Starting phenix.real_space_refine on Wed Aug 7 14:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b69_44250/08_2024/9b69_44250.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b69_44250/08_2024/9b69_44250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b69_44250/08_2024/9b69_44250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b69_44250/08_2024/9b69_44250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b69_44250/08_2024/9b69_44250.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b69_44250/08_2024/9b69_44250.cif" } resolution = 3.69 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 Anisotropic ADP refinement not supported. Converting 10695 atoms to isotropic. 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 36 5.16 5 C 7264 2.51 5 N 1875 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 25": "OE1" <-> "OE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D GLU 266": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2763 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ARG:plan': 11, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2774 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2814 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2871 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.65, per 1000 atoms: 0.67 Number of scatterers: 11370 At special positions: 0 Unit cell: (145.14, 123.82, 94.3, 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 36 16.00 O 2195 8.00 N 1875 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 901 " - " ASN B 355 " " NAG E 1 " - " ASN C 241 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 241 " " NAG H 1 " - " ASN D 241 " Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.2 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 41.6% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.885A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.045A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.551A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 324 through 334 removed outlier: 4.083A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 187 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.789A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.611A pdb=" N ILE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.540A pdb=" N LYS B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 173 " --> pdb=" O ASN B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 173' Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.394A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.732A pdb=" N ILE B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.742A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 172 through 187 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 231 through 235 removed outlier: 4.050A pdb=" N LYS D 234 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.095A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 303 Processing helix chain 'D' and resid 325 through 335 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.612A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.414A pdb=" N LYS C 132 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 49 removed outlier: 7.229A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.451A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 364 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.617A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.764A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 164 removed outlier: 4.988A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 362 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.365A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.450A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 543 hydrogen bonds defined for protein. 1587 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: 3.54 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3711 1.34 - 1.46: 2734 1.46 - 1.58: 5116 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 11617 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 11612 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.21: 182 106.21 - 113.15: 6319 113.15 - 120.09: 3882 120.09 - 127.03: 5366 127.03 - 133.97: 104 Bond angle restraints: 15853 Sorted by residual: angle pdb=" CA LYS D 187 " pdb=" CB LYS D 187 " pdb=" CG LYS D 187 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 angle pdb=" CB LYS D 187 " pdb=" CG LYS D 187 " pdb=" CD LYS D 187 " ideal model delta sigma weight residual 111.30 118.17 -6.87 2.30e+00 1.89e-01 8.93e+00 angle pdb=" C LEU D 186 " pdb=" N LYS D 187 " pdb=" CA LYS D 187 " ideal model delta sigma weight residual 122.31 116.56 5.75 2.00e+00 2.50e-01 8.27e+00 angle pdb=" N LYS D 187 " pdb=" CA LYS D 187 " pdb=" CB LYS D 187 " ideal