Starting phenix.real_space_refine on Mon Mar 18 07:19:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/03_2024/7w6s_32334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/03_2024/7w6s_32334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/03_2024/7w6s_32334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/03_2024/7w6s_32334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/03_2024/7w6s_32334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/03_2024/7w6s_32334.pdb" } resolution = 2.8 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= 0.002 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 136 5.16 5 C 13040 2.51 5 N 3408 2.21 5 O 3684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E ASP 178": "OD1" <-> "OD2" Residue "E ARG 226": "NH1" <-> "NH2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 267": "OD1" <-> "OD2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G ASP 178": "OD1" <-> "OD2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 267": "OD1" <-> "OD2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H ARG 139": "NH1" <-> "NH2" Residue "H ARG 171": "NH1" <-> "NH2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "H ARG 308": "NH1" <-> "NH2" Residue "H PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H GLU 473": "OE1" <-> "OE2" 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: 20268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Chain: "C" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Time building chain proxies: 10.66, per 1000 atoms: 0.53 Number of scatterers: 20268 At special positions: 0 Unit cell: (161.226, 161.226, 127.764, 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 136 16.00 O 3684 8.00 N 3408 7.00 C 13040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.25 Conformation dependent library (CDL) restraints added in 3.6 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.947A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.719A pdb=" N ASN A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.645A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.932A pdb=" N LYS A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.746A pdb=" N ASP A 267 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 268 " --> pdb=" O LEU A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 268' Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.610A pdb=" N ILE B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.531A pdb=" N GLU B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 203 removed outlier: 4.023A pdb=" N PHE B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.667A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.519A pdb=" N ILE B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Proline residue: B 269 - end of helix removed outlier: 3.632A pdb=" N GLY B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.004A pdb=" N ASP B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.914A pdb=" N ARG B 296 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.595A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 3.634A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 4.136A pdb=" N TRP B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 396 removed outlier: 3.847A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 446 removed outlier: 4.448A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.938A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.714A pdb=" N ASN C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.556A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.937A pdb=" N LYS C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.757A pdb=" N ASP C 267 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 268 " --> pdb=" O LEU C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.607A pdb=" N ILE D 128 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 179 through 203 removed outlier: 4.068A pdb=" N PHE D 191 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 removed outlier: 3.657A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.523A pdb=" N ILE D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 3.594A pdb=" N GLY D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.971A pdb=" N ASP D 281 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 292 Processing helix chain 'D' and resid 293 through 303 removed outlier: 3.927A pdb=" N ARG D 296 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.595A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 344 removed outlier: 3.631A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 4.135A pdb=" N TRP D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D 360 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 396 removed outlier: 3.846A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 446 removed outlier: 4.448A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 124 through 133 removed outlier: 3.924A pdb=" N LYS E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.752A pdb=" N ASN E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 Processing helix chain 'E' and resid 176 through 189 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.544A pdb=" N ILE E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 Processing helix chain 'E' and resid 246 through 255 removed outlier: 3.940A pdb=" N LYS E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.754A pdb=" N ASP E 267 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 268 " --> pdb=" O LEU E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 264 through 268' Processing helix chain 'F' and resid 8 through 16 Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.596A pdb=" N ILE F 128 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 133 through 148 Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.532A pdb=" N GLU F 174 " --> pdb=" O TRP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 203 removed outlier: 4.015A pdb=" N PHE F 191 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 192 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 222 through 247 removed outlier: 3.655A pdb=" N LEU F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 276 removed outlier: 3.514A pdb=" N ILE F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.632A pdb=" N GLY F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET F 276 " --> pdb=" O ILE F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.991A pdb=" N ASP F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 