Starting phenix.real_space_refine on Sat May 17 01:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn2_27552/05_2025/8dn2_27552_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn2_27552/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dn2_27552/05_2025/8dn2_27552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn2_27552/05_2025/8dn2_27552.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn2_27552/05_2025/8dn2_27552_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn2_27552/05_2025/8dn2_27552_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.92, per 1000 atoms: 0.63 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: 3.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.61 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: 4.62 Time building geometry restraints manager: 4.27 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: 1.170 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.440 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- 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 : 14.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (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 TRP 0.010 0.001 TRP D 68 HIS 0.002 0.001 HIS A 311 PHE 0.011 0.001 PHE D 412 TYR 0.015 0.001 TYR D 301 ARG 0.003 0.000 ARG B 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 1.51756 ( 15) hydrogen bonds : bond 0.15680 ( 654) hydrogen bonds : angle 5.98792 ( 2061) SS BOND : bond 0.00255 ( 10) SS BOND : angle 1.36639 ( 20) covalent geometry : bond 0.00347 (14412) covalent geometry : angle 0.65209 (19420) Misc. bond : bond 0.32254 ( 10) *********************** 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 : 1.641 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: 0.2431 time to fit residues: 165.3439 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 : 1.568 ------------------------------------------------------------------------------- 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 141 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 0.0070 overall best weight: 1.8102 ------------------------------------------------------------------------------- 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 E 200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103806 restraints weight = 29461.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107159 restraints weight = 15919.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109279 restraints weight = 10422.113| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14437 Z= 0.160 Angle : 0.681 8.886 19455 Z= 0.339 Chirality : 0.045 0.242 2151 Planarity : 0.004 0.047 2406 Dihedral : 9.767 84.179 2138 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.08 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1673 helix: 2.00 (0.21), residues: 592 sheet: -0.21 (0.28), residues: 352 loop : -1.35 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.004 0.001 HIS C 109 PHE 0.016 0.001 PHE B 409 TYR 0.022 0.002 TYR B 78 ARG 0.009 0.001 ARG D 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 5) link_NAG-ASN : angle 2.79387 ( 15) hydrogen bonds : bond 0.04482 ( 654) hydrogen bonds : angle 4.68816 ( 2061) SS BOND : bond 0.00722 ( 10) SS BOND : angle 1.91792 ( 20) covalent geometry : bond 0.00349 (14412) covalent geometry : angle 0.67473 (19420) Misc. bond : bond 0.00142 ( 10) *********************** 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 408 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 346 time to evaluate : 1.495 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: 0.8293 (mp0) cc_final: 0.8034 (mp0) REVERT: D 242 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: D 404 MET cc_start: 0.7839 (mtp) cc_final: 0.7447 (ptt) REVERT: D 411 MET cc_start: 0.6215 (mmt) cc_final: 0.5996 (mmt) REVERT: A 172 GLU cc_start: 0.8322 (pm20) cc_final: 0.7476 (pm20) REVERT: A 192 GLU cc_start: 0.8334 (pm20) cc_final: 0.7863 (mm-30) REVERT: A 217 GLU cc_start: 0.8467 (tp30) cc_final: 0.8235 (tp30) REVERT: A 219 GLN cc_start: 0.8509 (mp10) cc_final: 0.8175 (mp-120) REVERT: A 383 MET cc_start: 0.7844 (ppp) cc_final: 0.7174 (ppp) REVERT: B 41 CYS cc_start: 0.8973 (p) cc_final: 0.8307 (p) REVERT: B 131 ARG cc_start: 0.9036 (ttt-90) cc_final: 0.8620 (ttt90) REVERT: B 170 TRP cc_start: 0.8358 (m100) cc_final: 0.7925 (m100) REVERT: B 252 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: B 393 LYS cc_start: 0.7544 (mttm) cc_final: 0.7085 (pttt) REVERT: C 17 LEU cc_start: 0.9186 (mt) cc_final: 0.8815 (mt) REVERT: C 85 LEU cc_start: 0.7602 (tp) cc_final: 0.7335 (tp) REVERT: C 116 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8715 (mtpp) REVERT: C 147 MET cc_start: 0.7970 (mtp) cc_final: 0.7519 (tpt) REVERT: C 192 GLU cc_start: 