Starting phenix.real_space_refine on Sat Aug 23 22:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn2_27552/08_2025/8dn2_27552_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn2_27552/08_2025/8dn2_27552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dn2_27552/08_2025/8dn2_27552_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn2_27552/08_2025/8dn2_27552_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dn2_27552/08_2025/8dn2_27552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn2_27552/08_2025/8dn2_27552.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9267 2.51 5 N 2258 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14102 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2814 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain breaks: 1 Chain: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2778 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2755 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2726 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2692 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Unusual residues: {'HEX': 3, 'HP6': 4, 'NAG': 1, 'OCT': 1, 'UND': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Unusual residues: {'DD9': 1, 'HEX': 3, 'NAG': 1, 'NBU': 1, 'OCT': 2, 'UND': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {'HEX': 2, 'HP6': 1, 'NAG': 1, 'UND': 1} Inner-chain residues flagged as termini: ['pdbres="GLY B 502 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 58 Unusual residues: {'HEX': 1, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'OCT': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Unusual residues: {'D10': 1, 'DD9': 1, 'HEX': 1, 'HP6': 2, 'NAG': 1, 'OCT': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.17, per 1000 atoms: 0.30 Number of scatterers: 14102 At special positions: 0 Unit cell: (107.07, 126.99, 134.46, 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 102 16.00 O 2475 8.00 N 2258 7.00 C 9267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=10, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 38 " " NAG B 503 " - " ASN B 38 " " NAG C 502 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 663.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 25 sheets defined 40.1% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.759A pdb=" N PHE D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.548A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 243 Proline residue: D 230 - end of helix removed outlier: 3.854A pdb=" N PHE D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 Processing helix chain 'D' and resid 282 through 311 removed outlier: 3.596A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 417 Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.538A pdb=" N LEU A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 271 removed outlier: 3.513A pdb=" N LEU A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.905A pdb=" N TRP A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 419 Proline residue: A 403 - end of helix removed outlier: 3.653A pdb=" N ILE A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 18 removed outlier: 3.520A pdb=" N PHE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 244 Proline residue: B 230 - end of helix removed outlier: 3.761A pdb=" N ILE B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 272 removed outlier: 3.652A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 removed outlier: 3.611A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 419 removed outlier: 3.663A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Proline residue: B 403 - end of helix removed outlier: 3.576A pdb=" N ILE B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 244 Proline residue: C 230 - end of helix removed outlier: 3.574A pdb=" N ILE C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 272 removed outlier: 3.678A pdb=" N ALA C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 310 removed outlier: 4.071A pdb=" N ILE C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 419 Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 34 through 43 removed outlier: 3.966A pdb=" N LEU E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.534A pdb=" N LYS E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 109 through 116 removed outlier: 3.986A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 251 through 266 Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 277 through 296 removed outlier: 4.226A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 Processing helix chain 'E' and resid 446 through 475 removed outlier: 3.936A pdb=" N ILE E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.225A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 106 through 107 removed outlier: 3.594A pdb=" N HIS D 107 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 133 " --> pdb=" O HIS D 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 99 through 100 removed outlier: 4.717A pdb=" N HIS D 215 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLU D 192 " --> pdb=" O HIS D 215 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLU D 217 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS D 190 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 85 removed outlier: 4.749A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.615A pdb=" N HIS A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 133 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.564A pdb=" N ALA A 212 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.564A pdb=" N ALA A 212 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.550A pdb=" N LYS A 200 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 37 through 40 Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.641A pdb=" N THR B 133 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 107 