model delta sigma weight residual 110.46 114.67 -4.21 1.54e+00 4.22e-01 7.46e+00 angle pdb=" CA LEU C 233 " pdb=" CB LEU C 233 " pdb=" CG LEU C 233 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 ... (remaining 15848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 6298 21.82 - 43.65: 462 43.65 - 65.47: 74 65.47 - 87.29: 25 87.29 - 109.11: 8 Dihedral angle restraints: 6867 sinusoidal: 2543 harmonic: 4324 Sorted by residual: dihedral pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" SG CYS C 315 " pdb=" CB CYS C 315 " ideal model delta sinusoidal sigma weight residual -86.00 -48.10 -37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.60 109.11 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.62 108.33 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1596 0.055 - 0.111: 223 0.111 - 0.166: 33 0.166 - 0.221: 2 0.221 - 0.276: 2 Chirality restraints: 1856 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LYS D 187 " pdb=" N LYS D 187 " pdb=" C LYS D 187 " pdb=" CB LYS D 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1853 not shown) Planarity restraints: 2045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO D 99 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO C 99 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 99 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.016 5.00e-02 4.00e+02 ... (remaining 2042 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 455 2.72 - 3.27: 11559 3.27 - 3.81: 19355 3.81 - 4.36: 22231 4.36 - 4.90: 39070 Nonbonded interactions: 92670 Sorted by model distance: nonbonded pdb=" OE1 GLU A 25 " pdb=" OG SER A 282 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP C 116 " pdb=" OH TYR C 356 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR D 135 " pdb=" OD2 ASP D 195 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 71 " pdb=" O ILE B 306 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 128 " pdb=" OE2 GLU D 362 " model vdw 2.247 3.040 ... (remaining 92665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 78 or (resid 79 throu \ gh 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 155 or (resid 156 through 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 183 or (resid 184 through 190 and \ (name N or name CA or name C or name O or name CB )) or resid 191 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 230 or (resid 231 through 232 and (name N or name CA or name C or nam \ e O or name CB )) or resid 233 or (resid 234 through 236 and (name N or name CA \ or name C or name O or name CB )) or resid 237 through 256 or (resid 257 and (na \ me N or name CA or name C or name O or name CB )) or resid 258 through 265 or (r \ esid 266 through 269 and (name N or name CA or name C or name O or name CB )) or \ resid 270 through 273 or (resid 274 and (name N or name CA or name C or name O \ or name CB )) or resid 275 through 278 or (resid 279 and (name N or name CA or n \ ame C or name O or name CB )) or resid 280 through 296 or (resid 297 and (name N \ or name CA or name C or name O or name CB )) or resid 298 through 301 or (resid \ 302 through 303 and (name N or name CA or name C or name O or name CB )) or res \ id 304 through 333 or (resid 334 through 335 and (name N or name CA or name C or \ name O or name CB )) or resid 336 through 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB )) or resid 347 through 351 or (resid 352 and \ (name N or name CA or name C or name O or name CB )) or resid 353 through 383)) \ selection = (chain 'B' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 103 or (resid 104 and (name N or name CA or name C or name O or name CB )) \ or resid 105 through 115 or (resid 116 and (name N or name CA or name C or name \ O or name CB )) or resid 117 through 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 155 or (resid 156 through 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 through \ 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) or r \ esid 171 through 177 or (resid 178 and (name N or name CA or name C or name O or \ name CB )) or resid 179 through 183 or (resid 184 through 190 and (name N or na \ me CA or name C or name O or name CB )) or resid 191 through 199 or (resid 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 205 \ or (resid 206 and (name N or name CA or name C or name O or name CB )) or resid \ 207 through 212 or (resid 213 and (name N or name CA or name C or name O or nam \ e CB )) or resid 214 through 215 or (resid 216 and (name N or name CA or name C \ or name O or name CB )) or resid 217 through 230 or (resid 231 through 232 and ( \ name N or name CA or name C or name O or name CB )) or resid 233 or (resid 234 t \ hrough 236 and (name N or name CA or name C or name O or name CB )) or resid 