0.8628 (tp30) cc_final: 0.8379 (tp30) REVERT: E 170 MET cc_start: 0.9166 (mtm) cc_final: 0.8879 (mtm) REVERT: E 235 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 247 TYR cc_start: 0.8543 (m-80) cc_final: 0.8155 (m-80) REVERT: E 285 LEU cc_start: 0.7921 (mt) cc_final: 0.7454 (tt) REVERT: E 329 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 449 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7568 (ptpp) outliers start: 62 outliers final: 42 residues processed: 379 average time/residue: 0.2027 time to fit residues: 118.5833 Evaluate side-chains 360 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 200 GLN Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 301 VAL 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 19 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105434 restraints weight = 29416.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108868 restraints weight = 15751.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111182 restraints weight = 10244.930| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14437 Z= 0.134 Angle : 0.665 9.864 19455 Z= 0.328 Chirality : 0.044 0.285 2151 Planarity : 0.004 0.040 2406 Dihedral : 8.688 81.607 2125 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.95 % Allowed : 17.83 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1673 helix: 2.02 (0.21), residues: 587 sheet: -0.01 (0.29), residues: 338 loop : -1.41 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.017 0.001 PHE E 282 TYR 0.020 0.001 TYR E 325 ARG 0.004 0.000 ARG D 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 5) link_NAG-ASN : angle 2.16150 ( 15) hydrogen bonds : bond 0.04174 ( 654) hydrogen bonds : angle 4.45812 ( 2061) SS BOND : bond 0.00430 ( 10) SS BOND : angle 2.26951 ( 20) covalent geometry : bond 0.00291 (14412) covalent geometry : angle 0.65843 (19420) Misc. bond : bond 0.00414 ( 10) *********************** 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: 60 poor density : 339 time to evaluate : 1.568 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: 0.8329 (mp0) cc_final: 0.8070 (mp0) REVERT: D 108 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: D 203 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7616 (p0) REVERT: D 298 LEU cc_start: 0.9211 (tp) cc_final: 0.8993 (tp) REVERT: D 404 MET cc_start: 0.7769 (mtp) cc_final: 0.7369 (ptt) REVERT: A 192 GLU cc_start: 0.8292 (pm20) cc_final: 0.7854 (mm-30) REVERT: A 219 GLN cc_start: 0.8534 (mp10) cc_final: 0.8023 (mp-120) REVERT: A 383 MET cc_start: 0.7893 (ppp) cc_final: 0.7275 (ppp) REVERT: B 41 CYS cc_start: 0.9004 (p) cc_final: 0.8419 (p) REVERT: B 131 ARG cc_start: 0.9004 (ttt-90) cc_final: 0.8592 (ttt90) REVERT: B 170 TRP cc_start: 0.8331 (m100) cc_final: 0.7924 (m100) REVERT: B 252 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7884 (mmm-85) REVERT: B 279 TYR cc_start: 0.8284 (p90) cc_final: 0.7677 (p90) REVERT: B 393 LYS cc_start: 0.7531 (mttm) cc_final: 0.7078 (pttt) REVERT: C 17 LEU cc_start: 0.9161 (mt) cc_final: 0.8823 (mt) REVERT: C 116 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8743 (mtpp) REVERT: C 147 MET cc_start: 0.8104 (mtp) cc_final: 0.7545 (tpt) REVERT: C 172 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8807 (mm-30) REVERT: C 192 GLU cc_start: 0.8627 (tp30) cc_final: 0.8413 (tp30) REVERT: E 200 GLN cc_start: 0.7382 (pt0) cc_final: 0.7152 (pt0) REVERT: E 247 TYR cc_start: 0.8510 (m-80) cc_final: 0.8136 (m-80) REVERT: E 268 ILE cc_start: 0.9311 (mt) cc_final: 0.9053 (mp) REVERT: E 329 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7869 (tm-30) REVERT: E 449 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7584 (ptpp) outliers start: 60 outliers final: 39 residues processed: 377 average time/residue: 0.2165 time to fit residues: 124.6264 Evaluate side-chains 351 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 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 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 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 15 ASP 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 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 221 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 301 VAL 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 55 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 16 optimal weight: 0.0370 chunk 157 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN E 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106286 restraints weight = 29300.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109795 restraints weight = 15492.