Processing helix chain 'F' and resid 293 through 303 removed outlier: 3.930A pdb=" N ARG F 296 " --> pdb=" O ARG F 293 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG F 302 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 317 removed outlier: 3.582A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 311 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 344 removed outlier: 3.653A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 366 removed outlier: 4.144A pdb=" N TRP F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR F 360 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 396 removed outlier: 3.876A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 446 removed outlier: 4.443A pdb=" N VAL F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'G' and resid 103 through 118 Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.969A pdb=" N LYS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.708A pdb=" N ASN G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 174 Processing helix chain 'G' and resid 176 through 189 Processing helix chain 'G' and resid 197 through 211 removed outlier: 3.613A pdb=" N ILE G 204 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 211 " --> pdb=" O SER G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 236 Processing helix chain 'G' and resid 246 through 255 removed outlier: 3.932A pdb=" N LYS G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 263 Processing helix chain 'G' and resid 264 through 268 removed outlier: 3.751A pdb=" N ASP G 267 " --> pdb=" O GLN G 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 268 " --> pdb=" O LEU G 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 264 through 268' Processing helix chain 'H' and resid 8 through 16 Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 90 through 100 Processing helix chain 'H' and resid 110 through 122 Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.621A pdb=" N ILE H 128 " --> pdb=" O PRO H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 166 through 174 removed outlier: 3.536A pdb=" N GLU H 174 " --> pdb=" O TRP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 203 removed outlier: 4.003A pdb=" N PHE H 191 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE H 192 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 222 through 247 removed outlier: 3.660A pdb=" N LEU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 276 removed outlier: 3.529A pdb=" N ILE H 261 " --> pdb=" O SER H 257 " (cutoff:3.500A) Proline residue: H 269 - end of helix removed outlier: 3.639A pdb=" N GLY H 273 " --> pdb=" O PRO H 269 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET H 276 " --> pdb=" O ILE H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 removed outlier: 4.004A pdb=" N ASP H 281 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 292 Processing helix chain 'H' and resid 293 through 303 removed outlier: 3.930A pdb=" N ARG H 296 " --> pdb=" O ARG H 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.636A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 311 " --> pdb=" O LEU H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 344 removed outlier: 3.648A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 366 removed outlier: 4.138A pdb=" N TRP H 359 " --> pdb=" O PRO H 355 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR H 360 " --> pdb=" O ALA H 356 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 396 removed outlier: 3.864A pdb=" N LEU H 389 " --> pdb=" O SER H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 446 removed outlier: 4.442A pdb=" N VAL H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS H 424 " --> pdb=" O ARG H 420 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 54 removed outlier: 3.595A pdb=" N GLU B 81 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'D' and resid 49 through 54 removed outlier: 3.617A pdb=" N GLU D 81 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'F' and resid 49 through 54 removed outlier: 3.607A pdb=" N GLU F 81 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'H' and resid 49 through 54 removed outlier: 3.552A pdb=" N GLU H 81 " --> pdb=" O ASN H 76 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3366 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: 5.61 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6460 1.34 - 1.46: 3692 1.46 - 1.57: 10380 1.57 - 1.69: 0 1.69 - 1.81: 212 Bond restraints: 20744 Sorted by residual: bond pdb=" C MET D 268 " pdb=" N PRO D 269 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.45e+00 bond pdb=" C MET H 268 " pdb=" N PRO H 269 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.41e+00 bond pdb=" C MET F 268 " pdb=" N PRO F 269 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.08e-02 8.57e+03 4.91e+00 bond pdb=" C MET B 268 " pdb=" N PRO B 269 " ideal model delta sigma weight residual 1.336 1.359 -0.024 1.08e-02 8.57e+03 4.78e+00 bond pdb=" C GLY E 213 " pdb=" O GLY E 213 " ideal model delta sigma weight residual 1.237 1.227 0.010 7.00e-03 2.04e+04 2.08e+00 ... (remaining 20739 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.51: 375 105.51 - 112.66: 10507 112.66 - 119.82: 7134 119.82 - 126.97: 9823 126.97 - 134.12: 189 Bond angle restraints: 28028 Sorted by residual: angle pdb=" N GLY C 121 " pdb=" CA GLY C 121 " pdb=" C GLY C 121 " ideal model delta sigma weight residual 113.18 104.70 8.48 2.37e+00 1.78e-01 1.28e+01 angle pdb=" N GLY E 121 " pdb=" CA GLY E 121 " pdb=" C GLY E 121 " ideal model delta sigma weight residual 113.18 104.72 8.46 2.37e+00 1.78e-01 1.27e+01 angle pdb=" N GLY A 121 " pdb=" CA GLY A 121 " pdb=" C GLY A 121 " ideal model delta sigma weight residual 113.18 104.73 8.45 2.37e+00 1.78e-01 1.27e+01 angle pdb=" N GLY G 121 " pdb=" CA GLY G 121 " pdb=" C GLY G 121 " ideal model delta sigma weight residual 113.18 104.79 8.39 2.37e+00 1.78e-01 1.25e+01 angle pdb=" N VAL B 22 " pdb=" CA VAL B 22 " pdb=" C VAL B 22 " ideal model delta sigma weight residual 112.80 108.85 3.95 1.15e+00 7.56e-01 1.18e+01 ... (remaining 28023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 11160 17.61 - 35.22: 1033 35.22 - 52.83: 136 52.83 - 70.44: 11 70.44 - 88.05: 16 Dihedral angle restraints: 12356 sinusoidal: 4996 harmonic: 7360 Sorted by residual: dihedral pdb=" CA GLY G 121 " pdb=" C GLY G 121 " pdb=" N ILE G 122 " pdb=" CA ILE G 122 " ideal model delta harmonic sigma weight residual -180.00 -143.86 -36.14 