.6799 (m-10) REVERT: I 187 TYR cc_start: 0.8750 (t80) cc_final: 0.8470 (t80) REVERT: I 212 GLU cc_start: 0.8555 (tp30) cc_final: 0.8230 (tp30) REVERT: I 236 LEU cc_start: 0.8670 (mt) cc_final: 0.8370 (tt) REVERT: I 255 TRP cc_start: 0.7626 (OUTLIER) cc_final: 0.7048 (m100) REVERT: K 209 ASP cc_start: 0.8979 (t0) cc_final: 0.8579 (t0) REVERT: K 243 MET cc_start: 0.7872 (ttm) cc_final: 0.7403 (ttm) REVERT: K 326 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8414 (tp-100) REVERT: L 96 ASP cc_start: 0.7543 (m-30) cc_final: 0.7101 (m-30) REVERT: O 84 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8177 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8630 (tt) REVERT: O 263 MET cc_start: 0.8368 (tpp) cc_final: 0.8093 (tpp) REVERT: O 276 MET cc_start: 0.8243 (ttp) cc_final: 0.7804 (ttp) REVERT: P 98 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7028 (t80) REVERT: M 190 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7977 (pp) REVERT: M 260 TRP cc_start: 0.8124 (t-100) cc_final: 0.7750 (t-100) REVERT: M 276 MET cc_start: 0.8464 (ttt) cc_final: 0.8034 (ttt) REVERT: M 303 PHE cc_start: 0.8398 (t80) cc_final: 0.8179 (t80) REVERT: N 79 TYR cc_start: 0.7392 (t80) cc_final: 0.6746 (m-10) REVERT: Q 204 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7955 (mp) REVERT: Q 240 MET cc_start: 0.9433 (ppp) cc_final: 0.9085 (tmm) REVERT: Q 345 MET cc_start: 0.8746 (mmm) cc_final: 0.8360 (mmm) REVERT: Q 381 LEU cc_start: 0.9268 (tp) cc_final: 0.9017 (tp) REVERT: R 91 MET cc_start: 0.7881 (tpp) cc_final: 0.7668 (tpp) REVERT: R 114 MET cc_start: 0.8982 (ttm) cc_final: 0.8558 (mtp) REVERT: R 161 THR cc_start: 0.9092 (m) cc_final: 0.8810 (t) REVERT: R 183 MET cc_start: 0.9105 (tmm) cc_final: 0.8838 (tmm) REVERT: R 256 MET cc_start: 0.8916 (mtm) cc_final: 0.8350 (mtm) REVERT: R 271 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: S 209 TYR cc_start: 0.8650 (t80) cc_final: 0.8415 (t80) REVERT: S 305 HIS cc_start: 0.9460 (t-90) cc_final: 0.8983 (t-90) REVERT: S 345 MET cc_start: 0.8680 (mmm) cc_final: 0.8260 (mmm) REVERT: S 366 ASN cc_start: 0.8977 (p0) cc_final: 0.8710 (p0) REVERT: S 381 LEU cc_start: 0.9409 (tp) cc_final: 0.9201 (tp) REVERT: S 396 MET cc_start: 0.9327 (tmm) cc_final: 0.8910 (tmm) REVERT: S 406 VAL cc_start: 0.8300 (p) cc_final: 0.8002 (m) REVERT: T 91 MET cc_start: 0.8173 (mmm) cc_final: 0.7802 (tpp) REVERT: T 102 TYR cc_start: 0.8708 (m-80) cc_final: 0.8270 (m-80) REVERT: T 114 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: T 391 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9079 (mm) outliers start: 156 outliers final: 117 residues processed: 518 average time/residue: 0.3932 time to fit residues: 330.2268 Evaluate side-chains 515 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 388 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 255 TRP Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 71 PHE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 323 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain S residue 408 LEU Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 114 MET Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 282 ASP Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 HIS Q 222 ASN R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 30472 Z= 0.259 Angle : 0.682 11.426 41114 Z= 0.334 Chirality : 0.043 0.425 4607 Planarity : 0.004 0.056 5208 Dihedral : 4.937 34.821 4023 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.06 % Allowed : 24.67 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3585 helix: 0.47 (0.11), residues: 2267 sheet: -1.57 (0.38), residues: 190 loop : -1.43 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 256 HIS 0.009 0.001 HIS Q 411 PHE 0.040 0.001 PHE T 252 TYR 