Starting phenix.real_space_refine on Mon Mar 18 21:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/03_2024/6kfg_9972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/03_2024/6kfg_9972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/03_2024/6kfg_9972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/03_2024/6kfg_9972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/03_2024/6kfg_9972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/03_2024/6kfg_9972.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14704 2.51 5 N 3632 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G ASP 249": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H ASP 249": "OD1" <-> "OD2" Residue "H PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.47, per 1000 atoms: 0.52 Number of scatterers: 22264 At special positions: 0 Unit cell: (126.896, 126.896, 107.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3832 8.00 N 3632 7.00 C 14704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.05 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.05 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.05 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.05 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.05 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.05 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.05 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.05 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 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: 8.50 Conformation dependent library (CDL) restraints added in 6.2 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 67.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.338A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.505A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.780A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.504A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.716A pdb=" N ARG B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.780A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 302 " --> pdb=" O TRP B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.505A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.718A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.781A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.338A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.505A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.601A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.716A pdb=" N ARG D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.780A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.505A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.601A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.083A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Proline residue: E 169 - end of helix removed outlier: 3.781A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU E 302 " --> pdb=" O TRP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 19 Processing helix chain 'F' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.452A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.505A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 removed outlier: 3.718A pdb=" N ARG F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Proline residue: F 169 - end of helix removed outlier: 3.779A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR F 301 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 302 " --> pdb=" O TRP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 19 Processing helix chain 'G' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.504A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Proline residue: G 169 - end of helix removed outlier: 3.781A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS G 275 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 301 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU G 302 " --> pdb=" O TRP G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 19 Processing helix chain 'H' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.452A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.505A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Proline residue: H 169 - end of helix removed outlier: 3.780A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS H 275 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 301 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU H 302 " --> pdb=" O TRP H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU A 264 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU B 264 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU C 264 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU D 264 " --> pdb=" O TRP D 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU E 264 " --> pdb=" O TRP E 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU F 264 " --> pdb=" O TRP F 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU G 264 " --> pdb=" O TRP G 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU H 264 " --> pdb=" O TRP H 59 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3627 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: 6.61 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6756 1.35 - 1.49: 6983 1.49 - 1.62: 9045 1.62 - 1.76: 8 1.76 - 1.89: 128 Bond restraints: 22920 Sorted by residual: bond pdb=" CB CYS H 58 " pdb=" SG CYS H 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" CB CYS C 58 " pdb=" SG CYS C 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.13e+00 bond pdb=" CB CYS A 58 " pdb=" SG CYS A 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB CYS D 58 " pdb=" SG CYS D 58 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB CYS E 58 " pdb=" SG CYS E 58 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 6.07e+00 ... (remaining 22915 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.28: 668 107.28 - 113.98: 12826 113.98 - 120.69: 10372 120.69 - 127.39: 7038 127.39 - 134.09: 312 Bond angle restraints: 31216 Sorted by residual: angle pdb=" CA CYS G 265 " pdb=" CB CYS G 265 " pdb=" SG CYS G 265 " ideal model delta sigma weight residual 114.40 127.15 -12.75 2.30e+00 1.89e-01 3.07e+01 angle pdb=" CA CYS E 265 " pdb=" CB CYS E 265 " pdb=" SG CYS E 265 " ideal model delta sigma weight residual 114.40 127.11 -12.71 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS C 265 " pdb=" CB CYS C 265 " pdb=" SG CYS C 265 " ideal model delta sigma weight residual 114.40 127.11 -12.71 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS H 265 " pdb=" CB CYS H 265 " pdb=" SG CYS H 265 " ideal model delta sigma weight residual 114.40 127.10 -12.70 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS F 265 " pdb=" CB CYS F 265 " pdb=" SG CYS F 265 " ideal model delta sigma weight residual 114.40 127.10 -12.70 2.30e+00 1.89e-01 3.05e+01 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 11402 15.58 - 31.17: 1407 31.17 - 46.75: 287 46.75 - 