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA GLY E 121 " pdb=" C GLY E 121 " pdb=" N ILE E 122 " pdb=" CA ILE E 122 " ideal model delta harmonic sigma weight residual 180.00 -143.99 -36.01 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA GLY A 121 " pdb=" C GLY A 121 " pdb=" N ILE A 122 " pdb=" CA ILE A 122 " ideal model delta harmonic sigma weight residual -180.00 -144.09 -35.91 0 5.00e+00 4.00e-02 5.16e+01 ... (remaining 12353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1677 0.031 - 0.063: 915 0.063 - 0.094: 370 0.094 - 0.126: 82 0.126 - 0.157: 24 Chirality restraints: 3068 Sorted by residual: chirality pdb=" CG LEU D 44 " pdb=" CB LEU D 44 " pdb=" CD1 LEU D 44 " pdb=" CD2 LEU D 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CG LEU B 44 " pdb=" CB LEU B 44 " pdb=" CD1 LEU B 44 " pdb=" CD2 LEU B 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CG LEU F 44 " pdb=" CB LEU F 44 " pdb=" CD1 LEU F 44 " pdb=" CD2 LEU F 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 3065 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 217 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO E 218 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 218 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 218 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 217 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO G 218 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 218 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 218 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 354 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO D 355 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 355 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 355 " 0.028 5.00e-02 4.00e+02 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1757 2.73 - 3.27: 21825 3.27 - 3.82: 33309 3.82 - 4.36: 40298 4.36 - 4.90: 67372 Nonbonded interactions: 164561 Sorted by model distance: nonbonded pdb=" O GLU C 248 " pdb=" OG SER C 252 " model vdw 2.191 2.440 nonbonded pdb=" O GLU G 248 " pdb=" OG SER G 252 " model vdw 2.196 2.440 nonbonded pdb=" NH2 ARG A 104 " pdb=" OE1 GLU H 77 " model vdw 2.196 2.520 nonbonded pdb=" O GLU E 248 " pdb=" OG SER E 252 " model vdw 2.196 2.440 nonbonded pdb=" O GLU A 248 " pdb=" OG SER A 252 " model vdw 2.198 2.440 ... (remaining 164556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.020 Extract box with map and model: 5.340 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 53.420 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.950 ------------------------------------------------------------------------------- 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 : 0.005 0.042 20744 Z= 0.346 Angle : 0.675 8.484 28028 Z= 0.394 Chirality : 0.044 0.157 3068 Planarity : 0.005 0.050 3576 Dihedral : 13.599 88.051 7604 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.18 % Allowed : 5.34 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.03 (0.14), residues: 2476 helix: -1.49 (0.11), residues: 1668 sheet: None (None), residues: 0 loop : -2.89 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 359 HIS 0.005 0.001 HIS B 477 PHE 0.021 0.002 PHE A 165 TYR 0.024 0.002 TYR C 132 ARG 0.022 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 539 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8426 (mt0) cc_final: 0.8185 (mt0) REVERT: A 125 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 129 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8064 (mtmt) REVERT: A 133 SER cc_start: 0.8739 (m) cc_final: 0.8362 (m) REVERT: A 134 GLN cc_start: 0.8440 (mm110) cc_final: 0.8008 (mm110) REVERT: A 192 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7998 (mmmt) REVERT: B 29 LEU cc_start: 0.8178 (mm) cc_final: 0.7928 (tp) REVERT: B 130 ASP cc_start: 0.7677 (m-30) cc_final: 0.7468 (m-30) REVERT: B 276 MET cc_start: 0.7864 (mpp) cc_final: 0.7306 (mpt) REVERT: B 315 LYS cc_start: 0.8421 (tppt) cc_final: 0.8035 (tttt) REVERT: B 429 ARG cc_start: 0.7577 (ttp-170) cc_final: 0.7349 (mtm-85) REVERT: C 125 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7345 (tm-30) REVERT: C 129 LYS cc_start: 0.8395 (mtmt) cc_final: 0.8044 (mtmt) REVERT: C 133 SER cc_start: 0.8808 (m) cc_final: 0.8442 (m) REVERT: C 134 GLN cc_start: 0.8421 (mm110) cc_final: 0.7948 (mm110) REVERT: C 192 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7964 (mmmt) REVERT: D 29 LEU cc_start: 0.8174 (mm) cc_final: 0.7941 (tp) REVERT: D 130 ASP cc_start: 0.7675 (m-30) cc_final: 0.7472 (m-30) REVERT: D 315 LYS cc_start: 0.8394 (tppt) cc_final: 0.8023 (tttt) REVERT: E 125 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 129 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8019 (mtmt) REVERT: E 133 SER cc_start: 0.8724 (m) cc_final: 0.8337 (m) REVERT: E 134 GLN cc_start: 0.8409 (mm110) cc_final: 0.7963 (mm110) REVERT: E 192 LYS cc_start: 0.8403 (mmtm) cc_final: 0.7959 (mmmt) REVERT: E 232 PHE cc_start: 0.8253 (t80) cc_final: 0.7809 (t80) REVERT: F 29 LEU cc_start: 0.8170 (mm) cc_final: 0.7927 (tp) REVERT: F 315 LYS cc_start: 0.8395 (tppt) cc_final: 0.8044 (tttt) REVERT: F 429 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.7276 (mtm-85) REVERT: G 125 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7228 (tm-30) REVERT: G 129 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8000 (mtmt) REVERT: G 133 SER cc_start: 0.8727 (m) cc_final: 0.8354 (m) REVERT: G 134 GLN cc_start: 0.8430 (mm110) cc_final: 0.8004 (mm110) REVERT: G 192 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7990 (mmmt) REVERT: G 232 PHE cc_start: 0.8284 (t80) cc_final: 0.7961 (t80) REVERT: H 29 LEU cc_start: 0.8168 (mm) cc_final: 0.7915 (tp) REVERT: H 230 ASP cc_start: 0.8134 (p0) cc_final: 0.7925 (p0) REVERT: H 315 LYS cc_start: 0.8394 (tppt) cc_final: 0.8024 (tttt) outliers start: 4 outliers final: 0 residues processed: 543 average time/residue: 1.3447 time to fit residues: 816.8278 Evaluate side-chains 373 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 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 97 GLN A 182 ASN A 264 GLN B 278 ASN B 405 ASN B 443 HIS C 97 GLN C 182 ASN D 278 ASN D 405 ASN D 443 HIS E 97 GLN E 182 ASN F 278 ASN F 405 ASN F 443 HIS G 97 GLN G 182 ASN H 278 ASN H 405 ASN H 443 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20744 Z= 0.198 Angle : 0.634 13.089 28028 Z= 0.322 Chirality : 0.042 0.166 3068 Planarity : 0.005 0.046 3576 Dihedral : 5.035 34.303 2772 