237 \ through 273 or (resid 274 and (name N or name CA or name C or name O or name CB \ )) or resid 275 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 through 298 or (res \ id 299 through 303 and (name N or name CA or name C or name O or name CB )) or r \ esid 304 through 305 or (resid 306 and (name N or name CA or name C or name O or \ name CB )) or resid 307 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB )) or resid 363 through 368 \ or (resid 369 through 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 383)) selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 103 or (resid 104 and (name N or name CA or name C or name O o \ r name CB )) or resid 105 through 115 or (resid 116 and (name N or name CA or na \ me C or name O or name CB )) or resid 117 through 139 or (resid 140 and (name N \ or name CA or name C or name O or name CB )) or resid 141 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 184 or (resid 185 through 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 212 or (resid 213 and (name N or n \ ame CA or name C or name O or name CB )) or resid 214 through 215 or (resid 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 26 \ 5 or (resid 266 through 269 and (name N or name CA or name C or name O or name C \ B )) or resid 270 through 273 or (resid 274 and (name N or name CA or name C or \ name O or name CB )) or resid 275 through 293 or (resid 294 through 295 and (nam \ e N or name CA or name C or name O or name CB )) or resid 296 or (resid 297 and \ (name N or name CA or name C or name O or name CB )) or resid 298 or (resid 299 \ through 303 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 4 through 305 or (resid 306 and (name N or name CA or name C or name O or name C \ B )) or resid 307 through 351 or (resid 352 and (name N or name CA or name C or \ name O or name CB )) or resid 353 through 383)) selection = (chain 'D' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 21 through 23 and (name N or na \ me CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 43 or ( \ resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 th \ rough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) o \ r resid 55 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA or \ name C or name O or name CB )) or resid 119 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 155 or (resi \ d 156 through 157 and (name N or name CA or name C or name O or name CB )) or re \ sid 158 through 169 or (resid 170 and (name N or name CA or name C or name O or \ name CB )) or resid 171 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB )) or resid 174 through 177 or (resid 178 and (name N or \ name CA or name C or name O or name CB )) or resid 179 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 or (resi \ d 184 through 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 through 196 or (resid 197 and (name N or name CA or name C or name O or \ name CB )) or resid 198 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 205 or (resid 206 and (name N or \ name CA or name C or name O or name CB )) or resid 207 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) or re \ sid 217 through 230 or (resid 231 through 232 and (name N or name CA or name C o \ r name O or name CB )) or resid 233 or (resid 234 through 236 and (name N or nam \ e CA or name C or name O or name CB )) or resid 237 through 260 or (resid 261 an \ d (name N or name CA or name C or name O or name CB )) or resid 262 through 265 \ or (resid 266 through 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 through 278 or (resid 279 and (name N or name CA or name C or na \ me O or name CB )) or resid 280 through 296 or (resid 297 and (name N or name CA \ or name C or name O or name CB )) or resid 298 or (resid 299 through 303 and (n \ ame N or name CA or name C or name O or name CB )) or resid 304 through 305 or ( \ resid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 \ or (resid 308 through 309 and (name N or name CA or name C or name O or name CB \ )) or resid 310 through 324 or (resid 325 and (name N or name CA or name C or na \ me O or name CB )) or resid 326 through 330 or (resid 331 through 332 and (name \ N or name CA or name C or name O or name CB )) or resid 333 or (resid 334 throug \ h 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thro \ ugh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) o \ r resid 347 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB )) or resid 353 through 361 or (resid 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 through 369 or (resid 370 and (name \ N or name CA or name C or name O or name CB )) or resid 371 through 383)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.160 