62.33: 72 62.33 - 77.91: 16 Dihedral angle restraints: 13184 sinusoidal: 5144 harmonic: 8040 Sorted by residual: dihedral pdb=" CB CYS E 58 " pdb=" SG CYS E 58 " pdb=" SG CYS E 265 " pdb=" CB CYS E 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.42 53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS G 58 " pdb=" SG CYS G 58 " pdb=" SG CYS G 265 " pdb=" CB CYS G 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.42 53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS F 58 " pdb=" SG CYS F 58 " pdb=" SG CYS F 265 " pdb=" CB CYS F 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.43 53.57 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2102 0.038 - 0.076: 951 0.076 - 0.114: 331 0.114 - 0.152: 56 0.152 - 0.190: 8 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA CYS B 265 " pdb=" N CYS B 265 " pdb=" C CYS B 265 " pdb=" CB CYS B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA CYS E 265 " pdb=" N CYS E 265 " pdb=" C CYS E 265 " pdb=" CB CYS E 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA CYS D 265 " pdb=" N CYS D 265 " pdb=" C CYS D 265 " pdb=" CB CYS D 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 3445 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 242 " 0.014 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE B 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 242 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 242 " 0.014 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE C 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 242 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 242 " 0.014 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE A 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 242 " 0.003 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 604 2.70 - 3.25: 24596 3.25 - 3.80: 35506 3.80 - 4.35: 41354 4.35 - 4.90: 69124 Nonbonded interactions: 171184 Sorted by model distance: nonbonded pdb=" OE1 GLN G 115 " pdb=" NE2 GLN G 206 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLN C 115 " pdb=" NE2 GLN C 206 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLN B 115 " pdb=" NE2 GLN B 206 " model vdw 2.148 2.520 nonbonded pdb=" OE1 GLN F 115 " pdb=" NE2 GLN F 206 " model vdw 2.149 2.520 nonbonded pdb=" OE1 GLN D 115 " pdb=" NE2 GLN D 206 " model vdw 2.149 2.520 ... (remaining 171179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.270 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: 2.710 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 59.260 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.007 0.082 22920 Z= 0.433 Angle : 0.770 12.750 31216 Z= 0.419 Chirality : 0.047 0.190 3448 Planarity : 0.003 0.029 3832 Dihedral : 14.038 77.914 7920 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.67 % Allowed : 8.15 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.13), residues: 2640 helix: -1.78 (0.11), residues: 1704 sheet: -3.36 (0.47), residues: 88 loop : -5.15 (0.13), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 222 HIS 0.004 0.001 HIS G 241 PHE 0.025 0.002 PHE B 242 TYR 0.012 0.001 TYR F 301 ARG 0.003 0.001 ARG H 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 934 time to evaluate : 2.555 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: A 69 VAL cc_start: 0.9055 (m) cc_final: 0.8784 (t) REVERT: A 127 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7711 (ttmm) REVERT: A 130 ILE cc_start: 0.9009 (tp) cc_final: 0.8624 (tp) REVERT: A 284 LEU cc_start: 0.8784 (tp) cc_final: 0.8579 (tp) REVERT: A 343 ASP cc_start: 0.8354 (t70) cc_final: 0.8094 (t70) REVERT: A 344 GLN cc_start: 0.9045 (mm110) cc_final: 0.8730 (mm110) REVERT: A 364 ILE cc_start: 0.8755 (tt) cc_final: 0.8466 (tt) REVERT: B 63 GLN cc_start: 0.8001 (pp30) cc_final: 0.7764 (pm20) REVERT: B 127 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7811 (ttmm) REVERT: B 130 ILE cc_start: 0.8881 (tp) cc_final: 0.8543 (tp) REVERT: B 166 GLU cc_start: 0.8445 (tp30) cc_final: 0.7718 (tp30) REVERT: B 202 ASN cc_start: 0.8922 (t0) cc_final: 0.8566 (t0) REVERT: B 210 LEU cc_start: 0.9314 (tp) cc_final: 0.9013 (tt) REVERT: B 211 THR cc_start: 0.9408 (m) cc_final: 0.9180 (p) REVERT: B 212 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8288 (mp10) REVERT: B 271 ILE cc_start: 0.9446 (tt) cc_final: 0.9244 (tt) REVERT: B 313 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8749 (ttmm) REVERT: B 344 GLN cc_start: 0.8991 (mm110) cc_final: 0.8757 (mm110) REVERT: B 364 ILE cc_start: 0.8650 (tt) cc_final: 0.8209 (tt) REVERT: C 105 TYR cc_start: 0.7005 (m-80) cc_final: 0.6802 (m-80) REVERT: C 127 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7768 (ttmm) REVERT: C 130 ILE cc_start: 0.9000 (tp) cc_final: 0.8662 (tp) REVERT: C 328 ASP cc_start: 0.9023 (m-30) cc_final: 0.8758 (p0) REVERT: C 343 ASP cc_start: 0.8305 (t70) cc_final: 0.8072 (t70) REVERT: C 344 GLN cc_start: 0.9050 (mm110) cc_final: 0.8739 (mm110) REVERT: C 364 ILE cc_start: 0.8750 (tt) cc_final: 0.8525 (tt) REVERT: D 63 GLN cc_start: 0.8026 (pp30) cc_final: 0.7760 (pm20) REVERT: D 127 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7794 (ttmm) REVERT: D 130 ILE cc_start: 0.8927 (tp) cc_final: 0.8609 (tp) REVERT: D 166 GLU cc_start: 0.8380 (tp30) cc_final: 0.7666 (tp30) REVERT: D 202 ASN cc_start: 0.8926 (t0) cc_final: 0.8553 (t0) REVERT: D 210 LEU cc_start: 0.9279 (tp) cc_final: 0.9031 (tt) REVERT: D 212 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8375 (mp10) REVERT: D 244 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7947 (mtt180) REVERT: D 271 ILE cc_start: 0.9475 (tt) cc_final: 0.9233 (tt) REVERT: D 344 GLN cc_start: 0.8953 (mm110) cc_final: 0.8710 (mm110) REVERT: D 364 ILE cc_start: 0.8533 (tt) cc_final: 0.8083 (tt) REVERT: E 127 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7740 (ttmm) REVERT: E 130 ILE cc_start: 0.9010 (tp) cc_final: 0.8640 (tp) REVERT: E 343 ASP cc_start: 0.8296 (t70) cc_final: 0.8029 (t70) REVERT: E 344 GLN cc_start: 0.9036 (mm110) cc_final: 0.8723 (mm110) REVERT: F 63 GLN cc_start: 0.8081 (pp30) cc_final: 0.7817 (pm20) REVERT: F 130 ILE cc_start: 0.8872 (tp) cc_final: 0.8553 (tp) REVERT: F 166 GLU cc_start: 0.8488 (tp30) cc_final: 0.7748 (tp30) REVERT: F 202 ASN cc_start: 0.8953 (t0) cc_final: 0.8614 (t0) REVERT: F 210 LEU cc_start: 0.9324 (tp) cc_final: 0.9103 (tt) REVERT: F 211 THR cc_start: 0.9329 (m) cc_final: 0.9024 (p) REVERT: F 212 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8431 (mp10) REVERT: F 271 ILE cc_start: 0.9464 (tt) cc_final: 0.9207 (tt) REVERT: F 344 GLN cc_start: 0.9006 (mm110) cc_final: 0.8746 (mm110) REVERT: F 364 ILE cc_start: 0.8609 (tt) cc_final: 0.8163 (tt) REVERT: G 69 VAL cc_start: 0.9003 (m) cc_final: 0.8546 (t) REVERT: G 105 TYR cc_start: 0.6993 (m-80) cc_final: 0.6787 (m-80) REVERT: G 127 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7818 (ttmm) REVERT: G 343 ASP cc_start: 0.8380 (t70) cc_final: 0.8115 (t70) REVERT: G 344 GLN cc_start: 0.9012 (mm110) cc_final: 0.8704 (mm110) REVERT: G 364 ILE cc_start: 0.8759 (tt) cc_final: 0.8520 (tt) REVERT: H 63 GLN cc_start: 0.8002 (pp30) cc_final: 0.7721 (pm20) REVERT: H 127 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7800 (ttmm) REVERT: H 130 ILE cc_start: 0.8905 (tp) cc_final: 0.8551 (tp) REVERT: H 166 GLU cc_start: 0.8379 (tp30) cc_final: 0.7755 (tp30) REVERT: H 202 ASN cc_start: 0.8936 (t0) cc_final: 0.8734 (t0) REVERT: H 210 LEU cc_start: 0.9323 (tp) cc_final: 0.9096 (tt) REVERT: H 212 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8630 (mp10) REVERT: H 244 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7893 (mtt180) REVERT: H 271 ILE cc_start: 0.9481 (tt) cc_final: 0.9218 (tt) REVERT: H 313 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8740 (ttmm) REVERT: H 344 GLN cc_start: 0.8970 (mm110) cc_final: 0.8701 (mm110) REVERT: H 364 ILE cc_start: 0.8602 (tt) cc_final: 0.8194 (tt) outliers start: 16 outliers final: 8 residues processed: 950 average time/residue: 0.3552 time to fit residues: 503.9424 Evaluate side-chains 731 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 723 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 225 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 134 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 73 ASN B 329 GLN C 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 73 ASN D 329 GLN E 73 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 73 ASN F 329 GLN G 73 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 73 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22920 Z= 0.197 Angle : 0.669 7.795 31216 Z= 0.345 Chirality : 0.042 0.167 3448 Planarity : 0.004 0.038 3832 Dihedral : 6.158 58.381 2960 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 5.77 % Allowed : 18.94 % Favored : 75.29 % 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: -2.71 (0.15), residues: 2640 helix: -0.45 (0.12), residues: 1728 sheet: -2.41 (0.42), residues: 144 loop : -4.82 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 59 HIS 0.002 0.001 HIS F 247 PHE 0.028 0.001 PHE B 242 TYR 0.025 0.002 TYR D 301 ARG 0.007 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 762 time to evaluate : 2.560 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: A 29 ARG cc_start: 0.8270 (mmp80) cc_final: 0.7591 (mmp80) REVERT: A 127 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7754 (ttmm) REVERT: A 130 ILE cc_start: 0.9000 (tp) cc_final: 0.8641 (tp) REVERT: A 166 GLU cc_start: 0.8789 (tp30) cc_final: 0.8471 (tp30) REVERT: A 244 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7610 (mtm-85) REVERT: A 328 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8695 (p0) REVERT: A 344 GLN cc_start: 0.8978 (mm110) cc_final: 0.8770 (mm110) REVERT: B 127 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7799 (ttmm) REVERT: B 130 ILE cc_start: 0.8864 (tp) cc_final: 0.8540 (tp) REVERT: B 199 GLN cc_start: 0.8774 (tp40) cc_final: 0.8404 (tt0) REVERT: B 244 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7904 (mtt180) REVERT: B 313 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8731 (pttp) REVERT: B 328 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8799 (p0) REVERT: B 342 MET cc_start: 0.8784 (mmm) cc_final: 0.8544 (mmm) REVERT: B 344 GLN cc_start: 0.8914 (mm110) cc_final: 0.8712 (mm110) REVERT: C 127 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7780 (ttmm) REVERT: C 130 ILE cc_start: 0.9004 (tp) cc_final: 0.8671 (tp) REVERT: C 153 ASP cc_start: 0.8399 (m-30) cc_final: 0.7982 (m-30) REVERT: C 213 LEU cc_start: 0.8453 (tp) cc_final: 0.8023 (tt) REVERT: C 328 ASP cc_start: 0.8974 (m-30) cc_final: 0.8715 (p0) REVERT: C 343 ASP cc_start: 0.8312 (t70) cc_final: 0.8042 (t70) REVERT: C 344 GLN cc_start: 0.8946 (mm110) cc_final: 0.8693 (mm110) REVERT: D 127 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7806 (ttmm) REVERT: D 130 ILE cc_start: 0.8998 (tp) cc_final: 0.8662 (tp) REVERT: D 202 ASN cc_start: 0.8717 (t0) cc_final: 0.8487 (t0) REVERT: D 244 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7669 (mtm-85) REVERT: D 328 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8819 (p0) REVERT: D 342 MET cc_start: 0.8798 (mmm) cc_final: 0.8586 (mmm) REVERT: E 213 LEU cc_start: 0.8441 (tp) cc_final: 0.8130 (tp) REVERT: E 328 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8685 (p0) REVERT: E 344 GLN cc_start: 0.8921 (mm110) cc_final: 0.8705 (mm110) REVERT: F 29 ARG cc_start: 0.8628 (mmp80) cc_final: 0.7857 (mmp80) REVERT: F 79 HIS cc_start: 0.8484 (t-90) cc_final: 0.8033 (t-90) REVERT: F 130 ILE cc_start: 0.8859 (tp) cc_final: 0.8523 (tp) REVERT: F 166 GLU cc_start: 0.8582 (tp30) cc_final: 0.7637 (tp30) REVERT: F 199 GLN cc_start: 0.8751 (tp40) cc_final: 0.8471 (tt0) REVERT: F 210 LEU cc_start: 0.9335 (tp) cc_final: 0.9051 (tt) REVERT: F 244 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7686 (mtt90) REVERT: F 328 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8774 (p0) REVERT: F 345 MET cc_start: 0.8857 (tpp) cc_final: 0.8602 (mmp) REVERT: F 364 ILE cc_start: 0.8322 (tt) cc_final: 0.7959 (tt) REVERT: G 344 GLN cc_start: 0.8913 (mm110) cc_final: 0.8698 (mm110) REVERT: H 29 ARG cc_start: 0.8571 (mmp80) cc_final: 0.7822 (mmp80) REVERT: H 65 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7230 (p0) REVERT: H 127 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7728 (ttmm) REVERT: H 130 ILE cc_start: 0.8850 (tp) cc_final: 0.8519 (tp) REVERT: H 199 GLN cc_start: 0.8760 (tp40) cc_final: 0.8474 (tt0) REVERT: H 210 LEU cc_start: 0.9324 (tp) cc_final: 0.9046 (tt) REVERT: H 244 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7658 (mtm-85) REVERT: H 313 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8716 (ttmm) REVERT: H 328 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8752 (p0) REVERT: H 342 MET cc_start: 0.8727 (mmm) cc_final: 0.8465 (mmm) outliers start: 138 outliers final: 90 residues processed: 806 average time/residue: 0.3159 time to fit residues: 397.0155 Evaluate side-chains 779 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 682 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 199 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 348 ASN B 294 ASN C 199 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN D 294 ASN E 199 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN E 348 ASN F 348 ASN G 73 ASN G 199 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 348 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22920 Z= 0.328 Angle : 0.707 13.022 31216 Z= 0.366 Chirality : 0.045 0.216 3448 Planarity : 0.004 0.034 3832 Dihedral : 6.127 55.117 2960 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 7.78 % Allowed : 21.66 % Favored : 70.57 % 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: -2.11 (0.16), residues: 2640 helix: 0.00 (0.12), residues: 1752 sheet: -1.89 (0.44), residues: 144 loop : -4.79 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 59 HIS 0.006 0.002 HIS G 241 PHE 0.060 0.001 PHE B 242 TYR 0.019 0.002 TYR C 132 ARG 0.009 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 719 time to evaluate : 2.381 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: A 127 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7812 (ttmm) REVERT: A 274 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.5632 (mp0) REVERT: A 328 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8715 (p0) REVERT: A 344 GLN cc_start: 0.9006 (mm110) cc_final: 0.8772 (mm110) REVERT: B 29 ARG cc_start: 0.8429 (mmp80) cc_final: 0.7662 (mmp80) REVERT: B 65 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7176 (p0) REVERT: B 79 HIS cc_start: 0.8592 (t-90) cc_final: 0.8106 (t-90) REVERT: B 127 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7842 (ttmm) REVERT: B 130 ILE cc_start: 0.8992 (tp) cc_final: 0.8609 (tp) REVERT: B 178 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8316 (ttp80) REVERT: B 199 GLN cc_start: 0.8799 (tp40) cc_final: 0.8409 (tt0) REVERT: B 210 LEU cc_start: 0.9270 (tp) cc_final: 0.8994 (tt) REVERT: B 244 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8083 (mtt180) REVERT: B 313 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8718 (ttmm) REVERT: B 328 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8784 (p0) REVERT: C 127 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7836 (ttmm) REVERT: C 213 LEU cc_start: 0.8605 (tp) cc_final: 0.8383 (tp) REVERT: C 343 ASP cc_start: 0.8270 (t70) cc_final: 0.7973 (t70) REVERT: C 344 GLN cc_start: 0.8991 (mm110) cc_final: 0.8747 (mm110) REVERT: D 29 ARG cc_start: 0.8386 (mmp80) cc_final: 0.7644 (mmp80) REVERT: D 127 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7797 (ttmm) REVERT: D 130 ILE cc_start: 0.8982 (tp) cc_final: 0.8634 (tp) REVERT: D 199 GLN cc_start: 0.8823 (tp40) cc_final: 0.8369 (tt0) REVERT: D 202 ASN cc_start: 0.8774 (t0) cc_final: 0.8553 (t0) REVERT: D 244 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7838 (mtt90) REVERT: D 274 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.5891 (mp0) REVERT: E 274 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.5750 (mp0) REVERT: E 328 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8740 (p0) REVERT: E 344 GLN cc_start: 0.8986 (mm110) cc_final: 0.8756 (mm110) REVERT: F 130 ILE cc_start: 0.8908 (tp) cc_final: 0.8508 (tp) REVERT: F 166 GLU cc_start: 0.8529 (tp30) cc_final: 0.7628 (tp30) REVERT: F 199 GLN cc_start: 0.8764 (tp40) cc_final: 0.8492 (tt0) REVERT: F 210 LEU cc_start: 0.9389 (tp) cc_final: 0.9179 (tt) REVERT: F 274 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.5757 (mp0) REVERT: F 328 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8759 (p0) REVERT: F 364 ILE cc_start: 0.8431 (tt) cc_final: 0.8099 (tt) REVERT: G 274 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.5641 (mp0) REVERT: H 65 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7084 (p0) REVERT: H 127 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7820 (ttmm) REVERT: H 130 ILE cc_start: 0.8924 (tp) cc_final: 0.8561 (tp) REVERT: H 166 GLU cc_start: 0.8451 (tp30) cc_final: 0.7665 (tp30) REVERT: H 199 GLN cc_start: 0.8779 (tp40) cc_final: 0.8460 (tt0) REVERT: H 210 LEU cc_start: 0.9373 (tp) cc_final: 0.9153 (tt) REVERT: H 274 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: H 313 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8745 (ttmm) REVERT: H 342 MET cc_start: 0.8734 (mmm) cc_final: 0.8519 (mmm) REVERT: H 364 ILE cc_start: 0.8221 (tp) cc_final: 0.8017 (tp) outliers start: 186 outliers final: 139 residues processed: 782 average time/residue: 0.3003 time to fit residues: 374.6646 Evaluate side-chains 800 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 649 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 277 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN D 79 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 79 HIS F 348 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22920 Z= 0.255 Angle : 0.658 10.137 31216 Z= 0.339 Chirality : 0.043 0.189 3448 Planarity : 0.003 0.035 3832 Dihedral : 5.855 53.608 2960 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 7.73 % Allowed : 24.25 % Favored : 68.02 % 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: -1.54 (0.17), residues: 2640 helix: 0.45 (0.13), residues: 1744 sheet: -1.75 (0.45), residues: 144 loop : -4.53 (0.17), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 107 HIS 0.007 0.001 HIS F 79 PHE 0.053 0.001 PHE B 242 TYR 0.021 0.002 TYR B 82 ARG 0.006 0.001 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 686 time to evaluate : 2.579 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: A 69 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 179 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8932 (tp) REVERT: A 274 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.5566 (mp0) REVERT: A 328 ASP cc_start: 0.9108 (m-30) cc_final: 0.8743 (p0) REVERT: A 344 GLN cc_start: 0.8966 (mm110) cc_final: 0.8753 (mm110) REVERT: A 345 MET cc_start: 0.8485 (mmp) cc_final: 0.8135 (mmm) REVERT: B 29 ARG cc_start: 0.8354 (mmp80) cc_final: 0.7829 (mmp80) REVERT: B 65 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7210 (p0) REVERT: B 69 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8520 (t) REVERT: B 79 HIS cc_start: 0.8545 (t-90) cc_final: 0.8039 (t-90) REVERT: B 127 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7815 (ttmm) REVERT: B 130 ILE cc_start: 0.8957 (tp) cc_final: 0.8583 (tp) REVERT: B 178 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8329 (ttp80) REVERT: B 199 GLN cc_start: 0.8745 (tp40) cc_final: 0.8485 (tt0) REVERT: B 210 LEU cc_start: 0.9240 (tp) cc_final: 0.8992 (tt) REVERT: B 244 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7787 (mtm-85) REVERT: B 328 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8804 (p0) REVERT: C 156 ASP cc_start: 0.8504 (p0) cc_final: 0.8281 (p0) REVERT: C 213 LEU cc_start: 0.8487 (tp) cc_final: 0.8077 (tt) REVERT: C 344 GLN cc_start: 0.8889 (mm110) cc_final: 0.8641 (mm110) REVERT: D 29 ARG cc_start: 0.8351 (mmp80) cc_final: 0.7840 (mmp80) REVERT: D 65 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.6890 (p0) REVERT: D 127 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7854 (ttmm) REVERT: D 130 ILE cc_start: 0.8964 (tp) cc_final: 0.8599 (tp) REVERT: D 199 GLN cc_start: 0.8777 (tp40) cc_final: 0.8459 (tt0) REVERT: D 202 ASN cc_start: 0.8778 (t0) cc_final: 0.8570 (t0) REVERT: D 244 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7943 (mtt180) REVERT: D 345 MET cc_start: 0.8912 (mmm) cc_final: 0.8401 (tpp) REVERT: E 69 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8438 (t) REVERT: E 274 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: E 328 ASP cc_start: 0.9121 (m-30) cc_final: 0.8736 (p0) REVERT: E 344 GLN cc_start: 