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.703A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 44 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 43 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 157 removed outlier: 4.882A pdb=" N HIS B 215 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU B 192 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU B 217 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS B 190 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 200 through 201 removed outlier: 3.553A pdb=" N LYS B 200 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.138A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.593A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 133 " --> pdb=" O HIS C 107 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS C 107 " --> pdb=" O THR C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.593A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 152 Processing sheet with id=AC2, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.745A pdb=" N LYS C 200 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 207 " --> pdb=" O LYS C 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 72 through 73 removed outlier: 3.502A pdb=" N TRP E 89 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 126 through 130 removed outlier: 6.514A pdb=" N GLU E 126 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER E 160 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER E 128 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP E 89 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AC6, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AC7, first strand: chain 'E' and resid 223 through 225 721 hydrogen bonds defined for protein. 2061 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: 2.75 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2441 1.33 - 1.45: 3822 1.45 - 1.58: 7977 1.58 - 1.70: 0 1.70 - 1.83: 172 Bond restraints: 14412 Sorted by residual: bond pdb=" CA PHE D 387 " pdb=" C PHE D 387 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.39e-02 5.18e+03 1.24e+01 bond pdb=" N THR D 55 " pdb=" CA THR D 55 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" N VAL B 37 " pdb=" CA VAL B 37 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" C PRO A 87 " pdb=" O PRO A 87 " ideal model delta sigma weight residual 1.237 1.201 0.037 1.26e-02 6.30e+03 8.42e+00 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.38e+00 ... (remaining 14407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19037 2.05 - 4.10: 315 4.10 - 6.16: 55 6.16 - 8.21: 5 8.21 - 10.26: 8 Bond angle restraints: 19420 Sorted by residual: angle pdb=" N ILE D 388 " pdb=" CA ILE D 388 " pdb=" C ILE D 388 " ideal model delta sigma weight residual 110.72 101.30 9.42 1.01e+00 9.80e-01 8.70e+01 angle pdb=" N LEU D 386 " pdb=" CA LEU D 386 " pdb=" C LEU D 386 " ideal model delta sigma weight residual 111.07 119.86 -8.79 1.07e+00 8.73e-01 6.74e+01 angle pdb=" N VAL A 294 " pdb=" CA VAL A 294 " pdb=" C VAL A 294 " ideal model delta sigma weight residual 110.42 117.91 -7.49 9.60e-01 1.09e+00 6.09e+01 angle pdb=" N GLN C 226 " pdb=" CA GLN C 226 " pdb=" C GLN C 226 " ideal model delta sigma weight residual 111.82 120.74 -8.92 1.16e+00 7.43e-01 5.91e+01 angle pdb=" N ILE D 388 " pdb=" CA ILE D 388 " pdb=" CB ILE D 388 " ideal model delta sigma weight residual 110.58 120.84 -10.26 1.50e+00 4.44e-01 4.68e+01 ... (remaining 19415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.96: 8245 19.96 - 39.92: 354 39.92 - 59.87: 64 59.87 - 79.83: 15 79.83 - 99.79: 12 Dihedral angle restraints: 8690 sinusoidal: 3691 harmonic: 4999 Sorted by residual: dihedral pdb=" CA ILE B 419 " pdb=" C ILE B 419 " pdb=" N VAL B 420 " pdb=" CA VAL B 420 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C1 NAG E 501 " pdb=" C2 NAG E 501 " pdb=" C3 NAG E 501 " pdb=" O3 NAG E 501 " ideal model delta sinusoidal sigma weight residual -175.09 -75.30 -99.79 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" C2 NAG D 501 " pdb=" C3 NAG D 501 " pdb=" C4 NAG D 501 " pdb=" C5 NAG D 501 " ideal model delta sinusoidal sigma weight residual 53.78 -45.81 99.59 1 3.00e+01 1.11e-03 1.24e+01 ... (remaining 8687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1927 0.076 - 0.152: 208 0.152 - 0.229: 11 0.229 - 0.305: 4 0.305 - 0.381: 1 Chirality restraints: 2151 Sorted by residual: chirality pdb=" CA LEU D 386 " pdb=" N LEU D 386 " pdb=" C LEU D 386 " pdb=" CB LEU D 386 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA LEU C 224 " pdb=" N LEU C 224 " pdb=" C LEU C 224 " pdb=" CB LEU C 224 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2148 not shown) Planarity restraints: 2411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 503 " 0.307 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C7 NAG B 503 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 503 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 503 " -0.450 2.00e-02 2.50e+03 pdb=" O7 NAG B 503 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 225 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ILE C 225 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE C 225 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN C 226 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 419 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ILE B 419 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE B 419 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL B 420 " -0.022 2.00e-02 2.50e+03 ... (remaining 2408 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 4 1.96 - 2.69: 398 2.69 - 3.43: 20551 3.43 - 4.16: 31694 4.16 - 4.90: 55903 Nonbonded interactions: 108550 Sorted by model distance: nonbonded pdb=" CD2 LEU D 261 " pdb=" CE1 PHE E 282 " model vdw 1.224 3.760 nonbonded pdb=" CZ3 TRP B 414 " pdb=" C5 UND B 504 " model