0.023 0.002 TYR R 249 ARG 0.013 0.000 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 392 time to evaluate : 3.790 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: G 84 PRO cc_start: 0.8885 (Cg_exo) cc_final: 0.8667 (Cg_endo) REVERT: G 263 MET cc_start: 0.7952 (tpp) cc_final: 0.7747 (mmp) REVERT: G 283 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.9095 (p) REVERT: C 161 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7771 (ptt-90) REVERT: C 209 ASP cc_start: 0.9139 (t0) cc_final: 0.8823 (t0) REVERT: A 117 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8358 (tm-30) REVERT: A 187 TYR cc_start: 0.8696 (t80) cc_final: 0.8320 (t80) REVERT: B 57 LEU cc_start: 0.9042 (mm) cc_final: 0.8695 (mp) REVERT: B 71 PHE cc_start: 0.8380 (m-80) cc_final: 0.8002 (m-80) REVERT: B 98 PHE cc_start: 0.8146 (t80) cc_final: 0.7756 (t80) REVERT: E 289 TYR cc_start: 0.8489 (t80) cc_final: 0.7693 (t80) REVERT: E 303 PHE cc_start: 0.8494 (t80) cc_final: 0.8267 (t80) REVERT: E 329 MET cc_start: 0.7562 (tpt) cc_final: 0.7268 (tmm) REVERT: F 79 TYR cc_start: 0.7091 (t80) cc_final: 0.6787 (m-10) REVERT: I 156 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8362 (tt) REVERT: I 187 TYR cc_start: 0.8804 (t80) cc_final: 0.8528 (t80) REVERT: I 212 GLU cc_start: 0.8588 (tp30) cc_final: 0.8289 (tp30) REVERT: I 236 LEU cc_start: 0.8759 (mt) cc_final: 0.8434 (tt) REVERT: I 255 TRP cc_start: 0.7688 (OUTLIER) cc_final: 0.7149 (m100) REVERT: J 97 ILE cc_start: 0.7780 (mm) cc_final: 0.7471 (mt) REVERT: K 209 ASP cc_start: 0.8981 (t0) cc_final: 0.8588 (t0) REVERT: K 243 MET cc_start: 0.7914 (ttm) cc_final: 0.7462 (ttm) REVERT: K 252 ARG cc_start: 0.6561 (mpt180) cc_final: 0.6172 (mpt180) REVERT: K 326 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8488 (tp-100) REVERT: L 96 ASP cc_start: 0.7572 (m-30) cc_final: 0.7108 (m-30) REVERT: O 84 PRO cc_start: 0.8582 (Cg_exo) cc_final: 0.8276 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8669 (tt) REVERT: O 263 MET cc_start: 0.8457 (tpp) cc_final: 0.8157 (tpp) REVERT: O 276 MET cc_start: 0.8274 (ttp) cc_final: 0.7844 (ttp) REVERT: P 98 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7056 (t80) REVERT: M 190 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8192 (pp) REVERT: M 276 MET cc_start: 0.8481 (ttt) cc_final: 0.7982 (ttt) REVERT: N 79 TYR cc_start: 0.7429 (t80) cc_final: 0.6778 (m-10) REVERT: Q 204 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (mp) REVERT: Q 240 MET cc_start: 0.9438 (ppp) cc_final: 0.9086 (tmm) REVERT: Q 345 MET cc_start: 0.8760 (mmm) cc_final: 0.8369 (mmm) REVERT: Q 381 LEU cc_start: 0.9287 (tp) cc_final: 0.9001 (tp) REVERT: R 114 MET cc_start: 0.8987 (ttm) cc_final: 0.8514 (mtp) REVERT: R 161 THR cc_start: 0.9109 (m) cc_final: 0.8846 (t) REVERT: R 183 MET cc_start: 0.9103 (tmm) cc_final: 0.8812 (tmm) REVERT: R 256 MET cc_start: 0.8930 (mtm) cc_final: 0.8369 (mtm) REVERT: R 271 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: S 209 TYR cc_start: 0.8653 (t80) cc_final: 0.8421 (t80) REVERT: S 305 HIS cc_start: 0.9458 (t-90) cc_final: 0.8975 (t-90) REVERT: S 345 MET cc_start: 0.8710 (mmm) cc_final: 0.8277 (mmm) REVERT: S 366 ASN cc_start: 0.8990 (p0) cc_final: 0.8786 (p0) REVERT: S 396 MET cc_start: 0.9318 (tmm) cc_final: 0.8878 (tmm) REVERT: T 91 MET cc_start: 0.8125 (mmm) cc_final: 0.7738 (tpp) REVERT: T 102 TYR cc_start: 0.8694 (m-80) cc_final: 0.8259 (m-80) REVERT: T 114 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: T 118 MET cc_start: 0.6565 (ttt) cc_final: 0.6349 (ttt) REVERT: T 278 MET cc_start: 0.8060 (tmm) cc_final: 0.7857 (tmm) REVERT: T 391 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9073 (mm) outliers start: 165 outliers final: 136 residues processed: 519 average