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112129 restraints weight = 9989.950| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2096 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= 0.122 Angle : 0.658 10.316 19455 Z= 0.322 Chirality : 0.043 0.301 2151 Planarity : 0.003 0.035 2406 Dihedral : 7.996 77.885 2117 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.75 % Allowed : 19.28 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1673 helix: 1.95 (0.21), residues: 593 sheet: 0.09 (0.29), residues: 338 loop : -1.40 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.019 0.001 PHE E 282 TYR 0.025 0.001 TYR B 78 ARG 0.009 0.000 ARG C 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 5) link_NAG-ASN : angle 2.04950 ( 15) hydrogen bonds : bond 0.03923 ( 654) hydrogen bonds : angle 4.41446 ( 2061) SS BOND : bond 0.00936 ( 10) SS BOND : angle 2.44813 ( 20) covalent geometry : bond 0.00262 (14412) covalent geometry : angle 0.65140 (19420) Misc. bond : bond 0.00156 ( 10) *********************** 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 393 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 336 time to evaluate : 1.490 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: 0.8310 (mp0) cc_final: 0.8106 (mp0) REVERT: D 108 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: D 163 MET cc_start: 0.8302 (mtm) cc_final: 0.7927 (mtp) REVERT: D 298 LEU cc_start: 0.9194 (tp) cc_final: 0.8966 (tp) REVERT: D 404 MET cc_start: 0.7759 (mtp) cc_final: 0.7359 (ptt) REVERT: A 169 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7124 (mm-30) REVERT: A 219 GLN cc_start: 0.8590 (mp10) cc_final: 0.8191 (mp10) REVERT: A 383 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7285 (ppp) REVERT: B 41 CYS cc_start: 0.8982 (p) cc_final: 0.8412 (p) REVERT: B 131 ARG cc_start: 0.8979 (ttt-90) cc_final: 0.8601 (ttt90) REVERT: B 170 TRP cc_start: 0.8323 (m100) cc_final: 0.7884 (m100) REVERT: B 252 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.7818 (mmm-85) REVERT: B 279 TYR cc_start: 0.8253 (p90) cc_final: 0.7575 (p90) REVERT: B 393 LYS cc_start: 0.7537 (mttm) cc_final: 0.7062 (pttt) REVERT: C 17 LEU cc_start: 0.9132 (mt) cc_final: 0.8820 (mt) REVERT: C 116 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8667 (mtmm) REVERT: C 147 MET cc_start: 0.8129 (mtp) cc_final: 0.7648 (tpt) REVERT: C 172 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8819 (mm-30) REVERT: E 235 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7744 (mt-10) REVERT: E 247 TYR cc_start: 0.8467 (m-80) cc_final: 0.8090 (m-80) REVERT: E 268 ILE cc_start: 0.9311 (mt) cc_final: 0.9070 (mp) REVERT: E 329 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7771 (tm-30) REVERT: E 449 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7731 (ptpp) outliers start: 57 outliers final: 42 residues processed: 363 average time/residue: 0.2249 time to fit residues: 126.5795 Evaluate side-chains 360 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 182 LEU 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 149 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 383 MET 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 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 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 284 ASP Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 113 TYR 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 285 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 446 THR Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103643 restraints weight = 29407.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107038 restraints weight = 15523.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109345 restraints weight = 10006.564| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14437 Z= 0.171 Angle : 0.661 10.064 19455 Z= 0.327 Chirality : 0.044 0.251 2151 Planarity : 0.004 0.032 2406 Dihedral : 7.897 72.508 2117 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.13 % Allowed : 19.67 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1673 helix: 2.03 (0.21), residues: 593 sheet: -0.13 (0.28), residues: 358 loop : -1.32 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.018 0.001 PHE E 282 TYR 0.020 0.001 TYR D 301 ARG 0.003 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 5) link_NAG-ASN : angle 2.09407 ( 15) hydrogen bonds : bond 0.04017 ( 654) hydrogen bonds : angle 4.43244 ( 2061) SS BOND : bond 0.00510 ( 10) SS BOND : angle 2.30642 ( 20) covalent geometry : bond 0.00386 (14412) covalent geometry : angle 0.65466 (19420) Misc. bond : bond 0.00043 ( 10) *********************** 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 408 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 330 time to evaluate : 1.561 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: 0.6704 (tpt170) cc_final: 0.6443 (tpt90) REVERT: D 53 GLU cc_start: 0.8413 (mp0) cc_final: 0.8132 (mp0) REVERT: D 108 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: D 163 MET cc_start: 0.8456 (mtm) cc_final: 0.8088 (mtp) REVERT: D 188 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9112 (mm) REVERT: D 298 LEU cc_start: 0.9287 (tp) cc_final: 0.9075 (tp) REVERT: D 300 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6481 (pp20) REVERT: D 404 MET cc_start: 0.7794 (mtp) cc_final: 0.7410 (ptt) REVERT: A 169 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7203 (mm-30) REVERT: A 192 GLU cc_start: 0.8327 (pm20) cc_final: 0.7880 (mm-30) REVERT: B 41 CYS cc_start: 0.8873 (p) cc_final: 0.8330 (p) REVERT: B 170 TRP cc_start: 0.8369 (m100) cc_final: 0.7854 (m100) REVERT: B 252 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.7876 (mmm-85) REVERT: B 279 TYR cc_start: 0.8298 (p90) cc_final: 0.7668 (p90) REVERT: B 287 MET cc_start: 0.8786 (ttt) cc_final: 0.8546 (ttt) REVERT: B 393 LYS cc_start: 0.7627 (mttm) cc_final: 0.7139 (pttt) REVERT: C 17 LEU cc_start: 0.9186 (mt) cc_final: 0.8874 (mt) REVERT: C 116 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8759 (mtmm) REVERT: C 147 MET cc_start: 0.8130 (mtp) cc_final: 0.7736 (tpt) REVERT: C 172 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8808 (mm-30) REVERT: E 235 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7677 (mt-10) REVERT: E 247 TYR cc_start: 0.8538 (m-80) cc_final: 0.8129 (m-80) REVERT: E 268 ILE cc_start: 0.9373 (mt) cc_final: 0.9136 (mp) REVERT: E 329 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 449 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7720 (ptpp) outliers start: 78 outliers final: 59 residues processed: 373 average time/residue: 0.2096 time to fit residues: 121.0550 Evaluate side-chains 374 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain D residue 188 ILE 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 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 293 PHE Chi-restraints excluded: chain A residue 417 TYR 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 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 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 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 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 285 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 VAL 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 475 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 94 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 0.0050 overall best weight: 1.9200 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103556 restraints weight = 29699.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106956 restraints weight = 15715.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109270 restraints weight = 10139.653| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2342 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= 0.152 Angle : 0.670 10.179 19455 Z= 0.327 Chirality : 0.044 0.395 2151 Planarity : 0.004 0.046 2406 Dihedral : 7.792 66.009 2117 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.33 % Allowed : 20.99 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1673 helix: 2.02 (0.21), residues: 592 sheet: -0.05 (0.28), residues: 344 loop : -1.37 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.022 0.001 PHE E 282 TYR 0.021 0.001 TYR E 325 ARG 0.002 0.000 ARG D 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 5) link_NAG-ASN : angle 2.12031 ( 15) hydrogen bonds : bond 0.04005 ( 654) hydrogen bonds : angle 4.41261 ( 2061) SS BOND : bond 0.00420 ( 10) SS BOND : angle 1.91265 ( 20) covalent geometry : bond 0.00346 (14412) covalent geometry : angle 0.66509 (19420) Misc. bond : bond 0.00045 ( 10) *********************** 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 410 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 329 time to evaluate : 1.629 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: 0.6698 (tpt170) cc_final: 0.6378 (tpt90) REVERT: D 53 GLU cc_start: 0.8393 (mp0) cc_final: 0.8134 (mp0) REVERT: D 116 LYS cc_start: 0.8449 (pttp) cc_final: 0.7967 (mtmm) REVERT: D 163 MET cc_start: 0.8513 (mtm) cc_final: 0.8121 (mtp) REVERT: D 298 LEU cc_start: 0.9281 (tp) cc_final: 0.9053 (tp) REVERT: D 300 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6355 (pp20) REVERT: D 404 MET cc_start: 0.7772 (mtp) cc_final: 0.7384 (ptt) REVERT: A 169 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7242 (mm-30) REVERT: A 219 GLN cc_start: 0.8601 (mp10) cc_final: 0.8231 (mp10) REVERT: A 383 MET cc_start: 0.7686 (ppp) cc_final: 0.6866 (ppp) REVERT: B 170 TRP cc_start: 0.8350 (m100) cc_final: 0.7825 (m100) REVERT: B 252 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.7865 (mmm-85) REVERT: B 279 TYR cc_start: 0.8296 (p90) cc_final: 0.7698 (p90) REVERT: B 393 LYS cc_start: 0.7594 (mttm) cc_final: 0.7095 (pttt) REVERT: C 17 LEU cc_start: 0.9188 (mt) cc_final: 0.8867 (mt) REVERT: C 147 MET cc_start: 0.8125 (mtp) cc_final: 0.7709 (tpt) REVERT: C 172 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8796 (mm-30) REVERT: C 239 TRP cc_start: 0.8435 (m-10) cc_final: 0.8218 (m100) REVERT: E 235 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7848 (mt-10) REVERT: E 247 TYR cc_start: 0.8513 (m-80) cc_final: 0.8095 (m-80) REVERT: E 268 ILE cc_start: 0.9387 (mt) cc_final: 0.9150 (mp) REVERT: E 329 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7763 (tm-30) REVERT: E 449 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7910 (ptpt) outliers start: 81 outliers final: 61 residues processed: 377 average time/residue: 0.2251 time to fit residues: 130.7482 Evaluate side-chains 377 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 182 LEU 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 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 253 VAL 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 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 208 THR 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 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 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 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 292 THR Chi-restraints excluded: chain E residue 298 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 468 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101523 restraints weight = 29871.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104867 restraints weight = 16001.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107103 restraints weight = 10438.110| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14437 Z= 0.198 Angle : 0.708 11.003 19455 Z= 0.349 Chirality : 0.045 0.454 2151 Planarity : 0.004 0.048 2406 Dihedral : 7.783 59.704 2117 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.59 % Allowed : 21.12 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1673 helix: 1.98 (0.21), residues: 585 sheet: -0.13 (0.28), residues: 347 loop : -1.34 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 239 HIS 0.004 0.001 HIS A 311 PHE 0.025 0.002 PHE E 282 TYR 0.020 0.002 TYR D 301 ARG 0.006 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 5) link_NAG-ASN : angle 2.25719 ( 15) hydrogen bonds : bond 0.04206 ( 654) hydrogen bonds : angle 4.53871 ( 2061) SS BOND : bond 0.00479 ( 10) SS BOND : angle 2.21172 ( 20) covalent geometry : bond 0.00452 (14412) covalent geometry : angle 0.70249 (19420) Misc. bond : bond 0.00057 ( 10) *********************** 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 412 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 327 time to evaluate : 1.580 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: 0.6675 (tpt170) cc_final: 0.6372 (tpt90) REVERT: D 116 LYS cc_start: 0.8455 (pttp) cc_final: 0.8211 (pttp) REVERT: D 163 MET cc_start: 0.8545 (mtm) cc_final: 0.8018 (mtp) REVERT: D 271 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6579 (mtm-85) REVERT: D 300 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6468 (pp20) REVERT: D 404 MET cc_start: 0.7757 (mtp) cc_final: 0.7374 (ptt) REVERT: A 211 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: A 383 MET cc_start: 0.7658 (ppp) cc_final: 0.6791 (ppp) REVERT: B 170 TRP cc_start: 0.8389 (m100) cc_final: 0.7899 (m100) REVERT: B 252 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7825 (mmm-85) REVERT: B 279 TYR cc_start: 0.8255 (p90) cc_final: 0.7608 (p90) REVERT: B 393 LYS cc_start: 0.7588 (mttm) cc_final: 0.7097 (pttt) REVERT: C 17 LEU cc_start: 0.9197 (mt) cc_final: 0.8796 (mt) REVERT: C 77 GLU cc_start: 0.8814 (mp0) cc_final: 0.8512 (pm20) REVERT: C 110 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 147 MET cc_start: 0.8187 (mtp) cc_final: 0.7856 (tpt) REVERT: C 239 TRP cc_start: 0.8388 (m-10) cc_final: 0.8144 (m100) REVERT: E 136 GLN cc_start: 0.9122 (tp40) cc_final: 0.8800 (tp-100) REVERT: E 235 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7781 (mt-10) REVERT: E 247 TYR cc_start: 0.8576 (m-80) cc_final: 0.8160 (m-80) REVERT: E 290 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8024 (mm-30) REVERT: E 294 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8149 (mm) REVERT: E 329 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7754 (tm-30) outliers start: 85 outliers final: 69 residues processed: 374 average time/residue: 0.2193 time to fit residues: 127.0067 Evaluate side-chains 384 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 313 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain D residue 