0.8948 (mm110) cc_final: 0.8720 (mm110) REVERT: F 65 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.6871 (p0) REVERT: F 130 ILE cc_start: 0.8958 (tp) cc_final: 0.8587 (tp) REVERT: F 166 GLU cc_start: 0.8536 (tp30) cc_final: 0.7667 (tp30) REVERT: F 210 LEU cc_start: 0.9381 (tp) cc_final: 0.9137 (tt) REVERT: F 328 ASP cc_start: 0.9014 (m-30) cc_final: 0.8744 (p0) REVERT: F 345 MET cc_start: 0.8511 (mmt) cc_final: 0.8222 (tpp) REVERT: G 274 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: H 65 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7067 (p0) REVERT: H 127 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7813 (ttmm) REVERT: H 130 ILE cc_start: 0.8971 (tp) cc_final: 0.8583 (tp) REVERT: H 210 LEU cc_start: 0.9371 (tp) cc_final: 0.9141 (tt) REVERT: H 313 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8741 (ttmm) outliers start: 185 outliers final: 136 residues processed: 755 average time/residue: 0.2967 time to fit residues: 356.5640 Evaluate side-chains 783 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 635 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 229 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN C 348 ASN D 70 ASN D 79 HIS D 206 GLN F 70 ASN F 79 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22920 Z= 0.236 Angle : 0.639 9.304 31216 Z= 0.330 Chirality : 0.043 0.189 3448 Planarity : 0.003 0.034 3832 Dihedral : 5.535 49.048 2958 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 8.36 % Allowed : 24.46 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2640 helix: 0.67 (0.13), residues: 1752 sheet: -1.71 (0.44), residues: 144 loop : -4.25 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 59 HIS 0.006 0.001 HIS D 79 PHE 0.047 0.001 PHE B 242 TYR 0.016 0.001 TYR C 301 ARG 0.005 0.000 ARG G 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 668 time to evaluate : 2.452 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: A 69 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8476 (t) REVERT: A 130 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 244 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7885 (mtm-85) REVERT: A 274 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.5624 (mp0) REVERT: A 328 ASP cc_start: 0.9099 (m-30) cc_final: 0.8746 (p0) REVERT: A 344 GLN cc_start: 0.8972 (mm110) cc_final: 0.8745 (mm110) REVERT: B 65 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 69 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8494 (t) REVERT: B 127 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7801 (ttmm) REVERT: B 130 ILE cc_start: 0.8949 (tp) cc_final: 0.8582 (tp) REVERT: B 199 GLN cc_start: 0.8697 (tp40) cc_final: 0.8378 (tt0) REVERT: B 210 LEU cc_start: 0.9267 (tp) cc_final: 0.8978 (tt) REVERT: B 273 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: B 345 MET cc_start: 0.8251 (mmp) cc_final: 0.7989 (mmm) REVERT: C 344 GLN cc_start: 0.8894 (mm110) cc_final: 0.8648 (mm110) REVERT: D 29 ARG cc_start: 0.8320 (mmp80) cc_final: 0.8112 (mmp80) REVERT: D 65 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.6898 (p0) REVERT: D 127 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7832 (ttmm) REVERT: D 130 ILE cc_start: 0.8953 (tp) cc_final: 0.8593 (tp) REVERT: D 155 ASP cc_start: 0.8350 (t0) cc_final: 0.8012 (t0) REVERT: D 199 GLN cc_start: 0.8754 (tp40) cc_final: 0.8418 (tt0) REVERT: D 328 ASP cc_start: 0.9004 (m-30) cc_final: 0.8791 (p0) REVERT: E 69 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8414 (t) REVERT: E 130 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8573 (tp) REVERT: E 179 LEU cc_start: 0.9233 (tp) cc_final: 0.8992 (tp) REVERT: E 274 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.5635 (mp0) REVERT: E 328 ASP cc_start: 0.9107 (m-30) cc_final: 0.8731 (p0) REVERT: E 344 GLN cc_start: 0.8953 (mm110) cc_final: 0.8714 (mm110) REVERT: E 345 MET cc_start: 0.8517 (mmp) cc_final: 0.8107 (mmm) REVERT: F 65 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.6842 (p0) REVERT: F 130 ILE cc_start: 0.8975 (tp) cc_final: 0.8586 (tp) REVERT: F 210 LEU cc_start: 0.9368 (tp) cc_final: 0.9090 (tt) REVERT: F 214 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7149 (mm) REVERT: F 284 LEU cc_start: 0.9230 (mt) cc_final: 0.8981 (mt) REVERT: F 328 ASP cc_start: 0.9003 (m-30) cc_final: 0.8736 (p0) REVERT: F 345 MET cc_start: 0.8496 (mmt) cc_final: 0.8213 (tpp) REVERT: G 130 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8522 (tp) REVERT: G 274 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.5487 (mp0) REVERT: H 65 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.6939 (p0) REVERT: H 210 LEU cc_start: 0.9352 (tp) cc_final: 0.9060 (tt) REVERT: H 313 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8734 (ttmm) REVERT: H 328 ASP cc_start: 0.9023 (m-30) cc_final: 0.8769 (p0) outliers start: 200 outliers final: 144 residues processed: 751 average time/residue: 0.2863 time to fit residues: 344.9615 Evaluate side-chains 780 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 621 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 277 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 337 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 255 optimal weight: 0.3980 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN C 294 ASN C 348 ASN D 79 HIS F 79 HIS F 206 GLN G 73 ASN G 348 ASN H 79 HIS H 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22920 Z= 0.361 Angle : 0.717 11.376 31216 Z= 0.369 Chirality : 0.045 0.175 3448 Planarity : 0.003 0.033 3832 Dihedral : 5.662 42.844 2957 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 9.78 % Allowed : 23.70 % Favored : 66.51 % 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: -1.37 (0.17), residues: 2640 helix: 0.63 (0.13), residues: 1760 sheet: -3.47 (0.44), residues: 96 loop : -4.27 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP G 59 HIS 0.006 0.002 HIS H 79 PHE 0.061 0.001 PHE B 242 TYR 0.019 0.002 TYR H 82 ARG 0.007 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 623 time to evaluate : 2.515 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: A 130 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 274 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: A 328 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8726 (p0) REVERT: A 344 GLN cc_start: 0.9011 (mm110) cc_final: 0.8767 (mm110) REVERT: B 65 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.6898 (p0) REVERT: B 69 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8567 (t) REVERT: B 127 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7804 (ttmm) REVERT: B 130 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 199 GLN cc_start: 0.8778 (tp40) cc_final: 0.8498 (tt0) REVERT: B 210 LEU cc_start: 0.9304 (tp) cc_final: 0.9023 (tt) REVERT: B 236 TRP cc_start: 0.8669 (p90) cc_final: 0.8289 (p90) REVERT: B 244 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7294 (mtm-85) REVERT: B 273 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: B 345 MET cc_start: 0.8440 (mmp) cc_final: 0.8197 (mmm) REVERT: C 59 TRP cc_start: 0.8210 (t-100) cc_final: 0.7777 (t-100) REVERT: C 130 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8570 (tp) REVERT: C 213 LEU cc_start: 0.8605 (tp) cc_final: 0.8358 (tp) REVERT: C 344 GLN cc_start: 0.8932 (mm110) cc_final: 0.8688 (mm110) REVERT: D 127 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7871 (ttmm) REVERT: D 130 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8565 (tp) REVERT: D 199 GLN cc_start: 0.8807 (tp40) cc_final: 0.8435 (tt0) REVERT: D 244 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7965 (mtt180) REVERT: D 274 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.5945 (mp0) REVERT: D 328 ASP cc_start: 0.9032 (m-30) cc_final: 0.8770 (p0) REVERT: E 69 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8539 (t) REVERT: E 130 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8590 (tp) REVERT: E 135 TYR cc_start: 0.8920 (t80) cc_final: 0.8621 (t80) REVERT: E 274 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.5679 (mp0) REVERT: E 328 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8736 (p0) REVERT: E 344 GLN cc_start: 0.8978 (mm110) cc_final: 0.8737 (mm110) REVERT: F 130 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8481 (tp) REVERT: F 210 LEU cc_start: 0.9409 (tp) cc_final: 0.9175 (tt) REVERT: F 284 LEU cc_start: 0.9256 (mt) cc_final: 0.9012 (mt) REVERT: F 328 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (p0) REVERT: G 130 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8565 (tp) REVERT: G 274 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.5612 (mp0) REVERT: H 65 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.6902 (p0) REVERT: H 130 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8514 (tp) REVERT: H 210 LEU cc_start: 0.9394 (tp) cc_final: 0.9155 (tt) REVERT: H 313 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8655 (ttmm) outliers start: 234 outliers final: 176 residues processed: 730 average time/residue: 0.2916 time to fit residues: 341.4010 Evaluate side-chains 772 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 576 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 277 PHE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 337 ASP Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 73 ASN B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 329 GLN F 73 ASN F 79 HIS H 70 ASN H 73 ASN H 79 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22920 Z= 0.201 Angle : 0.666 11.569 31216 Z= 0.338 Chirality : 0.042 0.191 3448 Planarity : 0.003 0.034 3832 Dihedral : 5.207 28.628 2954 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 6.15 % Allowed : 27.72 % Favored : 66.14 % 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: -0.75 (0.17), residues: 2640 helix: 0.99 (0.13), residues: 1752 sheet: -1.42 (0.46), residues: 144 loop : -4.08 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 68 HIS 0.006 0.001 HIS F 79 PHE 0.023 0.001 PHE B 242 TYR 0.020 0.001 TYR H 82 ARG 0.004 0.000 ARG F 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 667 time to evaluate : 2.379 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: A 69 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8453 (t) REVERT: A 130 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 244 ARG cc_start: 0.8321 (mtt180) cc_final: 0.7901 (mtm-85) REVERT: A 274 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: A 328 ASP cc_start: 0.9075 (m-30) cc_final: 0.8744 (p0) REVERT: B 65 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7152 (p0) REVERT: B 69 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8421 (t) REVERT: B 127 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7790 (ttmm) REVERT: B 130 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8564 (tp) REVERT: B 199 GLN cc_start: 0.8668 (tp40) cc_final: 0.8451 (tt0) REVERT: B 210 LEU cc_start: 0.9266 (tp) cc_final: 0.8978 (tt) REVERT: B 273 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: C 59 TRP cc_start: 0.7994 (t-100) cc_final: 0.7748 (t-100) REVERT: C 130 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 345 MET cc_start: 0.8462 (mmp) cc_final: 0.8088 (mmm) REVERT: D 65 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.6781 (p0) REVERT: D 127 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7883 (ttmm) REVERT: D 130 ILE cc_start: 0.8936 (tp) cc_final: 0.8592 (tp) REVERT: D 199 GLN cc_start: 0.8425 (tp40) cc_final: 0.8223 (tt0) REVERT: D 244 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7715 (mtm-85) REVERT: D 328 ASP cc_start: 0.9036 (m-30) cc_final: 0.8778 (p0) REVERT: D 345 MET cc_start: 0.8297 (mmp) cc_final: 0.8056 (mmm) REVERT: E 69 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8406 (t) REVERT: E 130 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8626 (tp) REVERT: E 212 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7933 (mp10) REVERT: E 274 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: E 328 ASP cc_start: 0.9083 (m-30) cc_final: 0.8731 (p0) REVERT: E 344 GLN cc_start: 0.8962 (mm110) cc_final: 0.8694 (mm110) REVERT: F 65 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.6717 (p0) REVERT: F 130 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8569 (tp) REVERT: F 210 LEU cc_start: 0.9345 (tp) cc_final: 0.9047 (tt) REVERT: F 310 LYS cc_start: 0.8633 (tppt) cc_final: 0.8301 (tptp) REVERT: F 328 ASP cc_start: 0.9033 (m-30) cc_final: 0.8741 (p0) REVERT: G 130 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8565 (tp) REVERT: G 274 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.5555 (mp0) REVERT: H 65 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.6820 (p0) REVERT: H 82 TYR cc_start: 0.8398 (p90) cc_final: 0.8017 (p90) REVERT: H 130 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8547 (tp) REVERT: H 210 LEU cc_start: 0.9341 (tp) cc_final: 0.9040 (tt) REVERT: H 313 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8729 (ttmm) REVERT: H 328 ASP cc_start: 0.8998 (m-30) cc_final: 0.8745 (p0) REVERT: H 345 MET cc_start: 0.8887 (mmm) cc_final: 0.8348 (tpp) outliers start: 147 outliers final: 100 residues processed: 728 average time/residue: 0.2928 time to fit residues: 343.6467 Evaluate side-chains 740 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 621 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 PHE Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 337 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN C 348 ASN D 79 HIS E 79 HIS F 79 HIS F 294 ASN H 79 HIS H 294 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22920 Z= 0.206 Angle : 0.682 11.336 31216 Z= 0.341 Chirality : 0.043 0.201 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.068 19.994 2952 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.98 % Allowed : 28.89 % Favored : 65.13 % 