time/residue: 0.3960 time to fit residues: 334.8675 Evaluate side-chains 528 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 381 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 255 TRP Chi-restraints excluded: chain I residue 276 MET Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 71 PHE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 323 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 ASN Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain S residue 408 LEU Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 114 MET Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 282 ASP Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 7.9990 chunk 330 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 290 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 HIS R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30472 Z= 0.255 Angle : 0.694 14.481 41114 Z= 0.338 Chirality : 0.043 0.380 4607 Planarity : 0.004 0.059 5208 Dihedral : 4.961 31.379 4023 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.85 % Allowed : 25.31 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3585 helix: 0.50 (0.11), residues: 2267 sheet: -1.78 (0.36), residues: 210 loop : -1.41 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 256 HIS 0.012 0.001 HIS C 159 PHE 0.043 0.001 PHE T 252 TYR 0.030 0.002 TYR R 249 ARG 0.014 0.000 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 383 time to evaluate : 3.739 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: G 84 PRO cc_start: 0.8972 (Cg_exo) cc_final: 0.8752 (Cg_endo) REVERT: G 303 PHE cc_start: 0.8503 (t80) cc_final: 0.8098 (t80) REVERT: C 161 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7839 (ptt-90) REVERT: C 209 ASP cc_start: 0.9137 (t0) cc_final: 0.8817 (t0) REVERT: D 86 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7883 (ttmm) REVERT: A 117 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 187 TYR cc_start: 0.8715 (t80) cc_final: 0.8339 (t80) REVERT: B 57 LEU cc_start: 0.9038 (mm) cc_final: 0.8727 (mp) REVERT: B 71 PHE cc_start: 0.8322 (m-80) cc_final: 0.8074 (m-80) REVERT: B 98 PHE cc_start: 0.8307 (t80) cc_final: 0.7911 (t80) REVERT: E 289 TYR cc_start: 0.8488 (t80) cc_final: 0.7692 (t80) REVERT: E 303 PHE cc_start: 0.8445 (t80) cc_final: 0.8189 (t80) REVERT: F 79 TYR cc_start: 0.7077 (t80) cc_final: 0.6794 (m-10) REVERT: I 156 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8365 (tt) REVERT: I 187 TYR cc_start: 0.8790 (t80) cc_final: 0.8502 (t80) REVERT: I 212 GLU cc_start: 0.8582 (tp30) cc_final: 0.8294 (tp30) REVERT: I 236 LEU cc_start: 0.8757 (mt) cc_final: 0.8432 (tt) REVERT: I 255 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.7119 (m100) REVERT: J 97 ILE cc_start: 0.7785 (mm) cc_final: 0.7474 (mt) REVERT: K 209 ASP cc_start: 0.8977 (t0) cc_final: 0.8585 (t0) REVERT: K 243 MET cc_start: 0.7911 (ttm) cc_final: 0.7509 (ttm) REVERT: K 326 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8522 (tp-100) REVERT: L 96 ASP cc_start: 0.7552 (m-30) cc_final: 0.7156 (m-30) REVERT: O 84 PRO cc_start: 0.8584 (Cg_exo) cc_final: 0.8275 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8659 (tt) REVERT: O 263 MET cc_start: 0.8491 (tpp) cc_final: 0.8235 (tpp) REVERT: O 276 MET cc_start: 0.8283 (ttp) cc_final: 0.7855 (ttp) REVERT: P 98 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7106 (t80) REVERT: M 190 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (pp) REVERT: M 276 MET cc_start: 0.8451 (ttt) cc_final: 0.7756 (ttt) REVERT: M 303 PHE cc_start: 0.8417 (t80) cc_final: 0.8184 (t80) REVERT: N 79 TYR cc_start: 0.7424 (t80) cc_final: 0.6761 (m-10) REVERT: Q 204 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8023 (mp) REVERT: Q 240 MET cc_start: 0.9437 (ppp) cc_final: 