vdw 1.382 2.992 nonbonded pdb=" CH2 TRP B 414 " pdb=" C6 UND B 504 " model vdw 1.765 2.992 nonbonded pdb=" CZ3 TRP B 414 " pdb=" C6 UND B 504 " model vdw 1.797 3.740 nonbonded pdb=" OG1 THR D 55 " pdb=" OD1 ASP D 57 " model vdw 2.064 3.040 ... (remaining 108545 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 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 308 or resid 386 through 419)) selection = (chain 'D' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.009 0.575 14437 Z= 0.871 Angle : 0.654 10.260 19455 Z= 0.390 Chirality : 0.046 0.381 2151 Planarity : 0.006 0.260 2406 Dihedral : 12.212 99.789 5420 Min Nonbonded Distance : 1.224 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.02 % Rotamer: Outliers : 2.83 % Allowed : 8.95 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.21), residues: 1673 helix: 1.90 (0.22), residues: 596 sheet: -0.46 (0.28), residues: 368 loop : -1.41 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 131 TYR 0.015 0.001 TYR D 301 PHE 0.011 0.001 PHE D 412 TRP 0.010 0.001 TRP D 68 HIS 0.002 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00347 (14412) covalent geometry : angle 0.65209 (19420) SS BOND : bond 0.00255 ( 10) SS BOND : angle 1.36639 ( 20) hydrogen bonds : bond 0.15680 ( 654) hydrogen bonds : angle 5.98792 ( 2061) Misc. bond : bond 0.32254 ( 10) link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 1.51756 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 437 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.8202 (pt0) cc_final: 0.7867 (pt0) REVERT: D 404 MET cc_start: 0.7747 (mtp) cc_final: 0.7451 (ptt) REVERT: A 18 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7132 (ptt) REVERT: A 73 LEU cc_start: 0.9385 (tp) cc_final: 0.9090 (tt) REVERT: A 220 MET cc_start: 0.7924 (mtt) cc_final: 0.7650 (mtm) REVERT: A 383 MET cc_start: 0.7454 (ppp) cc_final: 0.6668 (ppp) REVERT: B 55 THR cc_start: 0.9136 (p) cc_final: 0.8900 (p) REVERT: B 131 ARG cc_start: 0.8932 (ttt-90) cc_final: 0.8665 (ttt90) REVERT: B 170 TRP cc_start: 0.8339 (m100) cc_final: 0.8064 (m100) REVERT: B 211 GLU cc_start: 0.7407 (pm20) cc_final: 0.6806 (pm20) REVERT: B 252 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.7868 (mmm-85) REVERT: B 263 MET cc_start: 0.9188 (tpp) cc_final: 0.8891 (tpp) REVERT: B 276 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8172 (mtmt) REVERT: B 295 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8278 (t80) REVERT: B 393 LYS cc_start: 0.7678 (mttm) cc_final: 0.7160 (pttt) REVERT: C 17 LEU cc_start: 0.9307 (mt) cc_final: 0.9035 (mt) REVERT: C 55 THR cc_start: 0.9628 (OUTLIER) cc_final: 0.9240 (m) REVERT: C 98 LEU cc_start: 0.9152 (pt) cc_final: 0.8867 (pt) REVERT: C 147 MET cc_start: 0.7790 (mtp) cc_final: 0.7519 (tpt) REVERT: C 192 GLU cc_start: 0.8493 (tp30) cc_final: 0.8277 (tp30) REVERT: C 239 TRP cc_start: 0.8602 (m-10) cc_final: 0.8273 (m-10) REVERT: C 399 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6835 (ttm110) REVERT: E 154 ARG cc_start: 0.8857 (ttt-90) cc_final: 0.8298 (ttt-90) REVERT: E 235 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7722 (mt-10) REVERT: E 247 TYR cc_start: 0.8330 (m-80) cc_final: 0.7940 (m-80) REVERT: E 285 LEU cc_start: 0.8012 (mt) cc_final: 0.7629 (tt) REVERT: E 329 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8112 (tm-30) outliers start: 43 outliers final: 17 residues processed: 463 average time/residue: 0.1198 time to fit residues: 82.6957 Evaluate side-chains 341 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 320 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN D 203 ASN D 305 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 67 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102142 restraints weight = 29592.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105485 restraints weight = 15878.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107665 restraints weight = 10345.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109260 restraints weight = 7740.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110152 restraints weight = 6359.515| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14437 Z= 0.194 Angle : 0.693 8.792 19455 Z= 0.347 Chirality : 0.045 0.197 2151 Planarity : 0.004 0.050 2406 Dihedral : 9.900 83.803 2138 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.21 % Allowed : 16.58 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.21), residues: 1673 helix: 1.96 (0.21), residues: 593 sheet: -0.26 (0.28), residues: 352 loop : -1.38 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 309 TYR 0.021 0.002 TYR B 78 PHE 0.016 0.002 PHE B 409 TRP 0.011 0.001 TRP D 68 HIS 0.005 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00425 (14412) covalent geometry : angle 0.68588 (19420) SS BOND : bond 0.00530 ( 10) SS BOND : angle 1.94455 ( 20) hydrogen bonds : bond 0.04612 ( 654) hydrogen bonds : angle 4.74496 ( 2061) Misc. bond : bond 0.00199 ( 10) link_NAG-ASN : bond 0.00423 ( 5) link_NAG-ASN : angle 2.90718 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 GLU cc_start: 0.8311 (mp0) cc_final: 0.8033 (mp0) REVERT: D 242 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: D 404 MET cc_start: 0.7840 (mtp) cc_final: 0.7439 (ptt) REVERT: A 172 GLU cc_start: 0.8317 (pm20) cc_final: 0.7445 (pm20) REVERT: A 192 GLU cc_start: 0.8263 (pm20) cc_final: 0.7819 (mm-30) REVERT: A 219 GLN cc_start: 0.8447 (mp10) cc_final: 0.8130 (mp-120) REVERT: A 383 MET cc_start: 0.7791 (ppp) cc_final: 0.7120 (ppp) REVERT: B 41 CYS cc_start: 0.9053 (p) cc_final: 0.8324 (p) REVERT: B 170 TRP cc_start: 0.8362 (m100) cc_final: 0.7867 (m100) REVERT: B 252 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.7845 (mmm-85) REVERT: B 393 LYS cc_start: 0.7606 (mttm) cc_final: 0.7130 (pttt) REVERT: C 17 LEU cc_start: 0.9217 (mt) cc_final: 0.8834 (mt) REVERT: C 98 LEU