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.003 0.033 11617 Z= 0.180 Angle : 0.492 8.841 15853 Z= 0.255 Chirality : 0.041 0.276 1856 Planarity : 0.003 0.037 2040 Dihedral : 16.281 109.115 4087 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.36 % Allowed : 20.34 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.23), residues: 1488 helix: 2.10 (0.22), residues: 604 sheet: -0.99 (0.33), residues: 252 loop : -0.42 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.004 0.001 HIS A 46 PHE 0.010 0.001 PHE D 181 TYR 0.011 0.001 TYR A 77 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8844 (mm) cc_final: 0.8546 (mt) outliers start: 4 outliers final: 3 residues processed: 143 average time/residue: 0.2861 time to fit residues: 55.2503 Evaluate side-chains 141 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain D residue 13 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 GLN A 24 GLN B 207 GLN D 107 HIS D 170 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 11617 Z= 0.442 Angle : 0.605 6.343 15853 Z= 0.317 Chirality : 0.045 0.159 1856 Planarity : 0.004 0.043 2040 Dihedral : 8.583 59.510 1834 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.55 % Allowed : 18.03 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.05 (0.22), residues: 1488 helix: 1.39 (0.21), residues: 612 sheet: -1.38 (0.32), residues: 260 loop : -0.61 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 323 HIS 0.007 0.002 HIS D 93 PHE 0.014 0.002 PHE D 76 TYR 0.022 0.002 TYR C 77 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8706 (mt) REVERT: C 180 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7443 (tp) REVERT: C 267 GLU cc_start: 0.7976 (tp30) cc_final: 0.7658 (tp30) REVERT: C 280 TYR cc_start: 0.7050 (p90) cc_final: 0.6696 (p90) REVERT: C 339 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7210 (tm-30) REVERT: C 359 ASN cc_start: 0.8278 (t0) cc_final: 0.8053 (m-40) REVERT: C 360 ILE cc_start: 0.8198 (mp) cc_final: 0.7993 (mp) REVERT: A 202 ASN cc_start: 0.7643 (m110) cc_final: 0.7022 (t0) REVERT: D 318 ASN cc_start: 0.7820 (p0) cc_final: 0.7591 (p0) REVERT: D 344 ASN cc_start: 0.8015 (t0) cc_final: 0.7708 (t0) REVERT: D 380 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8072 (tpp) outliers start: 40 outliers final: 22 residues processed: 185 average time/residue: 0.2651 time to fit residues: 69.0186 Evaluate side-chains 168 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 290 GLN B 112 GLN D 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11617 Z= 0.155 Angle : 0.459 7.012 15853 Z= 0.242 Chirality : 0.041 0.141 1856 Planarity : 0.003 0.039 2040 Dihedral : 6.650 59.526 1826 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.22 % Allowed : 18.56 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.39 (0.22), residues: 1488 helix: 1.81 (0.21), residues: 608 sheet: -1.22 (0.32), residues: 252 loop : -0.59 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 262 HIS 0.005 0.001 HIS A 214 PHE 0.008 0.001 PHE D 133 TYR 0.018 0.001 TYR A 127 ARG 0.008 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8632 (mt) REVERT: C 339 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 71 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: A 190 ARG cc_start: 0.6989 (tpp80) cc_final: 0.6785 (mmm-85) REVERT: A 202 ASN cc_start: 0.7376 (m110) cc_final: 0.7018 (t0) REVERT: B 259 ILE cc_start: 0.7893 (mt) cc_final: 0.7625 (mm) REVERT: D 318 ASN cc_start: 0.7831 (p0) cc_final: 0.7575 (p0) REVERT: D 344 ASN cc_start: 0.7974 (t0) cc_final: 0.7758 (t0) REVERT: D 380 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8023 (tpp) outliers start: 25 outliers final: 14 residues processed: 175 average time/residue: 0.2603 time to fit residues: 63.4499 Evaluate side-chains 161 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 11617 Z= 0.450 Angle : 0.582 6.072 15853 Z= 0.307 Chirality : 0.044 0.166 1856 Planarity : 0.004 0.041 2040 Dihedral : 6.589 59.058 1826 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.44 % Allowed : 18.03 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.04 (0.22), residues: 1488 helix: 1.38 (0.21), residues: 612 sheet: -1.57 (0.31), residues: 268 loop : -0.64 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.005 0.001 HIS D 93 PHE 0.016 0.002 PHE B 258 TYR 0.022 0.002 TYR C 77 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8719 (mt) REVERT: C 339 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 50 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6442 (pp) REVERT: A 202 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7136 (t0) REVERT: A 338 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7786 (p) REVERT: A 380 MET cc_start: 0.6335 (ttp) cc_final: 0.6101 (ttp) REVERT: B 274 HIS cc_start: 