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.99 % Allowed : 15.53 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.88 (0.17), residues: 2476 helix: 0.12 (0.13), residues: 1664 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 54 HIS 0.009 0.001 HIS B 443 PHE 0.018 0.001 PHE E 165 TYR 0.021 0.001 TYR H 186 ARG 0.006 0.000 ARG H 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 445 time to evaluate : 2.408 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6805 (tm-30) REVERT: A 129 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7775 (mttt) REVERT: A 133 SER cc_start: 0.8583 (m) cc_final: 0.8253 (m) REVERT: A 134 GLN cc_start: 0.8186 (mm110) cc_final: 0.7973 (mm110) REVERT: A 232 PHE cc_start: 0.8118 (t80) cc_final: 0.7849 (t80) REVERT: A 241 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7206 (p0) REVERT: A 263 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7958 (tpp) REVERT: B 187 TYR cc_start: 0.8018 (m-10) cc_final: 0.7800 (m-10) REVERT: B 315 LYS cc_start: 0.8272 (tppt) cc_final: 0.7988 (ttmt) REVERT: C 125 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7002 (tm-30) REVERT: C 129 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7902 (mtpt) REVERT: C 133 SER cc_start: 0.8589 (m) cc_final: 0.8263 (m) REVERT: C 134 GLN cc_start: 0.8185 (mm110) cc_final: 0.7970 (mm110) REVERT: C 212 MET cc_start: 0.6866 (tpt) cc_final: 0.6611 (mmm) REVERT: C 226 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: C 263 MET cc_start: 0.8341 (ttm) cc_final: 0.7803 (tpp) REVERT: D 170 TRP cc_start: 0.7522 (t-100) cc_final: 0.7313 (t-100) REVERT: D 315 LYS cc_start: 0.8277 (tppt) cc_final: 0.7962 (ttmt) REVERT: E 125 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6971 (tm-30) REVERT: E 129 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7931 (mtmt) REVERT: E 133 SER cc_start: 0.8520 (m) cc_final: 0.8180 (m) REVERT: E 134 GLN cc_start: 0.8086 (mm110) cc_final: 0.7863 (mm110) REVERT: E 236 MET cc_start: 0.7468 (mtt) cc_final: 0.6853 (pp-130) REVERT: E 263 MET cc_start: 0.8400 (ttm) cc_final: 0.7888 (tpp) REVERT: F 21 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: F 315 LYS cc_start: 0.8292 (tppt) cc_final: 0.7972 (ttmt) REVERT: G 125 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7058 (tm-30) REVERT: G 129 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7947 (mtpt) REVERT: G 133 SER cc_start: 0.8576 (m) cc_final: 0.8249 (m) REVERT: G 212 MET cc_start: 0.6806 (tpt) cc_final: 0.6567 (mmm) REVERT: G 236 MET cc_start: 0.7587 (mtt) cc_final: 0.6789 (pp-130) REVERT: G 241 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7184 (p0) REVERT: G 263 MET cc_start: 0.8423 (ttm) cc_final: 0.7864 (tpp) REVERT: H 21 PRO cc_start: 0.8715 (Cg_exo) cc_final: 0.8475 (Cg_endo) REVERT: H 187 TYR cc_start: 0.8085 (m-10) cc_final: 0.7837 (m-10) REVERT: H 315 LYS cc_start: 0.8285 (tppt) cc_final: 0.7968 (ttmt) outliers start: 66 outliers final: 24 residues processed: 490 average time/residue: 1.2136 time to fit residues: 674.6483 Evaluate side-chains 406 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 379 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 241 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 443 HIS C 97 GLN C 264 GLN D 443 HIS E 97 GLN F 443 HIS G 97 GLN G 254 GLN H 443 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20744 Z= 0.190 Angle : 0.634 13.141 28028 Z= 0.315 Chirality : 0.041 0.156 3068 Planarity : 0.004 0.060 3576 Dihedral : 4.775 32.272 2772 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.58 % Allowed : 19.34 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.20 (0.17), residues: 2476 helix: 0.63 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.72 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.004 0.001 HIS H 477 PHE 0.016 0.001 PHE G 136 TYR 0.017 0.001 TYR D 186 ARG 0.006 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 439 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6935 (tm-30) REVERT: A 129 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8006 (mtpt) REVERT: A 133 SER cc_start: 0.8505 (m) cc_final: 0.8231 (m) REVERT: A 212 MET cc_start: 0.6916 (mmm) cc_final: 0.6652 (mmm) REVERT: A 226 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.8030 (mmm-85) REVERT: B 315 LYS cc_start: 0.8225 (tppt) cc_final: 0.7948 (ttmt) REVERT: C 129 LYS cc_start: 0.8310 (mtmt) cc_final: 0.8005 (mtpt) REVERT: C 130 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7627 (tp-100) REVERT: C 133 SER cc_start: 0.8558 (m) cc_final: 0.8239 (m) REVERT: C 134 GLN cc_start: 0.8162 (mm110) cc_final: 0.7943 (mm110) REVERT: C 163 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: C 212 MET cc_start: 0.6815 (tpt) cc_final: 0.6261 (mmm) REVERT: C 226 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.8032 (mmm-85) REVERT: D 20 MET cc_start: 0.8970 (mmt) cc_final: 0.8503 (mpm) REVERT: D 315 LYS cc_start: 0.8222 (tppt) cc_final: 0.7947 (ttmt) REVERT: E 125 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6868 (tm-30) REVERT: E 129 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7824 (mttt) REVERT: E 133 SER cc_start: 0.8460 (m) cc_final: 0.8191 (m) REVERT: E 192 LYS cc_start: 0.8699 (mppt) cc_final: 0.8490 (mmtm) REVERT: E 212 MET cc_start: 0.6781 (tpt) cc_final: 0.6568 (mmm) REVERT: E 232 PHE cc_start: 0.7969 (t80) cc_final: 0.7766 (t80) REVERT: F 315 LYS cc_start: 0.8262 (tppt) cc_final: 0.7989 (ttmt) REVERT: G 129 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8011 (mtpt) REVERT: G 133 SER cc_start: 0.8485 (m) cc_final: 0.8239 (m) REVERT: G 212 MET cc_start: 0.6852 (tpt) cc_final: 0.6123 (mmm) REVERT: G 226 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8032 (mmm-85) REVERT: G 254 GLN cc_start: 0.8713 (tp40) cc_final: 0.8499 (tp-100) REVERT: H 315 LYS cc_start: 0.8251 (tppt) cc_final: 0.7992 (ttmt) outliers start: 57 outliers final: 13 residues processed: 483 average time/residue: 1.2086 time to fit residues: 662.5573 Evaluate side-chains 396 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 382 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.0970 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 443 HIS B 478 HIS C 97 GLN C 186 ASN C 264 GLN D 177 HIS D 443 HIS D 478 HIS E 97 GLN F 177 HIS F 443 HIS F 478 HIS G 97 GLN H 443 HIS H 478 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20744 Z= 0.168 Angle : 0.622 12.314 28028 Z= 0.306 Chirality : 0.040 0.160 3068 Planarity : 0.004 0.051 3576 Dihedral : 4.575 30.034 2772 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.90 % Allowed : 21.51 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.21 (0.17), residues: 2476 helix: 0.94 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.57 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 54 HIS 0.015 0.001 HIS H 478 PHE 0.013 0.001 PHE E 165 TYR 0.016 0.001 TYR H 186 ARG 0.008 0.000 ARG H 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 426 time to evaluate : 2.187 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7888 (mmtm) REVERT: A 129 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7910 (mttt) REVERT: A 133 SER cc_start: 0.8443 (m) cc_final: 0.8118 (m) REVERT: A 163 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: A 226 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7997 (mmm-85) REVERT: A 236 MET cc_start: 0.6728 (pp-130) cc_final: 0.6528 (pp-130) REVERT: A 260 MET cc_start: 0.8259 (mpp) cc_final: 0.7960 (mmt) REVERT: B 238 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8726 (p) REVERT: B 268 MET cc_start: 0.8015 (ptp) cc_final: 0.7764 (ptm) REVERT: B 315 LYS cc_start: 0.8201 (tppt) cc_final: 0.7918 (ttmt) REVERT: C 130 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7721 (tp-100) REVERT: C 133 SER cc_start: 0.8453 (m) cc_final: 0.8132 (m) REVERT: C 163 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: C 212 MET cc_start: 0.6761 (tpt) cc_final: 0.6342 (mmm) REVERT: C 226 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8026 (mmm-85) REVERT: C 260 MET cc_start: 0.8279 (mpp) cc_final: 0.7752 (mmt) REVERT: D 20 MET cc_start: 0.8930 (mmt) cc_final: 0.8587 (mpm) REVERT: D 268 MET cc_start: 0.8020 (ptp) cc_final: 0.7800 (ptm) REVERT: D 315 LYS cc_start: 0.8260 (tppt) cc_final: 0.7969 (ttmt) REVERT: E 105 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7794 (mmtp) REVERT: E 129 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7940 (mttt) REVERT: E 133 SER cc_start: 0.8438 (m) cc_final: 0.8100 (m) REVERT: E 212 MET cc_start: 0.6721 (tpt) cc_final: 0.6256 (mmm) REVERT: E 226 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7955 (mmm-85) REVERT: F 20 MET cc_start: 0.8925 (mmt) cc_final: 0.8560 (mpm) REVERT: F 27 MET cc_start: 0.7356 (tmt) cc_final: 0.6956 (tmt) REVERT: F 268 MET cc_start: 0.7674 (ptm) cc_final: 0.7370 (ptp) REVERT: F 315 LYS cc_start: 0.8235 (tppt) cc_final: 0.7953 (ttmt) REVERT: G 129 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7902 (mttt) REVERT: G 133 SER cc_start: 0.8424 (m) cc_final: 0.8076 (m) REVERT: G 212 MET cc_start: 0.6724 (tpt) cc_final: 0.6276 (mmm) REVERT: G 254 GLN cc_start: 0.8742 (tp40) cc_final: 0.8529 (tp-100) REVERT: H 20 MET cc_start: 0.8948 (mmt) cc_final: 0.8564 (mpm) REVERT: H 27 MET cc_start: 0.7342 (tmt) cc_final: 0.6933 (tmt) REVERT: H 315 LYS cc_start: 0.8195 (tppt) cc_final: 0.7938 (ttmt) REVERT: H 415 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7590 (ptp-110) outliers start: 64 outliers final: 28 residues processed: 474 average time/residue: 1.2316 time to fit residues: 660.6411 Evaluate side-chains 416 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 385 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 478 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 478 HIS C 97 GLN D 478 HIS E 97 GLN G 97 GLN H 478 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20744 Z= 0.239 Angle : 0.650 10.041 28028 Z= 0.320 Chirality : 0.042 0.160 3068 Planarity : 0.004 0.048 3576 Dihedral : 4.617 30.261 2772 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.80 % Allowed : 22.28 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2476 helix: 0.99 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.42 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.015 0.002 HIS D 478 PHE 0.017 0.002 PHE A 136 TYR 0.018 0.001 TYR H 186 ARG 0.009 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 400 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8225 (mmmm) cc_final: 0.7943 (mmtm) REVERT: A 125 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 129 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7832 (mttt) REVERT: A 133 SER cc_start: 0.8527 (m) cc_final: 0.8159 (m) REVERT: A 163 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 260 MET cc_start: 0.8252 (mpp) cc_final: 0.7645 (mmt) REVERT: B 20 MET cc_start: 0.8875 (mmt) cc_final: 0.8443 (mpm) REVERT: B 315 LYS cc_start: 0.8250 (tppt) cc_final: 0.7961 (ttmt) REVERT: C 105 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7889 (mmtm) REVERT: C 125 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7116 (tm-30) REVERT: C 129 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7941 (mttt) REVERT: C 130 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7817 (tp-100) REVERT: C 133 SER cc_start: 0.8612 (m) cc_final: 0.8252 (m) REVERT: C 163 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: C 212 MET cc_start: 0.6798 (tpt) cc_final: 0.6341 (mmm) REVERT: C 226 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8018 (mmm-85) REVERT: D 20 MET cc_start: 0.8909 (mmt) cc_final: 0.8549 (mpm) REVERT: D 268 MET cc_start: 0.7978 (ptp) cc_final: 0.7749 (ptm) REVERT: D 315 LYS cc_start: 0.8329 (tppt) cc_final: 0.8029 (ttmt) REVERT: E 105 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7891 (mmtm) REVERT: E 129 LYS cc_start: 0.8224 (mtmt) cc_final: 0.8016 (mtpt) REVERT: E 133 SER cc_start: 0.8525 (m) cc_final: 0.8186 (m) REVERT: E 157 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7868 (p0) REVERT: E 212 MET cc_start: 0.6681 (tpt) cc_final: 0.6241 (mmm) REVERT: E 226 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7971 (mmm-85) REVERT: E 260 MET cc_start: 0.8513 (mmt) cc_final: 0.7732 (mmt) REVERT: F 20 MET cc_start: 0.8944 (mmt) cc_final: 0.8577 (mpm) REVERT: F 183 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5584 (tt) REVERT: F 187 TYR cc_start: 0.7834 (m-10) cc_final: 0.7613 (m-10) REVERT: F 268 MET cc_start: 0.7663 (ptm) cc_final: 0.7359 (ptp) REVERT: F 315 LYS cc_start: 0.8345 (tppt) cc_final: 0.8012 (ttmt) REVERT: G 129 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7969 (mtpt) REVERT: G 133 SER cc_start: 0.8534 (m) cc_final: 0.8182 (m) REVERT: G 157 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7839 (p0) REVERT: G 212 MET cc_start: 0.6791 (tpt) cc_final: 0.6279 (mmm) REVERT: G 254 GLN cc_start: 0.8702 (tp40) cc_final: 0.8451 (tp-100) REVERT: G 260 MET cc_start: 0.8112 (mpp) cc_final: 0.7653 (mmt) REVERT: H 20 MET cc_start: 0.8905 (mmt) cc_final: 0.8521 (mpm) REVERT: H 268 MET cc_start: 0.7456 (ptm) cc_final: 0.7200 (ptp) REVERT: H 315 LYS cc_start: 0.8283 (tppt) cc_final: 0.7989 (ttmt) outliers start: 84 outliers final: 48 residues processed: 465 average time/residue: 1.2442 time to fit residues: 654.6715 Evaluate side-chains 432 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 379 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 437 SER Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 478 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 254 GLN B 478 HIS C 97 GLN C 264 GLN D 478 HIS E 97 GLN G 97 GLN H 478 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20744 Z= 0.176 Angle : 0.654 12.070 28028 Z= 0.317 Chirality : 0.040 0.231 3068 Planarity : 0.004 0.049 3576 Dihedral : 4.510 29.656 2772 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.12 % Allowed : 22.64 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2476 helix: 1.14 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.37 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.013 0.001 HIS B 478 PHE 0.019 0.001 PHE C 136 TYR 0.017 0.001 TYR D 186 ARG 0.011 0.000 ARG D 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 394 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8521 (m) cc_final: 0.8167 (m) REVERT: A 157 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7835 (p0) REVERT: A 199 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6484 (pp20) REVERT: A 260 MET cc_start: 0.8132 (mpp) cc_final: 0.7858 (mmt) REVERT: B 20 MET cc_start: 0.8841 (mmt) cc_final: 0.8478 (mpm) REVERT: B 315 LYS cc_start: 0.8247 (tppt) cc_final: 0.7947 (ttmt) REVERT: C 125 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6989 (tm-30) REVERT: C 129 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7937 (mttt) REVERT: C 130 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7901 (tp-100) REVERT: C 133 SER cc_start: 0.8631 (m) cc_final: 0.8293 (m) REVERT: C 157 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7896 (p0) REVERT: C 163 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: C 212 MET cc_start: 0.6771 (tpt) cc_final: 0.6398 (mmm) REVERT: C 226 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: C 260 MET cc_start: 0.8184 (mpp) cc_final: 0.7664 (mmt) REVERT: D 20 MET cc_start: 0.8882 (mmt) cc_final: 0.8561 (mpm) REVERT: D 315 LYS cc_start: 0.8279 (tppt) cc_final: 0.7980 (ttmt) REVERT: E 129 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7947 (mtpt) REVERT: E 133 SER cc_start: 0.8480 (m) cc_final: 0.8172 (m) REVERT: E 212 MET cc_start: 0.6729 (tpt) cc_final: 0.6241 (mmm) REVERT: F 20 MET cc_start: 0.8893 (mmt) cc_final: 0.8513 (mpm) REVERT: F 187 TYR cc_start: 0.7816 (m-10) cc_final: 0.7611 (m-10) REVERT: F 268 MET cc_start: 0.7584 (ptm) cc_final: 0.7290 (ptp) REVERT: F 315 LYS cc_start: 0.8305 (tppt) cc_final: 0.7997 (ttmt) REVERT: G 129 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7904 (mttt) REVERT: G 133 SER cc_start: 0.8533 (m) cc_final: 0.8197 (m) REVERT: G 212 MET cc_start: 0.6662 (tpt) cc_final: 0.6219 (mmm) REVERT: G 254 GLN cc_start: 0.8653 (tp40) cc_final: 0.8433 (tp-100) REVERT: G 260 MET cc_start: 0.8106 (mpp) cc_final: 0.7829 (mmt) REVERT: H 20 MET cc_start: 0.8892 (mmt) cc_final: 0.8551 (mpm) REVERT: H 268 MET cc_start: 0.7409 (ptm) cc_final: 0.7170 (ptp) REVERT: H 315 LYS cc_start: 0.8302 (tppt) cc_final: 0.8005 (ttmt) outliers start: 91 outliers final: 48 residues processed: 461 average time/residue: 1.1973 time to fit residues: 625.9631 Evaluate side-chains 419 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 367 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 478 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 198 optimal weight: 0.0670 chunk 131 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 254 GLN A 264 GLN B 478 HIS C 97 GLN C 254 GLN D 478 HIS E 97 GLN E 254 GLN G 97 GLN H 478 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20744 Z= 0.193 Angle : 0.698 15.299 28028 Z= 0.331 Chirality : 0.041 0.246 3068 Planarity : 0.004 0.049 3576 Dihedral : 4.446 28.472 2772 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.89 % Allowed : 23.46 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2476 helix: 1.20 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 54 HIS 0.008 0.001 HIS B 478 PHE 0.018 0.001 PHE C 136 TYR 0.019 0.001 TYR H 186 ARG 0.010 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 382 time to evaluate : 2.523 Fit side-chains REVERT: A 133 SER cc_start: 0.8523 (m) cc_final: 0.8193 (m) REVERT: A 157 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7828 (p0) REVERT: A 199 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6492 (pp20) REVERT: A 260 MET cc_start: 0.8278 (mpp) cc_final: 0.7528 (mmt) REVERT: B 20 MET cc_start: 0.8837 (mmt) cc_final: 0.8457 (mpm) REVERT: B 183 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5659 (tt) REVERT: B 259 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7365 (mtt) REVERT: B 315 LYS cc_start: 0.8232 (tppt) cc_final: 0.7940 (ttmt) REVERT: C 130 GLN cc_start: 0.8313 (tp-100) cc_final: 0.8049 (tp-100) REVERT: C 133 SER cc_start: 0.8584 (m) cc_final: 0.8271 (m) REVERT: C 157 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7878 (p0) REVERT: C 163 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: C 195 CYS cc_start: 0.7143 (p) cc_final: 0.6896 (p) REVERT: C 212 MET cc_start: 0.6808 (tpt) cc_final: 0.6415 (mmm) REVERT: C 217 TYR cc_start: 0.4520 (OUTLIER) cc_final: 0.2239 (m-80) REVERT: C 260 MET cc_start: 0.8123 (mpp) cc_final: 0.7819 (mmt) REVERT: C 261 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7960 (tmt170) REVERT: D 20 MET cc_start: 0.8894 (mmt) cc_final: 0.8582 (mpm) REVERT: D 315 LYS cc_start: 0.8272 (tppt) cc_final: 0.7974 (ttmt) REVERT: E 133 SER cc_start: 0.8492 (m) cc_final: 0.8205 (m) REVERT: E 212 MET cc_start: 0.6788 (tpt) cc_final: 0.6339 (mmm) REVERT: E 217 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.2365 (m-80) REVERT: E 260 MET cc_start: 0.8282 (mpp) cc_final: 0.7570 (mmt) REVERT: F 20 MET cc_start: 0.8948 (mmt) cc_final: 0.8579 (mpm) REVERT: F 183 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5583 (tt) REVERT: F 187 TYR cc_start: 0.7798 (m-10) cc_final: 0.7562 (m-10) REVERT: F 268 MET cc_start: 0.7549 (ptm) cc_final: 0.7252 (ptp) REVERT: F 315 LYS cc_start: 0.8288 (tppt) cc_final: 0.7983 (ttmt) REVERT: G 133 SER cc_start: 0.8525 (m) cc_final: 0.8218 (m) REVERT: G 199 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6512 (pp20) REVERT: G 212 MET cc_start: 0.6727 (tpt) cc_final: 0.6278 (mmm) REVERT: G 260 MET cc_start: 0.8204 (mpp) cc_final: 0.7580 (mmt) REVERT: H 20 MET cc_start: 0.8891 (mmt) cc_final: 0.8522 (mpm) REVERT: H 183 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.5630 (tt) REVERT: H 268 MET cc_start: 0.7407 (ptm) cc_final: 0.7157 (ptp) REVERT: H 315 LYS cc_start: 0.8299 (tppt) cc_final: 0.8003 (ttmt) outliers start: 86 outliers final: 51 residues processed: 446 average time/residue: 1.2528 time to fit residues: 636.5182 Evaluate side-chains 428 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 366 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 478 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 254 GLN B 478 HIS C 97 GLN C 264 GLN D 443 HIS D 478 HIS E 97 GLN G 97 GLN H 478 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20744 Z= 0.228 Angle : 0.726 18.431 28028 Z= 0.344 Chirality : 0.043 0.288 3068 Planarity : 0.005 0.049 3576 Dihedral : 4.450 28.997 2772 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.76 % Allowed : 24.37 % Favored : 71.88 % 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: 0.68 (0.17), residues: 2476 helix: 1.23 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.21 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 54 HIS 0.014 0.001 HIS B 478 PHE 0.018 0.001 PHE C 136 TYR 0.018 0.001 TYR B 186 ARG 0.011 0.001 ARG H 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 376 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8550 (m) cc_final: 0.8258 (m) REVERT: A 157 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 199 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6558 (pp20) REVERT: A 260 MET cc_start: 0.8198 (mpp) cc_final: 0.7867 (mmt) REVERT: B 20 MET cc_start: 0.8816 (mmt) cc_final: 0.8425 (mpm) REVERT: B 183 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.5654 (tt) REVERT: B 315 LYS cc_start: 0.8258 (tppt) cc_final: 0.7952 (ttmt) REVERT: B 431 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7496 (tmm-80) REVERT: C 129 LYS cc_start: 0.8286 (mtpt) cc_final: 0.8043 (mppt) REVERT: C 130 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8021 (tp-100) REVERT: C 133 SER cc_start: 0.8611 (m) cc_final: 0.8353 (m) REVERT: C 157 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7858 (p0) REVERT: C 195 CYS cc_start: 0.7169 (p) cc_final: 0.6920 (p) REVERT: C 212 MET cc_start: 0.6839 (tpt) cc_final: 0.6330 (mmm) REVERT: C 217 TYR cc_start: 0.4553 (OUTLIER) cc_final: 0.2263 (m-80) REVERT: C 260 MET cc_start: 0.8274 (mpp) cc_final: 0.7635 (mmt) REVERT: D 20 MET cc_start: 0.8897 (mmt) cc_final: 0.8471 (mpm) REVERT: D 315 LYS cc_start: 0.8307 (tppt) cc_final: 0.7998 (ttmt) REVERT: D 431 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7475 (tmm-80) REVERT: E 133 SER cc_start: 0.8455 (m) cc_final: 0.8210 (m) REVERT: E 212 MET cc_start: 0.6718 (tpt) cc_final: 0.6163 (mmm) REVERT: E 217 TYR cc_start: 0.4622 (OUTLIER) cc_final: 0.2317 (m-80) REVERT: F 20 MET cc_start: 0.8952 (mmt) cc_final: 0.8571 (mpm) REVERT: F 183 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5520 (tt) REVERT: F 187 TYR cc_start: 0.7810 (m-10) cc_final: 0.7586 (m-10) REVERT: F 268 MET cc_start: 0.7551 (ptm) cc_final: 0.7256 (ptp) REVERT: F 315 LYS cc_start: 0.8309 (tppt) cc_final: 0.7994 (ttmt) REVERT: G 133 SER cc_start: 0.8527 (m) cc_final: 0.8248 (m) REVERT: G 195 CYS cc_start: 0.7084 (p) cc_final: 0.6827 (p) REVERT: G 199 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6557 (pp20) REVERT: G 212 MET cc_start: 0.6748 (tpt) cc_final: 0.6276 (mmm) REVERT: G 260 MET cc_start: 0.8170 (mpp) cc_final: 0.7752 (mmt) REVERT: H 20 MET cc_start: 0.8892 (mmt) cc_final: 0.8519 (mpm) REVERT: H 183 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.5662 (tt) REVERT: H 268 MET cc_start: 0.7399 (ptm) cc_final: 0.7152 (ptp) REVERT: H 315 LYS cc_start: 0.8313 (tppt) cc_final: 0.8010 (ttmt) outliers start: 83 outliers final: 58 residues processed: 435 average time/residue: 1.1714 time to fit residues: 581.2544 Evaluate side-chains 433 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 366 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 478 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 0.0060 chunk 67 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 443 HIS B 478 HIS C 97 GLN D 443 HIS ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 254 GLN F 443 HIS G 97 GLN H 443 HIS ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20744 Z= 0.243 Angle : 0.733 16.232 28028 Z= 0.350 Chirality : 0.043 0.251 3068 Planarity : 0.005 0.049 3576 Dihedral : 4.506 28.825 2772 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.58 % Allowed : 24.86 % Favored : 71.56 % 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: 0.73 (0.17), residues: 2476 helix: 1.25 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 54 HIS 0.006 0.001 HIS F 477 PHE 0.017 0.001 PHE G 136 TYR 0.018 0.001 TYR H 186 ARG 0.010 0.001 ARG F 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 372 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8531 (m) cc_final: 0.8252 (m) REVERT: A 156 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7004 (m90) REVERT: A 157 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7777 (p0) REVERT: A 195 CYS cc_start: 0.7117 (p) cc_final: 0.6823 (p) REVERT: A 199 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6637 (pp20) REVERT: A 260 MET cc_start: 0.8250 (mpp) cc_final: 0.7451 (mmt) REVERT: B 20 MET cc_start: 0.8832 (mmt) cc_final: 0.8433 (mpm) REVERT: B 315 LYS cc_start: 0.8320 (tppt) cc_final: 0.7983 (ttmt) REVERT: B 431 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7545 (tmm-80) REVERT: C 129 LYS cc_start: 0.8279 (mtpt) cc_final: 0.8022 (mppt) REVERT: C 130 GLN cc_start: 0.8362 (tp-100) cc_final: 0.8070 (tp-100) REVERT: C 133 SER cc_start: 0.8654 (m) cc_final: 0.8414 (m) REVERT: C 157 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7799 (p0) REVERT: C 195 CYS cc_start: 0.7214 (p) cc_final: 0.6951 (p) REVERT: C 212 MET cc_start: 0.6823 (tpt) cc_final: 0.6198 (mmm) REVERT: C 217 TYR cc_start: 0.4621 (OUTLIER) cc_final: 0.2325 (m-80) REVERT: C 260 MET cc_start: 0.8151 (mpp) cc_final: 0.7643 (mmt) REVERT: D 315 LYS cc_start: 0.8364 (tppt) cc_final: 0.8023 (ttmt) REVERT: D 431 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7523 (tmm-80) REVERT: E 157 