cc_start: 0.9151 (pt) cc_final: 0.8945 (pt) REVERT: C 116 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8702 (mtpp) REVERT: C 147 MET cc_start: 0.8019 (mtp) cc_final: 0.7590 (tpt) REVERT: C 192 GLU cc_start: 0.8629 (tp30) cc_final: 0.8386 (tp30) REVERT: E 170 MET cc_start: 0.9187 (mtm) cc_final: 0.8918 (mtm) REVERT: E 235 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 247 TYR cc_start: 0.8579 (m-80) cc_final: 0.8203 (m-80) REVERT: E 329 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8048 (tm-30) REVERT: E 449 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7573 (ptpp) outliers start: 64 outliers final: 46 residues processed: 375 average time/residue: 0.1033 time to fit residues: 60.7115 Evaluate side-chains 360 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN D 203 ASN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN E 138 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104528 restraints weight = 29563.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107907 restraints weight = 15844.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110224 restraints weight = 10346.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111663 restraints weight = 7734.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112616 restraints weight = 6420.904| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14437 Z= 0.137 Angle : 0.672 9.569 19455 Z= 0.332 Chirality : 0.044 0.295 2151 Planarity : 0.004 0.040 2406 Dihedral : 8.769 81.099 2125 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.28 % Allowed : 17.89 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1673 helix: 2.04 (0.21), residues: 586 sheet: -0.09 (0.29), residues: 335 loop : -1.44 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 309 TYR 0.020 0.001 TYR E 325 PHE 0.018 0.001 PHE E 282 TRP 0.025 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00300 (14412) covalent geometry : angle 0.66600 (19420) SS BOND : bond 0.00365 ( 10) SS BOND : angle 2.27486 ( 20) hydrogen bonds : bond 0.04227 ( 654) hydrogen bonds : angle 4.52153 ( 2061) Misc. bond : bond 0.00404 ( 10) link_NAG-ASN : bond 0.00437 ( 5) link_NAG-ASN : angle 2.19896 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 334 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 GLU cc_start: 0.8299 (mp0) cc_final: 0.8014 (mp0) REVERT: D 108 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: D 203 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7621 (p0) REVERT: D 242 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: D 298 LEU cc_start: 0.9212 (tp) cc_final: 0.9000 (tp) REVERT: D 404 MET cc_start: 0.7767 (mtp) cc_final: 0.7365 (ptt) REVERT: A 219 GLN cc_start: 0.8565 (mp10) cc_final: 0.8109 (mp-120) REVERT: A 383 MET cc_start: 0.7886 (ppp) cc_final: 0.7254 (ppp) REVERT: B 41 CYS cc_start: 0.9010 (p) cc_final: 0.8422 (p) REVERT: B 131 ARG cc_start: 0.9017 (ttt-90) cc_final: 0.8569 (ttt90) REVERT: B 170 TRP cc_start: 0.8311 (m100) cc_final: 0.7892 (m100) REVERT: B 252 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.7862 (mmm-85) REVERT: B 279 TYR cc_start: 0.8283 (p90) cc_final: 0.7668 (p90) REVERT: B 393 LYS cc_start: 0.7555 (mttm) cc_final: 0.7094 (pttt) REVERT: C 17 LEU cc_start: 0.9176 (mt) cc_final: 0.8860 (mt) REVERT: C 147 MET cc_start: 0.8090 (mtp) cc_final: 0.7617 (tpt) REVERT: C 192 GLU cc_start: 0.8589 (tp30) cc_final: 0.8329 (tp30) REVERT: E 200 GLN cc_start: 0.7436 (pt0) cc_final: 0.7198 (pt0) REVERT: E 247 TYR cc_start: 0.8504 (m-80) cc_final: 0.8090 (m-80) REVERT: E 268 ILE cc_start: 0.9344 (mt) cc_final: 0.9095 (mp) REVERT: E 329 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 449 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7742 (ptpp) outliers start: 65 outliers final: 45 residues processed: 375 average time/residue: 0.1047 time to fit residues: 61.1703 Evaluate side-chains 354 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 134 optimal weight: 6.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 203 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104163 restraints weight = 29360.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107582 restraints weight = 15528.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109861 restraints weight = 10024.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111345 restraints weight = 7455.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112381 restraints weight = 6166.020| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14437 Z= 0.141 Angle : 0.665 9.590 19455 Z= 0.328 Chirality : 0.044 0.303 2151 Planarity : 0.004 0.044 2406 Dihedral : 8.119 77.168 2118 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.00 % Allowed : 18.55 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1673 helix: 1.94 (0.21), residues: 593 sheet: -0.09 (0.28), residues: 348 loop : -1.37 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 399 TYR 0.020 0.001 TYR E 325 PHE 0.019 0.001 PHE E 282 TRP 0.037 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00315 (14412) covalent geometry : angle 0.65800 (19420) SS BOND : bond 0.00447 ( 10) SS BOND : angle 2.43384 ( 20) hydrogen bonds : bond 0.04071 ( 654) hydrogen bonds : angle 4.47441 ( 2061) Misc. bond : bond 0.00123 ( 10) link_NAG-ASN : bond 0.00494 ( 5) link_NAG-ASN : angle 2.13992 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 GLU cc_start: 0.8264 (mp0) cc_final: 0.8053 (mp0) REVERT: D 108 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: D 163 MET cc_start: 0.8342 (mtm) cc_final: 0.8063 (mtp) REVERT: D 242 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: D 298 LEU cc_start: 0.9225 (tp) cc_final: 0.9003 (tp) REVERT: D 404 MET cc_start: 0.7740 (mtp) cc_final: 0.7376 (ptt) REVERT: A 192 GLU cc_start: 0.8292 (pm20) cc_final: 0.7822 (mm-30) REVERT: A 287 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8234 (ttm) REVERT: A 383 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7267 (ppp) REVERT: B 41 CYS cc_start: 0.8920 (p) cc_final: 0.8321 (p) REVERT: B 170 TRP cc_start: 0.8316 (m100) cc_final: 0.7848 (m100) REVERT: B 252 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: B 279 TYR cc_start: 0.8309 (p90) cc_final: 0.7718 (p90) REVERT: B 393 LYS cc_start: 0.7632 (mttm) cc_final: 0.7115 (pttt) REVERT: C 17 LEU cc_start: 0.9211 (mt) cc_final: 0.8884 (mt) REVERT: C 147 MET cc_start: 0.8091 (mtp) cc_final: 0.7650 (tpt) REVERT: C 192 GLU cc_start: 0.8574 (tp30) cc_final: 0.8338 (tp30) REVERT: E 170 MET cc_start: 0.9142 (mtm) cc_final: 0.8929 (mtm) REVERT: E 235 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7773 (mt-10) REVERT: E 247 TYR cc_start: 0.8488 (m-80) cc_final: 0.8089 (m-80) REVERT: E 268 ILE cc_start: 0.9391 (mt) cc_final: 0.9144 (mp) REVERT: E 329 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 449 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7805 (ptpp) outliers start: 76 outliers final: 52 residues processed: 379 average time/residue: 0.1009 time to fit residues: 60.1354 Evaluate side-chains 370 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 131 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104550 restraints weight = 29400.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107981 restraints weight = 15505.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110285 restraints weight = 10005.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111841 restraints weight = 7418.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112746 restraints weight = 6078.946| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14437 Z= 0.133 Angle : 0.656 9.562 19455 Z= 0.321 Chirality : 0.044 0.267 2151 Planarity : 0.004 0.041 2406 Dihedral : 7.985 72.165 2117 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.13 % Allowed : 19.87 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1673 helix: 1.96 (0.21), residues: 593 sheet: -0.06 (0.28), residues: 348 loop : -1.35 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 80 TYR 0.020 0.001 TYR E 325 PHE 0.022 0.001 PHE E 282 TRP 0.048 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00299 (14412) covalent geometry : angle 0.64961 (19420) SS BOND : bond 0.00554 ( 10) SS BOND : angle 2.40574 ( 20) hydrogen bonds : bond 0.03962 ( 654) hydrogen bonds : angle 4.39592 ( 2061) Misc. bond : bond 0.00038 ( 10) link_NAG-ASN : bond 0.00496 ( 5) link_NAG-ASN : angle 2.05331 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6684 (tpt170) cc_final: 0.6425 (tpt90) REVERT: D 53 GLU cc_start: 0.8396 (mp0) cc_final: 0.8101 (mp0) REVERT: D 108 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: D 163 MET cc_start: 0.8435 (mtm) cc_final: 0.8078 (mtp) REVERT: D 242 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: D 298 LEU cc_start: 0.9237 (tp) cc_final: 0.9032 (tp) REVERT: D 404 MET cc_start: 0.7752 (mtp) cc_final: 0.7361 (ptt) REVERT: A 169 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7175 (mm-30) REVERT: A 383 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7048 (ppp) REVERT: B 170 TRP cc_start: 0.8296 (m100) cc_final: 0.7814 (m100) REVERT: B 252 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.7838 (mmm-85) REVERT: B 279 TYR cc_start: 0.8212 (p90) cc_final: 0.7545 (p90) REVERT: B 393 LYS cc_start: 0.7575 (mttm) cc_final: 0.7086 (pttt) REVERT: C 17 LEU cc_start: 0.9166 (mt) cc_final: 0.8736 (mt) REVERT: C 98 LEU cc_start: 0.9212 (pt) cc_final: 0.8935 (pt) REVERT: C 147 MET cc_start: 0.8145 (mtp) cc_final: 0.7729 (tpt) REVERT: C 172 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8799 (mm-30) REVERT: C 192 GLU cc_start: 0.8593 (tp30) cc_final: 0.8368 (tp30) REVERT: C 237 LEU cc_start: 0.9013 (tp) cc_final: 0.8811 (tt) REVERT: C 263 MET cc_start: 0.7684 (tpt) cc_final: 0.7423 (tpt) REVERT: E 136 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8982 (tp40) REVERT: E 170 MET cc_start: 0.9140 (mtm) cc_final: 0.8935 (mtm) REVERT: E 235 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7655 (mt-10) REVERT: E 247 TYR cc_start: 0.8485 (m-80) cc_final: 0.8075 (m-80) REVERT: E 268 ILE cc_start: 0.9353 (mt) cc_final: 0.9118 (mp) REVERT: E 329 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 449 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7692 (ptpp) outliers start: 78 outliers final: 56 residues processed: 370 average time/residue: 0.1009 time to fit residues: 58.9264 Evaluate side-chains 374 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 15 optimal weight: 0.0770 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098514 restraints weight = 30593.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101926 restraints weight = 15772.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104249 restraints weight = 10111.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105782 restraints weight = 7461.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106579 restraints weight = 6101.015| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14437 Z= 0.259 Angle : 0.717 11.926 19455 Z= 0.360 Chirality : 0.046 0.441 2151 Planarity : 0.004 0.051 2406 Dihedral : 8.152 65.685 2117 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 6.18 % Allowed : 19.61 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.21), residues: 1673 helix: 1.91 (0.21), residues: 592 sheet: -0.14 (0.29), residues: 337 loop : -1.38 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.022 0.002 TYR D 301 PHE 0.019 0.002 PHE E 282 TRP 0.054 0.002 TRP C 239 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00583 (14412) covalent geometry : angle 0.71118 (19420) SS BOND : bond 0.00434 ( 10) SS BOND : angle 2.28029 ( 20) hydrogen bonds : bond 0.04382 ( 654) hydrogen bonds : angle 4.64440 ( 2061) Misc. bond : bond 0.00076 ( 10) link_NAG-ASN : bond 0.00601 ( 5) link_NAG-ASN : angle 2.30955 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 321 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6740 (tpt170) cc_final: 0.6425 (tpt90) REVERT: D 163 MET cc_start: 0.8509 (mtm) cc_final: 0.8082 (mtp) REVERT: D 404 MET cc_start: 0.7796 (mtp) cc_final: 0.7449 (ptt) REVERT: A 211 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: A 219 GLN cc_start: 0.8621 (mp10) cc_final: 0.8292 (mp10) REVERT: A 383 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7273 (ppp) REVERT: B 170 TRP cc_start: 0.8439 (m100) cc_final: 0.7899 (m100) REVERT: B 252 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.7923 (mmm-85) REVERT: B 279 TYR cc_start: 0.8339 (p90) cc_final: 0.7826 (p90) REVERT: B 393 LYS cc_start: 0.7698 (mttm) cc_final: 0.7150 (tttt) REVERT: C 17 LEU cc_start: 0.9201 (mt) cc_final: 0.8864 (mt) REVERT: C 110 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8002 (mm-30) REVERT: C 147 MET cc_start: 0.8106 (mtp) cc_final: 0.7814 (tpt) REVERT: C 192 GLU cc_start: 0.8675 (tp30) cc_final: 0.8436 (tp30) REVERT: E 208 GLN cc_start: 0.8686 (pt0) cc_final: 0.8467 (pt0) REVERT: E 235 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 268 ILE cc_start: 0.9461 (mt) cc_final: 0.9240 (mp) REVERT: E 290 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8088 (mm-30) REVERT: E 294 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8230 (mm) REVERT: E 329 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7832 (tm-30) outliers start: 94 outliers final: 74 residues processed: 374 average time/residue: 0.0999 time to fit residues: 59.1413 Evaluate side-chains 388 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 311 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103265 restraints weight = 29312.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106663 restraints weight = 15546.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108918 restraints weight = 10076.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110436 restraints weight = 7517.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111334 restraints weight = 6181.777| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14437 Z= 0.136 Angle : 0.691 12.023 19455 Z= 0.334 Chirality : 0.045 0.458 2151 Planarity : 0.003 0.035 2406 Dihedral : 7.809 67.344 2117 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.26 % Allowed : 21.78 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.21), residues: 1673 helix: 1.91 (0.21), residues: 591 sheet: -0.09 (0.29), residues: 335 loop : -1.37 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 65 TYR 0.020 0.001 TYR E 325 PHE 0.024 0.001 PHE E 282 TRP 0.045 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00305 (14412) covalent geometry : angle 0.68619 (19420) SS BOND : bond 0.00402 ( 10) SS BOND : angle 1.88974 ( 20) hydrogen bonds : bond 0.04035 ( 654) hydrogen bonds : angle 4.47605 ( 2061) Misc. bond : bond 0.00038 ( 10) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 2.20415 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 324 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6724 (tpt170) cc_final: 0.6413 (tpt90) REVERT: D 53 GLU cc_start: 0.8302 (mp0) cc_final: 0.8089 (mp0) REVERT: D 116 LYS cc_start: 0.8477 (pttp) cc_final: 0.7626 (ptmt) REVERT: D 163 MET cc_start: 0.8536 (mtm) cc_final: 0.8070 (mtp) REVERT: D 404 MET cc_start: 0.7706 (mtp) cc_final: 0.7323 (ptt) REVERT: A 89 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7880 (ppp) REVERT: A 136 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8472 (pp) REVERT: A 169 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7216 (mm-30) REVERT: A 211 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: A 219 GLN cc_start: 0.8494 (mp10) cc_final: 0.8069 (mp-120) REVERT: A 383 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7167 (ppp) REVERT: B 170 TRP cc_start: 0.8299 (m100) cc_final: 0.7943 (m100) REVERT: B 252 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.7805 (mmm-85) REVERT: B 279 TYR cc_start: 0.8217 (p90) cc_final: 0.7559 (p90) REVERT: B 393 LYS cc_start: 0.7594 (mttm) cc_final: 0.7086 (pttt) REVERT: C 17 LEU cc_start: 0.9139 (mt) cc_final: 0.8799 (mt) REVERT: C 56 MET cc_start: 0.8860 (mmm) cc_final: 0.8654 (mmm) REVERT: C 98 LEU cc_start: 0.9247 (pt) cc_final: 0.9007 (pt) REVERT: C 147 MET cc_start: 0.8080 (mtp) cc_final: 0.7698 (tpt) REVERT: C 239 TRP cc_start: 0.8520 (m-10) cc_final: 0.8263 (m100) REVERT: E 136 GLN cc_start: 0.9090 (tp40) cc_final: 0.8758 (tp-100) REVERT: E 208 GLN cc_start: 0.8577 (pt0) cc_final: 0.8247 (pt0) REVERT: E 235 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7623 (mt-10) REVERT: E 247 TYR cc_start: 0.8490 (m-80) cc_final: 0.8099 (m-80) REVERT: E 268 ILE cc_start: 0.9440 (mt) cc_final: 0.9190 (mp) REVERT: E 290 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8057 (mm-30) REVERT: E 294 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8112 (mm) REVERT: E 329 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7741 (tm-30) REVERT: E 449 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7791 (ptpp) outliers start: 80 outliers final: 58 residues processed: 368 average time/residue: 0.1016 time to fit residues: 58.8936 Evaluate side-chains 375 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 43 optimal weight: 3.9990 chunk 142 optimal weight: 0.0770 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 0.0020 chunk 11 optimal weight: 10.0000 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104606 restraints weight = 29218.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108050 restraints weight = 15483.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110353 restraints weight = 10004.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111897 restraints weight = 7432.