0.5446 (OUTLIER) cc_final: 0.3908 (t70) REVERT: B 380 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7709 (ttt) REVERT: D 344 ASN cc_start: 0.8005 (t0) cc_final: 0.7710 (t0) REVERT: D 380 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8056 (tpp) outliers start: 50 outliers final: 32 residues processed: 185 average time/residue: 0.2655 time to fit residues: 67.2276 Evaluate side-chains 177 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11617 Z= 0.168 Angle : 0.466 6.085 15853 Z= 0.247 Chirality : 0.041 0.160 1856 Planarity : 0.003 0.035 2040 Dihedral : 6.142 59.587 1826 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.29 % Allowed : 19.18 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.33 (0.22), residues: 1488 helix: 1.73 (0.21), residues: 616 sheet: -1.29 (0.32), residues: 252 loop : -0.60 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 262 HIS 0.007 0.001 HIS D 46 PHE 0.010 0.001 PHE D 76 TYR 0.014 0.001 TYR A 128 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 71 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.5821 (m-80) REVERT: A 380 MET cc_start: 0.6244 (ttp) cc_final: 0.5757 (ttp) REVERT: D 304 ILE cc_start: 0.8646 (mm) cc_final: 0.8357 (mt) REVERT: D 380 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8053 (tpp) outliers start: 37 outliers final: 24 residues processed: 180 average time/residue: 0.2517 time to fit residues: 63.0956 Evaluate side-chains 172 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.0980 chunk 128 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 214 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11617 Z= 0.257 Angle : 0.493 6.239 15853 Z= 0.260 Chirality : 0.041 0.162 1856 Planarity : 0.003 0.034 2040 Dihedral : 6.155 58.994 1826 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.09 % Allowed : 19.09 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.28 (0.22), residues: 1488 helix: 1.68 (0.21), residues: 616 sheet: -1.28 (0.32), residues: 252 loop : -0.63 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 262 HIS 0.004 0.001 HIS D 46 PHE 0.011 0.001 PHE B 258 TYR 0.014 0.001 TYR A 77 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 47 ILE cc_start: 0.8946 (mm) cc_final: 0.8499 (pt) REVERT: A 50 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6248 (pp) REVERT: A 380 MET cc_start: 0.6234 (ttp) cc_final: 0.5924 (ttp) REVERT: B 274 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.3554 (t70) REVERT: B 380 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7750 (ttp) REVERT: D 304 ILE cc_start: 0.8658 (mm) cc_final: 0.8364 (mt) REVERT: D 380 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8034 (tpp) outliers start: 46 outliers final: 30 residues processed: 182 average time/residue: 0.2520 time to fit residues: 63.5370 Evaluate side-chains 178 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11617 Z= 0.162 Angle : 0.462 7.031 15853 Z= 0.243 Chirality : 0.040 0.159 1856 Planarity : 0.003 0.031 2040 Dihedral : 5.890 57.376 1826 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.73 % Allowed : 19.09 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1488 helix: 1.84 (0.21), residues: 616 sheet: -1.22 (0.32), residues: 252 loop : -0.59 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.005 0.001 HIS D 46 PHE 0.010 0.001 PHE D 76 TYR 0.010 0.001 TYR A 77 ARG 0.007 0.001 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8573 (mt) REVERT: A 47 ILE cc_start: 0.8899 (mm) cc_final: 0.8435 (pt) REVERT: A 50 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6176 (pp) REVERT: A 190 ARG cc_start: 0.6798 (mmm-85) cc_final: 0.6202 (mmm-85) REVERT: A 279 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7261 (mtmm) REVERT: B 68 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6711 (ttp-110) REVERT: B 274 HIS cc_start: 0.5322 (OUTLIER) cc_final: 0.3509 (t70) REVERT: B 380 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7761 (ttp) REVERT: D 304 ILE cc_start: 0.8648 (mm) cc_final: 0.8353 (mt) REVERT: D 380 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (tpp) outliers start: 42 outliers final: 28 residues processed: 184 average time/residue: 0.2588 time to fit residues: 65.8507 Evaluate side-chains 179 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 350 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11617 Z= 0.313 Angle : 0.527 7.305 15853 Z= 0.279 Chirality : 0.043 0.168 1856 Planarity : 0.003 0.034 2040 Dihedral : 6.030 58.203 1826 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.82 % Allowed : 19.98 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.20 (0.22), residues: 1488 helix: 1.62 (0.21), residues: 616 sheet: -1.45 (0.31), residues: 268 loop : -0.58 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 