231 SER 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 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 253 VAL 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 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 135 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 208 THR 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 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 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 292 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 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 468 VAL Chi-restraints excluded: chain E residue 475 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103855 restraints weight = 29420.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107281 restraints weight = 15521.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109611 restraints weight = 9998.939| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2570 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= 0.145 Angle : 0.724 13.263 19455 Z= 0.345 Chirality : 0.045 0.434 2151 Planarity : 0.003 0.040 2406 Dihedral : 7.601 65.620 2117 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.74 % Allowed : 22.83 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1673 helix: 1.87 (0.21), residues: 591 sheet: -0.01 (0.29), residues: 338 loop : -1.35 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.029 0.001 PHE E 282 TYR 0.021 0.001 TYR E 325 ARG 0.002 0.000 ARG B 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 5) link_NAG-ASN : angle 2.24755 ( 15) hydrogen bonds : bond 0.04034 ( 654) hydrogen bonds : angle 4.47428 ( 2061) SS BOND : bond 0.00564 ( 10) SS BOND : angle 2.13848 ( 20) covalent geometry : bond 0.00330 (14412) covalent geometry : angle 0.71828 (19420) Misc. bond : bond 0.00046 ( 10) *********************** 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 407 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 335 time to evaluate : 1.536 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: 0.6736 (tpt170) cc_final: 0.6432 (tpt90) REVERT: D 116 LYS cc_start: 0.8329 (pttp) cc_final: 0.8065 (pttp) REVERT: D 163 MET cc_start: 0.8573 (mtm) cc_final: 0.8081 (mtp) REVERT: D 271 ARG cc_start: 0.6932 (mtm-85) cc_final: 0.6497 (mtm-85) REVERT: D 300 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6543 (pp20) REVERT: D 404 MET cc_start: 0.7740 (mtp) cc_final: 0.7359 (ptt) REVERT: A 169 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7212 (mm-30) REVERT: A 192 GLU cc_start: 0.8274 (pm20) cc_final: 0.7749 (mm-30) REVERT: A 211 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7634 (pp20) REVERT: A 383 MET cc_start: 0.7693 (ppp) cc_final: 0.6692 (ppp) REVERT: B 170 TRP cc_start: 0.8344 (m100) cc_final: 0.7857 (m100) REVERT: B 252 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: B 279 TYR cc_start: 0.8240 (p90) cc_final: 0.7576 (p90) REVERT: B 393 LYS cc_start: 0.7574 (mttm) cc_final: 0.7070 (pttt) REVERT: C 17 LEU cc_start: 0.9090 (mt) cc_final: 0.8770 (mt) REVERT: C 77 GLU cc_start: 0.8803 (mp0) cc_final: 0.8530 (pm20) REVERT: C 239 TRP cc_start: 0.8399 (m-10) cc_final: 0.8186 (m100) REVERT: C 301 TYR cc_start: 0.8772 (t80) cc_final: 0.8563 (t80) REVERT: E 136 GLN cc_start: 0.9117 (tp40) cc_final: 0.8804 (tp-100) REVERT: E 235 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7859 (mt-10) REVERT: E 247 TYR cc_start: 0.8494 (m-80) cc_final: 0.8082 (m-80) REVERT: E 266 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7903 (t80) REVERT: E 290 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7997 (mm-30) REVERT: E 294 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8110 (mm) REVERT: E 329 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7725 (tm-30) outliers start: 72 outliers final: 63 residues processed: 379 average time/residue: 0.2071 time to fit residues: 121.1104 Evaluate side-chains 380 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 314 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 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 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 260 VAL 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 295 PHE 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 147 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 ILE 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 B residue 416 ILE 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 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 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 266 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 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 132 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104364 restraints weight = 29725.