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112899 restraints weight = 6090.892| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14437 Z= 0.132 Angle : 0.692 10.502 19455 Z= 0.335 Chirality : 0.045 0.444 2151 Planarity : 0.004 0.068 2406 Dihedral : 7.454 69.510 2115 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.87 % Allowed : 22.43 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.21), residues: 1673 helix: 1.89 (0.21), residues: 591 sheet: -0.10 (0.28), residues: 356 loop : -1.27 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 309 TYR 0.020 0.001 TYR E 325 PHE 0.017 0.001 PHE E 282 TRP 0.037 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00293 (14412) covalent geometry : angle 0.68597 (19420) SS BOND : bond 0.00389 ( 10) SS BOND : angle 1.97268 ( 20) hydrogen bonds : bond 0.03942 ( 654) hydrogen bonds : angle 4.43742 ( 2061) Misc. bond : bond 0.00034 ( 10) link_NAG-ASN : bond 0.00818 ( 5) link_NAG-ASN : angle 2.43639 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 332 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6738 (tpt170) cc_final: 0.6427 (tpt90) REVERT: D 116 LYS cc_start: 0.8466 (pttp) cc_final: 0.7594 (ptmt) REVERT: D 163 MET cc_start: 0.8568 (mtm) cc_final: 0.8054 (mtp) REVERT: D 404 MET cc_start: 0.7696 (mtp) cc_final: 0.7319 (ptt) REVERT: A 169 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7189 (mm-30) REVERT: A 211 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: A 219 GLN cc_start: 0.8497 (mp10) cc_final: 0.8045 (mp-120) REVERT: A 220 MET cc_start: 0.7848 (mtm) cc_final: 0.7400 (tpp) REVERT: A 246 MET cc_start: 0.9002 (pmm) cc_final: 0.8792 (pmm) REVERT: A 383 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7171 (ppp) REVERT: B 170 TRP cc_start: 0.8441 (m100) cc_final: 0.8057 (m100) REVERT: B 252 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: B 279 TYR cc_start: 0.8238 (p90) cc_final: 0.7512 (p90) REVERT: B 393 LYS cc_start: 0.7581 (mttm) cc_final: 0.7066 (pttt) REVERT: C 17 LEU cc_start: 0.9128 (mt) cc_final: 0.8797 (mt) REVERT: C 147 MET cc_start: 0.8103 (mtp) cc_final: 0.7716 (tpt) REVERT: C 211 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 239 TRP cc_start: 0.8461 (m-10) cc_final: 0.8178 (m100) REVERT: C 283 ILE cc_start: 0.8756 (tp) cc_final: 0.8502 (mm) REVERT: E 120 ASP cc_start: 0.9189 (p0) cc_final: 0.8832 (p0) REVERT: E 136 GLN cc_start: 0.9084 (tp40) cc_final: 0.8738 (tp-100) REVERT: E 235 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7797 (mt-10) REVERT: E 247 TYR cc_start: 0.8479 (m-80) cc_final: 0.8084 (m-80) REVERT: E 290 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8066 (mm-30) REVERT: E 294 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8079 (mm) REVERT: E 329 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7747 (tm-30) REVERT: E 449 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7771 (ptpp) outliers start: 74 outliers final: 64 residues processed: 377 average time/residue: 0.1015 time to fit residues: 60.8902 Evaluate side-chains 378 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 76 optimal weight: 0.1980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103110 restraints weight = 29497.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106492 restraints weight = 15669.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108751 restraints weight = 10163.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110289 restraints weight = 7580.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111257 restraints weight = 6227.183| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14437 Z= 0.160 Angle : 0.722 10.663 19455 Z= 0.349 Chirality : 0.045 0.424 2151 Planarity : 0.004 0.040 2406 Dihedral : 7.304 72.546 2113 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.93 % Allowed : 22.50 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.21), residues: 1673 helix: 1.82 (0.21), residues: 591 sheet: -0.00 (0.29), residues: 335 loop : -1.33 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 399 TYR 0.021 0.001 TYR C 301 PHE 0.024 0.001 PHE E 282 TRP 0.044 0.002 TRP C 239 HIS 0.006 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00368 (14412) covalent geometry : angle 0.71678 (19420) SS BOND : bond 0.00455 ( 10) SS BOND : angle 2.07958 ( 20) hydrogen bonds : bond 0.04044 ( 654) hydrogen bonds : angle 4.49448 ( 2061) Misc. bond : bond 0.00048 ( 10) link_NAG-ASN : bond 0.00710 ( 5) link_NAG-ASN : angle 2.21011 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 317 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6756 (tpt170) cc_final: 0.6455 (tpt90) REVERT: D 116 LYS cc_start: 0.8500 (pttp) cc_final: 0.7586 (ptmt) REVERT: D 163 MET cc_start: 0.8536 (mtm) cc_final: 0.8045 (mtp) REVERT: D 404 MET cc_start: 0.7705 (mtp) cc_final: 0.7327 (ptt) REVERT: A 169 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7183 (mm-30) REVERT: A 211 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7637 (pp20) REVERT: A 219 GLN cc_start: 0.8541 (mp10) cc_final: 0.8089 (mp10) REVERT: A 383 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7147 (ppp) REVERT: B 170 TRP cc_start: 0.8444 (m100) cc_final: 0.8132 (m100) REVERT: B 279 TYR cc_start: 0.8282 (p90) cc_final: 0.7623 (p90) REVERT: B 393 LYS cc_start: 0.7588 (mttm) cc_final: 0.7082 (pttt) REVERT: C 17 LEU cc_start: 0.9160 (mt) cc_final: 0.8834 (mt) REVERT: C 98 LEU cc_start: 0.9255 (pt) cc_final: 0.9003 (pt) REVERT: C 110 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7936 (mm-30) REVERT: C 147 MET cc_start: 0.8121 (mtp) cc_final: 0.7744 (tpt) REVERT: C 283 ILE cc_start: 0.8773 (tp) cc_final: 0.8524 (mm) REVERT: E 136 GLN cc_start: 0.9149 (tp40) cc_final: 0.8803 (tp-100) REVERT: E 208 GLN cc_start: 0.8570 (pt0) cc_final: 0.8239 (pt0) REVERT: E 235 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7851 (mt-10) REVERT: E 247 TYR cc_start: 0.8516 (m-80) cc_final: 0.8117 (m-80) REVERT: E 266 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7907 (t80) REVERT: E 290 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8097 (mm-30) REVERT: E 294 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8134 (mm) REVERT: E 329 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7748 (tm-30) REVERT: E 449 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7767 (ptpp) outliers start: 75 outliers final: 64 residues processed: 363 average time/residue: 0.0935 time to fit residues: 54.3448 Evaluate side-chains 379 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 311 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 417 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 76 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104098 restraints weight = 29728.