0.9076 (tmm) REVERT: Q 345 MET cc_start: 0.8763 (mmm) cc_final: 0.8345 (mmm) REVERT: Q 381 LEU cc_start: 0.9306 (tp) cc_final: 0.9019 (tp) REVERT: R 114 MET cc_start: 0.8982 (ttm) cc_final: 0.8506 (mtp) REVERT: R 161 THR cc_start: 0.9094 (m) cc_final: 0.8826 (t) REVERT: R 183 MET cc_start: 0.9140 (tmm) cc_final: 0.8841 (tmm) REVERT: R 256 MET cc_start: 0.8924 (mtm) cc_final: 0.8391 (mtm) REVERT: R 271 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: S 209 TYR cc_start: 0.8649 (t80) cc_final: 0.8416 (t80) REVERT: S 240 MET cc_start: 0.9408 (tmm) cc_final: 0.9072 (tmm) REVERT: S 305 HIS cc_start: 0.9457 (t-90) cc_final: 0.8970 (t-90) REVERT: S 345 MET cc_start: 0.8706 (mmm) cc_final: 0.8261 (mmm) REVERT: S 396 MET cc_start: 0.9302 (tmm) cc_final: 0.8919 (tmm) REVERT: T 91 MET cc_start: 0.8129 (mmm) cc_final: 0.7767 (tpp) REVERT: T 102 TYR cc_start: 0.8550 (m-80) cc_final: 0.8244 (m-80) REVERT: T 114 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8316 (tpp) REVERT: T 258 ASN cc_start: 0.8150 (m-40) cc_final: 0.7846 (p0) REVERT: T 278 MET cc_start: 0.8075 (tmm) cc_final: 0.7856 (tmm) REVERT: T 335 MET cc_start: 0.8610 (mmm) cc_final: 0.8272 (mmm) REVERT: T 391 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9064 (mm) outliers start: 158 outliers final: 138 residues processed: 503 average time/residue: 0.4045 time to fit residues: 330.6295 Evaluate side-chains 525 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 376 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 255 TRP Chi-restraints excluded: chain I residue 276 MET Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 323 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 ASN Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 114 MET Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 282 ASP Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 356 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 284 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 ASN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 30472 Z= 0.329 Angle : 0.738 15.467 41114 Z= 0.359 Chirality : 0.045 0.396 4607 Planarity : 0.004 0.066 5208 Dihedral : 5.050 32.003 4023 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.97 % Allowed : 25.25 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3585 helix: 0.47 (0.11), residues: 2259 sheet: -1.83 (0.36), residues: 210 loop : -1.39 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 256 HIS 0.017 0.002 HIS Q 411 PHE 0.047 0.002 PHE T 252 TYR 0.028 0.002 TYR R 249 ARG 0.015 0.000 ARG S 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 373 time to evaluate : 3.762 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: G 84 PRO cc_start: 0.8989 (Cg_exo) cc_final: 0.8773 (Cg_endo) REVERT: G 303 PHE cc_start: 0.8500 (t80) cc_final: 0.8106 (t80) REVERT: C 161 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7766 (ptt-90) REVERT: C 209 ASP cc_start: 0.9134 (t0) cc_final: 0.8820 (t0) REVERT: A 187 TYR cc_start: 0.8731 (t80) cc_final: 0.8347 (t80) REVERT: A 263 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7769 (tpp) REVERT: B 57 LEU cc_start: 0.9101 (mm) cc_final: 0.8768 (mp) REVERT: B 71 PHE cc_start: 0.8399 (m-80) cc_final: 0.8046 (m-80) REVERT: B 98 PHE cc_start: 0.8317 (t80) cc_final: 0.7906 (t80) REVERT: E 289 TYR cc_start: 0.8514 (t80) cc_final: 0.7744 (t80) REVERT: I 187 TYR cc_start: 0.8820 (t80) cc_final: 0.8556 (t80) REVERT: I 212 GLU cc_start: 0.8577 (tp30) cc_final: 0.8301 (tp30) REVERT: I 236 LEU cc_start: 0.8806 (mt) cc_final: 0.8465 (tt) REVERT: I 255 TRP cc_start: 0.7696 (OUTLIER) cc_final: 0.7191 (m100) REVERT: J 79 TYR cc_start: 0.6551 (t80) cc_final: 0.6002 (m-10) REVERT: K 209 ASP cc_start: 0.8986 (t0) cc_final: 0.8598 (t0) REVERT: K 243 MET cc_start: 0.7923 (ttm) cc_final: 0.7704 (ttm) REVERT: L 96 ASP cc_start: 0.7555 (m-30) cc_final: 0.7161 (m-30) REVERT: O 84 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8320 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8673 (tt) REVERT: O 263 MET cc_start: 0.8451 (tpp) cc_final: 0.8175 (tpp) REVERT: O 276 MET cc_start: 0.8344 (ttp) cc_final: 0.7926 (ttp) REVERT: P 98 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7177 (t80) REVERT: M 190 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8223 (pp) REVERT: M 276 MET cc_start: 0.8464 (ttt) cc_final: 0.7727 (ttt) REVERT: M 303 PHE cc_start: 0.8442 (t80) cc_final: 0.8202 (t80) REVERT: N 79 TYR cc_start: 0.7492 (t80) cc_final: 0.6861 (m-10) REVERT: Q 204 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8074 (mp) REVERT: Q 240 MET cc_start: 0.9441 (ppp) cc_final: 0.9078 (tmm) REVERT: Q 345 MET cc_start: 0.8777 (mmm) cc_final: 0.8367 (mmm) REVERT: Q 381 LEU cc_start: 0.9335 (tp) cc_final: 0.9059 (tp) REVERT: R 114 MET cc_start: 0.8988 (ttm) cc_final: 0.8545 (mtp) REVERT: R 161 THR cc_start: 0.9113 (m) cc_final: 0.8857 (t) REVERT: R 183 MET cc_start: 0.9164 (tmm) cc_final: 0.8864 (tmm) REVERT: R 256 MET cc_start: 0.8935 (mtm) cc_final: 0.8445 (mtm) REVERT: R 271 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: S 209 TYR cc_start: 0.8654 (t80) cc_final: 0.8439 (t80) REVERT: S 240 MET cc_start: 0.9412 (tmm) cc_final: 0.9071 (tmm) REVERT: S 305 HIS cc_start: 0.9461 (t-90) cc_final: 0.8883 (t70) REVERT: S 345 MET cc_start: 0.8716 (mmm) cc_final: 0.8265 (mmm) REVERT: S 396 MET cc_start: 0.9321 (tmm) cc_final: 0.8932 (tmm) REVERT: T 91 MET cc_start: 0.8159 (mmm) cc_final: 0.7779 (tpp) REVERT: T 102 TYR cc_start: 0.8576 (m-80) cc_final: 0.8289 (m-80) REVERT: T 114 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: T 258 ASN cc_start: 0.8149 (m-40) cc_final: 0.7820 (p0) REVERT: T 278 MET cc_start: 0.8093 (tmm) cc_final: 0.7865 (tmm) REVERT: T 335 MET cc_start: 0.8607 (mmm) cc_final: 0.8274 (mmm) REVERT: T 391 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9020 (mm) outliers start: 162 outliers final: 140 residues processed: 499 average time/residue: 0.3801 time to fit residues: 307.9149 Evaluate side-chains 519 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 369 time to evaluate : 4.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 255 TRP Chi-restraints excluded: chain I residue 276 MET Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 323 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 114 MET Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 282 ASP Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 292 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 ASN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.104912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.078383 restraints weight = 91141.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.080999 restraints weight = 41797.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.082663 restraints weight = 25198.690| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 30472 Z= 0.220 Angle : 0.700 15.945 41114 Z= 0.337 Chirality : 0.043 0.377 4607 Planarity : 0.004 0.065 5208 Dihedral : 4.924 31.948 4023 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.51 % Allowed : 25.68 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3585 helix: 0.58 (0.11), residues: 2259 sheet: -1.80 (0.36), residues: 210 loop : -1.33 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 286 HIS 0.012 0.001 HIS C 159 PHE 0.042 0.001 PHE T 252 TYR 0.027 0.001 TYR R 249 ARG 0.015 0.000 ARG S 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6509.03 seconds wall clock time: 119 minutes 20.34 seconds (7160.34 seconds total)