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107978 restraints weight = 15285.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110425 restraints weight = 9723.789| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2707 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= 0.131 Angle : 0.741 14.390 19455 Z= 0.352 Chirality : 0.045 0.396 2151 Planarity : 0.003 0.032 2406 Dihedral : 7.181 69.224 2114 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.47 % Allowed : 23.62 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1673 helix: 1.82 (0.22), residues: 589 sheet: 0.03 (0.28), residues: 346 loop : -1.30 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.024 0.001 PHE E 282 TYR 0.020 0.001 TYR E 325 ARG 0.003 0.000 ARG C 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00927 ( 5) link_NAG-ASN : angle 2.73235 ( 15) hydrogen bonds : bond 0.04024 ( 654) hydrogen bonds : angle 4.45218 ( 2061) SS BOND : bond 0.00428 ( 10) SS BOND : angle 1.76613 ( 20) covalent geometry : bond 0.00291 (14412) covalent geometry : angle 0.73599 (19420) Misc. bond : bond 0.00032 ( 10) *********************** 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 399 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 331 time to evaluate : 1.535 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: 0.6804 (tpt170) cc_final: 0.6509 (tpt90) REVERT: D 116 LYS cc_start: 0.8421 (pttp) cc_final: 0.8151 (pttp) REVERT: D 163 MET cc_start: 0.8548 (mtm) cc_final: 0.8120 (mtp) REVERT: D 404 MET cc_start: 0.7742 (mtp) cc_final: 0.7390 (ptt) REVERT: A 97 ASP cc_start: 0.8266 (p0) cc_final: 0.7967 (p0) REVERT: A 169 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7291 (mm-30) REVERT: A 220 MET cc_start: 0.7714 (mtm) cc_final: 0.7373 (tpp) REVERT: A 383 MET cc_start: 0.7851 (ppp) cc_final: 0.6941 (ppp) REVERT: B 170 TRP cc_start: 0.8486 (m100) cc_final: 0.8067 (m100) REVERT: B 279 TYR cc_start: 0.8374 (p90) cc_final: 0.7735 (p90) REVERT: B 393 LYS cc_start: 0.7634 (mttm) cc_final: 0.7109 (pttt) REVERT: C 17 LEU cc_start: 0.9121 (mt) cc_final: 0.8786 (mt) REVERT: C 77 GLU cc_start: 0.8751 (mp0) cc_final: 0.8476 (pm20) REVERT: C 140 MET cc_start: 0.8787 (tpp) cc_final: 0.8567 (tpp) REVERT: C 172 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8815 (mm-30) REVERT: C 239 TRP cc_start: 0.8405 (m-10) cc_final: 0.8151 (m100) REVERT: C 283 ILE cc_start: 0.8818 (tp) cc_final: 0.8571 (mm) REVERT: C 301 TYR cc_start: 0.8729 (t80) cc_final: 0.8521 (t80) REVERT: E 120 ASP cc_start: 0.9115 (p0) cc_final: 0.8787 (p0) REVERT: E 136 GLN cc_start: 0.9091 (tp40) cc_final: 0.8790 (tp-100) REVERT: E 170 MET cc_start: 0.8673 (mtm) cc_final: 0.8323 (ptp) REVERT: E 235 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 247 TYR cc_start: 0.8412 (m-80) cc_final: 0.8012 (m-80) REVERT: E 266 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7855 (t80) REVERT: E 290 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7961 (mm-30) REVERT: E 294 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8148 (mm) REVERT: E 329 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7771 (tm-30) outliers start: 68 outliers final: 58 residues processed: 372 average time/residue: 0.2140 time to fit residues: 123.1363 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 : 1.588 ------------------------------------------------------------------------------- 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 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 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 238 SER Chi-restraints excluded: chain A residue 241 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 412 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 ILE 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 B residue 416 ILE 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 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 266 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 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 95 optimal weight: 0.9980 chunk 8 optimal weight: 0.0040 chunk 27 optimal weight: 0.0970 chunk 161 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105951 restraints weight = 29866.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109643 restraints weight = 15228.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112130 restraints weight = 9623.933| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2890 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= 0.127 Angle : 0.740 14.033 19455 Z= 0.352 Chirality : 0.045 0.332 2151 Planarity : 0.003 0.035 2406 Dihedral : 6.992 71.421 2114 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.82 % Allowed : 24.