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107495 restraints weight = 15860.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109795 restraints weight = 10286.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111321 restraints weight = 7649.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112321 restraints weight = 6286.322| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14437 Z= 0.148 Angle : 0.742 14.423 19455 Z= 0.355 Chirality : 0.046 0.403 2151 Planarity : 0.004 0.033 2406 Dihedral : 7.208 78.111 2113 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.54 % Allowed : 23.42 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.21), residues: 1673 helix: 1.75 (0.22), residues: 590 sheet: 0.01 (0.28), residues: 346 loop : -1.28 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 399 TYR 0.021 0.001 TYR E 325 PHE 0.026 0.001 PHE E 282 TRP 0.056 0.002 TRP C 239 HIS 0.005 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00340 (14412) covalent geometry : angle 0.73719 (19420) SS BOND : bond 0.00487 ( 10) SS BOND : angle 2.22695 ( 20) hydrogen bonds : bond 0.03989 ( 654) hydrogen bonds : angle 4.51554 ( 2061) Misc. bond : bond 0.00043 ( 10) link_NAG-ASN : bond 0.00637 ( 5) link_NAG-ASN : angle 2.16605 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 320 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 ARG cc_start: 0.6756 (tpt170) cc_final: 0.6457 (tpt90) REVERT: D 116 LYS cc_start: 0.8415 (pttp) cc_final: 0.7535 (ptmt) REVERT: D 163 MET cc_start: 0.8539 (mtm) cc_final: 0.8048 (mtp) REVERT: D 404 MET cc_start: 0.7681 (mtp) cc_final: 0.7311 (ptt) REVERT: A 89 MET cc_start: 0.7966 (ppp) cc_final: 0.7760 (ppp) REVERT: A 97 ASP cc_start: 0.8248 (p0) cc_final: 0.7916 (p0) REVERT: A 169 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7195 (mm-30) REVERT: A 211 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7584 (pp20) REVERT: A 219 GLN cc_start: 0.8523 (mp10) cc_final: 0.8071 (mp10) REVERT: A 220 MET cc_start: 0.8032 (mtm) cc_final: 0.7644 (tpp) REVERT: A 383 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7201 (ppp) REVERT: B 170 TRP cc_start: 0.8417 (m100) cc_final: 0.8101 (m100) REVERT: B 279 TYR cc_start: 0.8288 (p90) cc_final: 0.7628 (p90) REVERT: B 393 LYS cc_start: 0.7566 (mttm) cc_final: 0.7064 (pttt) REVERT: C 17 LEU cc_start: 0.9108 (mt) cc_final: 0.8790 (mt) REVERT: C 147 MET cc_start: 0.8139 (mtp) cc_final: 0.7767 (tpt) REVERT: C 283 ILE cc_start: 0.8773 (tp) cc_final: 0.8537 (mm) REVERT: E 136 GLN cc_start: 0.9159 (tp40) cc_final: 0.8821 (tp-100) REVERT: E 177 MET cc_start: 0.8467 (ttm) cc_final: 0.8119 (ttt) REVERT: E 202 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8127 (tm-30) REVERT: E 208 GLN cc_start: 0.8537 (pt0) cc_final: 0.8215 (pt0) REVERT: E 235 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7839 (mt-10) REVERT: E 247 TYR cc_start: 0.8489 (m-80) cc_final: 0.8091 (m-80) REVERT: E 266 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7865 (t80) REVERT: E 290 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8092 (mm-30) REVERT: E 294 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8075 (mm) REVERT: E 329 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7742 (tm-30) REVERT: E 449 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7793 (pttp) outliers start: 69 outliers final: 62 residues processed: 360 average time/residue: 0.0890 time to fit residues: 50.9962 Evaluate side-chains 379 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 313 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 44 optimal weight: 4.9990 chunk 124 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104114 restraints weight = 29440.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107518 restraints weight = 15624.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109812 restraints weight = 10130.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111380 restraints weight = 7536.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112312 restraints weight = 6171.202| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14437 Z= 0.147 Angle : 0.739 14.143 19455 Z= 0.352 Chirality : 0.045 0.376 2151 Planarity : 0.004 0.034 2406 Dihedral : 7.072 83.260 2113 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.67 % Allowed : 23.75 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1673 helix: 1.78 (0.21), residues: 588 sheet: 0.01 (0.28), residues: 346 loop : -1.25 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 399 TYR 0.020 0.001 TYR E 325 PHE 0.023 0.001 PHE E 282 TRP 0.046 0.001 TRP C 239 HIS 0.005 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00339 (14412) covalent geometry : angle 0.73426 (19420) SS BOND : bond 0.00402 ( 10) SS BOND : angle 2.16904 ( 20) hydrogen bonds : bond 0.03911 ( 654) hydrogen bonds : angle 4.50812 ( 2061) Misc. bond : bond 0.00045 ( 10) link_NAG-ASN : bond 0.00595 ( 5) link_NAG-ASN : angle 2.09766 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.56 seconds wall clock time: 43 minutes 4.33 seconds (2584.33 seconds total)