262 HIS 0.003 0.001 HIS D 46 PHE 0.022 0.001 PHE A 181 TYR 0.016 0.002 TYR A 77 ARG 0.008 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8635 (mt) REVERT: A 47 ILE cc_start: 0.8942 (mm) cc_final: 0.8482 (pt) REVERT: A 50 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6394 (pp) REVERT: A 190 ARG cc_start: 0.6892 (mmm-85) cc_final: 0.6208 (mmm-85) REVERT: A 279 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (mtmm) REVERT: A 361 MET cc_start: 0.6225 (ptp) cc_final: 0.5786 (ptp) REVERT: A 380 MET cc_start: 0.6322 (ttp) cc_final: 0.6036 (ttp) REVERT: B 274 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.3769 (t-170) REVERT: B 380 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (ttp) REVERT: D 304 ILE cc_start: 0.8684 (mm) cc_final: 0.8389 (mt) REVERT: D 380 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8020 (tpp) outliers start: 43 outliers final: 31 residues processed: 182 average time/residue: 0.2554 time to fit residues: 64.2033 Evaluate side-chains 185 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 112 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11617 Z= 0.172 Angle : 0.479 7.438 15853 Z= 0.252 Chirality : 0.041 0.156 1856 Planarity : 0.003 0.036 2040 Dihedral : 5.730 58.184 1826 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.73 % Allowed : 20.60 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.39 (0.22), residues: 1488 helix: 1.79 (0.21), residues: 616 sheet: -1.16 (0.32), residues: 252 loop : -0.63 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 262 HIS 0.007 0.001 HIS D 46 PHE 0.014 0.001 PHE A 181 TYR 0.010 0.001 TYR A 77 ARG 0.009 0.001 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8591 (mt) REVERT: A 47 ILE cc_start: 0.8901 (mm) cc_final: 0.8423 (pt) REVERT: A 50 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6135 (pp) REVERT: A 279 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7346 (mtmm) REVERT: A 361 MET cc_start: 0.6204 (ptp) cc_final: 0.5714 (ptp) REVERT: A 380 MET cc_start: 0.6221 (ttp) cc_final: 0.5914 (ttp) REVERT: B 274 HIS cc_start: 0.5332 (OUTLIER) cc_final: 0.3455 (t-170) REVERT: B 380 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7812 (ttp) REVERT: D 304 ILE cc_start: 0.8667 (mm) cc_final: 0.8367 (mt) outliers start: 42 outliers final: 34 residues processed: 180 average time/residue: 0.2637 time to fit residues: 65.7766 Evaluate side-chains 186 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 214 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11617 Z= 0.268 Angle : 0.522 6.601 15853 Z= 0.276 Chirality : 0.042 0.164 1856 Planarity : 0.003 0.038 2040 Dihedral : 5.773 57.815 1826 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.64 % Allowed : 20.60 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1488 helix: 1.69 (0.21), residues: 616 sheet: -1.17 (0.32), residues: 252 loop : -0.67 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.015 0.001 PHE A 181 TYR 0.013 0.001 TYR C 77 ARG 0.009 0.001 ARG B 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 47 ILE cc_start: 0.8902 (mm) cc_final: 0.8445 (pt) REVERT: A 50 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6241 (pp) REVERT: A 279 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7342 (mtmm) REVERT: A 361 MET cc_start: 0.6289 (ptp) cc_final: 0.5781 (ptp) REVERT: A 380 MET cc_start: 0.6270 (ttp) cc_final: 0.5963 (ttp) REVERT: B 274 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.3439 (t-170) REVERT: B 380 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7760 (ttp) REVERT: D 304 ILE cc_start: 0.8689 (mm) cc_final: 0.8392 (mt) outliers start: 41 outliers final: 35 residues processed: 177 average time/residue: 0.2535 time to fit residues: 62.3328 Evaluate side-chains 189 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0000 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102231 restraints weight = 18024.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102610 restraints weight = 12922.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103638 restraints weight = 14374.626| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11617 Z= 0.258 Angle : 0.514 6.936 15853 Z= 0.272 Chirality : 0.042 0.164 1856 Planarity : 0.003 0.037 2040 Dihedral : 5.758 58.629 1826 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.73 % Allowed : 20.60 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.27 (0.22), residues: 1488 helix: 1.65 (0.21), residues: 616 sheet: -1.16 (0.32), residues: 252 loop : -0.67 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.013 0.001 PHE A 181 TYR 0.014 0.001 TYR A 77 ARG 0.009 0.001 ARG B 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.14 seconds wall clock time: 41 minutes 5.68 seconds (2465.68 seconds total)