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7767 (p0) REVERT: E 212 MET cc_start: 0.6735 (tpt) cc_final: 0.6125 (mmm) REVERT: E 217 TYR cc_start: 0.4639 (OUTLIER) cc_final: 0.2338 (m-80) REVERT: E 260 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7657 (mmt) REVERT: F 20 MET cc_start: 0.8888 (mmt) cc_final: 0.8544 (mpm) REVERT: F 183 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5560 (tt) REVERT: F 187 TYR cc_start: 0.7798 (m-10) cc_final: 0.7535 (m-10) REVERT: F 268 MET cc_start: 0.7555 (ptm) cc_final: 0.7257 (ptp) REVERT: F 315 LYS cc_start: 0.8340 (tppt) cc_final: 0.8011 (ttmt) REVERT: G 133 SER cc_start: 0.8507 (m) cc_final: 0.8242 (m) REVERT: G 157 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.7831 (p0) REVERT: G 195 CYS cc_start: 0.7183 (p) cc_final: 0.6948 (p) REVERT: G 199 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6582 (pp20) REVERT: G 212 MET cc_start: 0.6764 (tpt) cc_final: 0.6197 (mmm) REVERT: G 260 MET cc_start: 0.8209 (mpp) cc_final: 0.7810 (mmt) REVERT: H 20 MET cc_start: 0.8871 (mmt) cc_final: 0.8499 (mpm) REVERT: H 183 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.5670 (tt) REVERT: H 268 MET cc_start: 0.7411 (ptm) cc_final: 0.7157 (ptp) REVERT: H 315 LYS cc_start: 0.8364 (tppt) cc_final: 0.8034 (ttmt) outliers start: 79 outliers final: 58 residues processed: 427 average time/residue: 1.1564 time to fit residues: 563.4132 Evaluate side-chains 439 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 369 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 193 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 443 HIS C 97 GLN D 443 HIS D 478 HIS E 97 GLN F 443 HIS G 97 GLN H 443 HIS ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20744 Z= 0.228 Angle : 0.740 15.449 28028 Z= 0.353 Chirality : 0.042 0.237 3068 Planarity : 0.005 0.056 3576 Dihedral : 4.497 29.108 2772 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.85 % Allowed : 24.59 % Favored : 71.56 % 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: 0.77 (0.17), residues: 2476 helix: 1.28 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.13 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 54 HIS 0.014 0.001 HIS H 478 PHE 0.016 0.001 PHE E 136 TYR 0.017 0.001 TYR B 186 ARG 0.013 0.001 ARG E 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 376 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8551 (m) cc_final: 0.8265 (m) REVERT: A 156 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6989 (m90) REVERT: A 157 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.7777 (p0) REVERT: A 195 CYS cc_start: 0.7103 (p) cc_final: 0.6806 (p) REVERT: B 20 MET cc_start: 0.8832 (mmt) cc_final: 0.8429 (mpm) REVERT: B 183 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.5631 (tt) REVERT: B 259 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7369 (mtt) REVERT: B 276 MET cc_start: 0.7217 (mmt) cc_final: 0.6973 (mpm) REVERT: B 315 LYS cc_start: 0.8314 (tppt) cc_final: 0.7977 (ttmt) REVERT: B 431 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7541 (tmm-80) REVERT: C 130 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8091 (tp-100) REVERT: C 133 SER cc_start: 0.8658 (m) cc_final: 0.8421 (m) REVERT: C 156 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6971 (m90) REVERT: C 157 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7793 (p0) REVERT: C 195 CYS cc_start: 0.7150 (p) cc_final: 0.6855 (p) REVERT: C 212 MET cc_start: 0.6820 (tpt) cc_final: 0.6139 (mmm) REVERT: C 217 TYR cc_start: 0.4576 (OUTLIER) cc_final: 0.2248 (m-80) REVERT: C 260 MET cc_start: 0.8142 (mpp) cc_final: 0.7764 (mmt) REVERT: D 315 LYS cc_start: 0.8357 (tppt) cc_final: 0.8019 (ttmt) REVERT: E 157 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7733 (p0) REVERT: E 212 MET cc_start: 0.6729 (tpt) cc_final: 0.6084 (mmm) REVERT: E 217 TYR cc_start: 0.4591 (OUTLIER) cc_final: 0.2291 (m-80) REVERT: E 260 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: F 20 MET cc_start: 0.8879 (mmt) cc_final: 0.8539 (mpm) REVERT: F 183 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5515 (tt) REVERT: F 187 TYR cc_start: 0.7799 (m-10) cc_final: 0.7538 (m-10) REVERT: F 268 MET cc_start: 0.7552 (ptm) cc_final: 0.7254 (ptp) REVERT: F 315 LYS cc_start: 0.8329 (tppt) cc_final: 0.8012 (ttmt) REVERT: G 133 SER cc_start: 0.8489 (m) cc_final: 0.8216 (m) REVERT: G 157 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7820 (p0) REVERT: G 195 CYS cc_start: 0.7111 (p) cc_final: 0.6847 (p) REVERT: G 199 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: G 212 MET cc_start: 0.6753 (tpt) cc_final: 0.6159 (mmm) REVERT: G 260 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7768 (mmt) REVERT: H 20 MET cc_start: 0.8868 (mmt) cc_final: 0.8501 (mpm) REVERT: H 183 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.5647 (tt) REVERT: H 238 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8710 (p) REVERT: H 268 MET cc_start: 0.7401 (ptm) cc_final: 0.7140 (ptp) REVERT: H 315 LYS cc_start: 0.8369 (tppt) cc_final: 0.8034 (ttmt) outliers start: 85 outliers final: 56 residues processed: 436 average time/residue: 1.1620 time to fit residues: 578.4245 Evaluate side-chains 444 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 372 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 0.0270 chunk 81 optimal weight: 0.5980 chunk 199 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 443 HIS B 478 HIS C 97 GLN D 443 HIS ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN F 443 HIS G 97 GLN H 443 HIS ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.155972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105623 restraints weight = 31316.071| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.67 r_work: 0.3229 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20744 Z= 0.190 Angle : 0.743 18.290 28028 Z= 0.350 Chirality : 0.042 0.267 3068 Planarity : 0.005 0.058 3576 Dihedral : 4.433 27.937 2772 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.17 % Allowed : 25.18 % Favored : 71.65 % 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: 0.83 (0.17), residues: 2476 helix: 1.33 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.10 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 54 HIS 0.020 0.001 HIS D 478 PHE 0.016 0.001 PHE E 136 TYR 0.016 0.001 TYR H 186 ARG 0.013 0.001 ARG D 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9925.99 seconds wall clock time: 174 minutes 37.71 seconds (10477.71 seconds total)