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: -0.60 (0.17), residues: 2640 helix: 1.13 (0.13), residues: 1720 sheet: -1.31 (0.45), residues: 144 loop : -3.90 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 59 HIS 0.007 0.001 HIS B 79 PHE 0.026 0.001 PHE B 242 TYR 0.020 0.001 TYR H 82 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 666 time to evaluate : 2.759 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: A 69 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8508 (t) REVERT: A 130 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8512 (tp) REVERT: A 182 LYS cc_start: 0.8541 (tptt) cc_final: 0.8249 (tptt) REVERT: A 244 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7926 (mtm-85) REVERT: A 274 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.5627 (mp0) REVERT: A 328 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8713 (p0) REVERT: A 329 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8129 (mp10) REVERT: B 65 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7081 (p0) REVERT: B 69 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8551 (t) REVERT: B 127 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7789 (ttmm) REVERT: B 130 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8567 (tp) REVERT: B 182 LYS cc_start: 0.8650 (tptt) cc_final: 0.8422 (tptt) REVERT: B 210 LEU cc_start: 0.9311 (tp) cc_final: 0.9011 (tt) REVERT: B 273 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: B 310 LYS cc_start: 0.8660 (tppt) cc_final: 0.8305 (tptp) REVERT: C 59 TRP cc_start: 0.7992 (t-100) cc_final: 0.7697 (t-100) REVERT: C 130 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8501 (tp) REVERT: C 182 LYS cc_start: 0.8445 (tptt) cc_final: 0.8183 (tptt) REVERT: C 329 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: D 65 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6653 (p0) REVERT: D 127 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7867 (ttmm) REVERT: D 130 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8585 (tp) REVERT: D 310 LYS cc_start: 0.8683 (tppt) cc_final: 0.8318 (tptp) REVERT: D 328 ASP cc_start: 0.9033 (m-30) cc_final: 0.8780 (p0) REVERT: D 345 MET cc_start: 0.8295 (mmp) cc_final: 0.8051 (mmm) REVERT: E 69 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8507 (t) REVERT: E 130 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8462 (tp) REVERT: E 274 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.5515 (mp0) REVERT: E 305 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8204 (pttp) REVERT: E 328 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8646 (p0) REVERT: E 329 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8129 (mp10) REVERT: E 344 GLN cc_start: 0.8961 (mm110) cc_final: 0.8730 (mm110) REVERT: F 65 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.6692 (p0) REVERT: F 130 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8482 (tp) REVERT: F 210 LEU cc_start: 0.9355 (tp) cc_final: 0.9041 (tt) REVERT: F 248 CYS cc_start: 0.8053 (p) cc_final: 0.7818 (p) REVERT: F 328 ASP cc_start: 0.9015 (m-30) cc_final: 0.8760 (p0) REVERT: F 345 MET cc_start: 0.8155 (mmp) cc_final: 0.7954 (mmm) REVERT: G 130 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8525 (tp) REVERT: G 274 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.5508 (mp0) REVERT: H 65 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.6807 (p0) REVERT: H 82 TYR cc_start: 0.8515 (p90) cc_final: 0.8085 (p90) REVERT: H 130 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8569 (tp) REVERT: H 210 LEU cc_start: 0.9372 (tp) cc_final: 0.9114 (tt) REVERT: H 328 ASP cc_start: 0.8989 (m-30) cc_final: 0.8744 (p0) outliers start: 143 outliers final: 102 residues processed: 734 average time/residue: 0.2952 time to fit residues: 345.8058 Evaluate side-chains 760 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 633 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 PHE Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 224 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 329 GLN A 348 ASN B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN C 348 ASN D 79 HIS E 329 GLN E 348 ASN F 79 HIS G 348 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22920 Z= 0.195 Angle : 0.696 11.353 31216 Z= 0.345 Chirality : 0.043 0.202 3448 Planarity : 0.003 0.033 3832 Dihedral : 4.951 20.198 2952 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.81 % Allowed : 28.68 % Favored : 65.51 % 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: -0.45 (0.17), residues: 2640 helix: 1.19 (0.13), residues: 1744 sheet: -1.21 (0.46), residues: 144 loop : -3.88 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 59 HIS 0.007 0.001 HIS B 79 PHE 0.021 0.001 PHE B 242 TYR 0.020 0.001 TYR H 82 ARG 0.006 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 665 time to evaluate : 2.548 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: A 69 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8471 (t) REVERT: A 130 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 244 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7921 (mtm-85) REVERT: A 274 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: A 328 ASP cc_start: 0.9035 (m-30) cc_final: 0.8707 (p0) REVERT: B 28 ASP cc_start: 0.8484 (m-30) cc_final: 0.8165 (m-30) REVERT: B 65 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.6973 (p0) REVERT: B 69 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8470 (t) REVERT: B 127 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7765 (ttmm) REVERT: B 130 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8560 (tp) REVERT: B 182 LYS cc_start: 0.8667 (tptt) cc_final: 0.8256 (tppt) REVERT: B 210 LEU cc_start: 0.9274 (tp) cc_final: 0.9005 (tt) REVERT: B 273 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: B 310 LYS cc_start: 0.8669 (tppt) cc_final: 0.8336 (tptp) REVERT: B 345 MET cc_start: 0.8341 (mmp) cc_final: 0.8131 (mmm) REVERT: C 130 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8489 (tp) REVERT: C 300 TYR cc_start: 0.8483 (t80) cc_final: 0.8260 (t80) REVERT: D 65 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6357 (p0) REVERT: D 127 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7836 (ttmm) REVERT: D 130 ILE cc_start: 0.8911 (tp) cc_final: 0.8571 (tp) REVERT: D 182 LYS cc_start: 0.8680 (tptt) cc_final: 0.8432 (tptt) REVERT: D 328 ASP cc_start: 0.9001 (m-30) cc_final: 0.8797 (p0) REVERT: D 345 MET cc_start: 0.8229 (mmp) cc_final: 0.7992 (mmm) REVERT: E 69 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8475 (t) REVERT: E 130 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8478 (tp) REVERT: E 178 ARG cc_start: 0.8425 (ttm170) cc_final: 0.8159 (ptp-110) REVERT: E 212 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: E 274 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5263 (mp0) REVERT: E 328 ASP cc_start: 0.9056 (m-30) cc_final: 0.8720 (p0) REVERT: E 344 GLN cc_start: 0.9011 (mm110) cc_final: 0.8772 (mm110) REVERT: F 65 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6389 (p0) REVERT: F 130 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8485 (tp) REVERT: F 248 CYS cc_start: 0.7853 (p) cc_final: 0.7547 (p) REVERT: F 328 ASP cc_start: 0.8996 (m-30) cc_final: 0.8755 (p0) REVERT: F 345 MET cc_start: 0.8296 (mmp) cc_final: 0.8040 (mmm) REVERT: G 28 ASP cc_start: 0.8582 (m-30) cc_final: 0.8324 (m-30) REVERT: G 130 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8492 (tp) REVERT: G 187 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7278 (p0) REVERT: G 274 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.5284 (mp0) REVERT: H 28 ASP cc_start: 0.8711 (m-30) cc_final: 0.8480 (m-30) REVERT: H 65 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.6953 (p0) REVERT: H 130 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8465 (tp) REVERT: H 210 LEU cc_start: 0.9370 (tp) cc_final: 0.9053 (tt) REVERT: H 248 CYS cc_start: 0.8081 (p) cc_final: 0.7740 (p) REVERT: H 328 ASP cc_start: 0.8990 (m-30) cc_final: 0.8765 (p0) outliers start: 139 outliers final: 105 residues processed: 726 average time/residue: 0.2869 time to fit residues: 334.4567 Evaluate side-chains 759 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 634 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 277 PHE Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 329 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.1980 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 0.3980 chunk 242 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 166 optimal weight: 0.0270 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 70 ASN B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 79 HIS E 329 GLN F 79 HIS H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22920 Z= 0.195 Angle : 0.712 11.066 31216 Z= 0.350 Chirality : 0.043 0.196 3448 Planarity : 0.003 0.034 3832 Dihedral : 4.877 19.915 2952 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.39 % Allowed : 29.35 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2640 helix: 1.22 (0.13), residues: 1728 sheet: -1.24 (0.45), residues: 144 loop : -3.74 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP C 59 HIS 0.007 0.001 HIS B 79 PHE 0.019 0.001 PHE A 64 TYR 0.017 0.001 TYR G 300 ARG 0.005 0.000 ARG D 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 651 time to evaluate : 2.537 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: A 69 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8497 (t) REVERT: A 130 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 274 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: A 327 ASP cc_start: 0.8239 (m-30) cc_final: 0.8031 (m-30) REVERT: A 328 ASP cc_start: 0.9052 (m-30) cc_final: 0.8719 (p0) REVERT: B 65 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.6898 (p0) REVERT: B 69 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8410 (t) REVERT: B 127 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7792 (ttmm) REVERT: B 130 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 182 LYS cc_start: 0.8681 (tptt) cc_final: 0.8283 (tppt) REVERT: B 210 LEU cc_start: 0.9290 (tp) cc_final: 0.9009 (tt) REVERT: B 273 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: B 310 LYS cc_start: 0.8688 (tppt) cc_final: 0.8363 (tptp) REVERT: B 345 MET cc_start: 0.8262 (mmp) cc_final: 0.8002 (mmm) REVERT: C 130 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 300 TYR cc_start: 0.8493 (t80) cc_final: 0.8275 (t80) REVERT: C 329 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: D 127 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7830 (ttmm) REVERT: D 130 ILE cc_start: 0.9026 (tp) cc_final: 0.8680 (tp) REVERT: D 182 LYS cc_start: 0.8645 (tptt) cc_final: 0.8396 (tptt) REVERT: D 345 MET cc_start: 0.8216 (mmp) cc_final: 0.7985 (mmm) REVERT: E 28 ASP cc_start: 0.8783 (m-30) cc_final: 0.8533 (m-30) REVERT: E 69 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8460 (t) REVERT: E 130 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 212 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: E 274 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5201 (mp0) REVERT: E 328 ASP cc_start: 0.8988 (m-30) cc_final: 0.8700 (p0) REVERT: E 344 GLN cc_start: 0.9011 (mm110) cc_final: 0.8767 (mm110) REVERT: F 130 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8475 (tp) REVERT: F 182 LYS cc_start: 0.8647 (tptt) cc_final: 0.8372 (tptt) REVERT: F 248 CYS cc_start: 0.7834 (p) cc_final: 0.7606 (p) REVERT: F 310 LYS cc_start: 0.8612 (tppt) cc_final: 0.8224 (tptp) REVERT: F 328 ASP cc_start: 0.8991 (m-30) cc_final: 0.8743 (p0) REVERT: F 345 MET cc_start: 0.8239 (mmp) cc_final: 0.7982 (mmm) REVERT: G 28 ASP cc_start: 0.8577 (m-30) cc_final: 0.8325 (m-30) REVERT: G 130 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8484 (tp) REVERT: G 187 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7120 (p0) REVERT: G 274 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5183 (mp0) REVERT: H 65 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6746 (p0) REVERT: H 130 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8464 (tp) REVERT: H 182 LYS cc_start: 0.8647 (tptt) cc_final: 0.8272 (tppt) REVERT: H 210 LEU cc_start: 0.9364 (tp) cc_final: 0.9084 (tt) REVERT: H 248 CYS cc_start: 0.7855 (p) cc_final: 0.7485 (p) REVERT: H 310 LYS cc_start: 0.8560 (tppt) cc_final: 0.8188 (tptp) REVERT: H 328 ASP cc_start: 0.8962 (m-30) cc_final: 0.8753 (p0) REVERT: H 345 MET cc_start: 0.8293 (mmp) cc_final: 0.8002 (mmm) outliers start: 129 outliers final: 101 residues processed: 704 average time/residue: 0.2890 time to fit residues: 325.7164 Evaluate side-chains 754 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 634 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 329 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 348 ASN B 79 HIS B 206 GLN C 329 GLN D 70 ASN D 79 HIS E 329 GLN E 348 ASN F 79 HIS G 348 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114391 restraints weight = 31191.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118378 restraints weight = 16827.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121119 restraints weight = 11240.478| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 22920 Z= 0.374 Angle : 0.773 11.677 31216 Z= 0.385 Chirality : 0.047 0.194 3448 Planarity : 0.004 0.038 3832 Dihedral : 5.189 21.493 2952 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 5.94 % Allowed : 29.14 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2640 helix: 1.14 (0.13), residues: 1720 sheet: -1.41 (0.45), residues: 144 loop : -3.84 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 59 HIS 0.006 0.002 HIS B 79 PHE 0.039 0.001 PHE B 242 TYR 0.018 0.002 TYR E 300 ARG 0.005 0.001 ARG C 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5873.12 seconds wall clock time: 105 minutes 28.29 seconds (6328.29 seconds total)