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1673 helix: 1.75 (0.22), residues: 589 sheet: -0.01 (0.28), residues: 356 loop : -1.19 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 243 HIS 0.003 0.001 HIS A 311 PHE 0.026 0.001 PHE E 282 TYR 0.021 0.001 TYR E 325 ARG 0.006 0.000 ARG C 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00797 ( 5) link_NAG-ASN : angle 2.15497 ( 15) hydrogen bonds : bond 0.03865 ( 654) hydrogen bonds : angle 4.41054 ( 2061) SS BOND : bond 0.00429 ( 10) SS BOND : angle 1.91009 ( 20) covalent geometry : bond 0.00282 (14412) covalent geometry : angle 0.73592 (19420) Misc. bond : bond 0.00029 ( 10) ********************** 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 395 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 1.493 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: 0.6758 (tpt170) cc_final: 0.6454 (tpt90) REVERT: D 163 MET cc_start: 0.8558 (mtm) cc_final: 0.8098 (mtp) REVERT: D 271 ARG cc_start: 0.8001 (mmp80) cc_final: 0.6953 (mtm110) REVERT: D 404 MET cc_start: 0.7730 (mtp) cc_final: 0.7366 (ptt) REVERT: A 89 MET cc_start: 0.7956 (ppp) cc_final: 0.7714 (ppp) REVERT: A 97 ASP cc_start: 0.8254 (p0) cc_final: 0.7962 (p0) REVERT: A 119 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8080 (ttm170) REVERT: A 169 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7293 (mm-30) REVERT: A 192 GLU cc_start: 0.8290 (pm20) cc_final: 0.7802 (mm-30) REVERT: A 211 GLU cc_start: 0.7844 (pp20) cc_final: 0.7452 (pm20) REVERT: A 220 MET cc_start: 0.7644 (mtm) cc_final: 0.7253 (tpp) REVERT: A 383 MET cc_start: 0.7779 (ppp) cc_final: 0.6958 (ppp) REVERT: B 8 MET cc_start: 0.6049 (tpt) cc_final: 0.5804 (mmt) REVERT: B 170 TRP cc_start: 0.8504 (m100) cc_final: 0.8069 (m100) REVERT: B 276 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8092 (mtmt) REVERT: B 279 TYR cc_start: 0.8362 (p90) cc_final: 0.7709 (p90) REVERT: B 393 LYS cc_start: 0.7580 (mttm) cc_final: 0.7070 (pttt) REVERT: C 17 LEU cc_start: 0.9104 (mt) cc_final: 0.8782 (mt) REVERT: C 77 GLU cc_start: 0.8752 (mp0) cc_final: 0.8477 (pm20) REVERT: C 140 MET cc_start: 0.8809 (tpp) cc_final: 0.8584 (tpp) REVERT: C 172 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8840 (mm-30) REVERT: C 239 TRP cc_start: 0.8377 (m-10) cc_final: 0.8155 (m100) REVERT: C 287 MET cc_start: 0.6619 (tpt) cc_final: 0.6237 (ttm) REVERT: C 301 TYR cc_start: 0.8684 (t80) cc_final: 0.8482 (t80) REVERT: E 120 ASP cc_start: 0.9112 (p0) cc_final: 0.8806 (p0) REVERT: E 136 GLN cc_start: 0.9112 (tp40) cc_final: 0.8834 (tp-100) REVERT: E 170 MET cc_start: 0.8661 (mtm) cc_final: 0.8349 (ptp) REVERT: E 235 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 247 TYR cc_start: 0.8391 (m-80) cc_final: 0.8022 (m-80) REVERT: E 290 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7985 (mm-30) REVERT: E 294 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8087 (mm) REVERT: E 329 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7689 (tm-30) REVERT: E 331 MET cc_start: 0.8726 (mmt) cc_final: 0.8522 (mmt) outliers start: 58 outliers final: 45 residues processed: 372 average time/residue: 0.2178 time to fit residues: 123.9509 Evaluate side-chains 362 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 316 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain A residue 37 VAL 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 238 SER Chi-restraints excluded: chain A residue 241 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 412 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 416 ILE 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 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 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 294 LEU Chi-restraints excluded: chain E residue 301 VAL 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 153 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 0.0020 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107475 restraints weight = 29525.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111006 restraints weight = 15579.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113381 restraints weight = 10031.263| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14437 Z= 0.130 Angle : 0.759 13.655 19455 Z= 0.358 Chirality : 0.045 0.296 2151 Planarity : 0.003 0.035 2406 Dihedral : 6.723 72.889 2112 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.36 % Allowed : 25.26 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1673 helix: 1.73 (0.21), residues: 591 sheet: 0.05 (0.28), residues: 347 loop : -1.23 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 239 HIS 0.003 0.001 HIS A 311 PHE 0.027 0.001 PHE E 282 TYR 0.020 0.001 TYR E 325 ARG 0.008 0.000 ARG D 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 5) link_NAG-ASN : angle 2.06881 ( 15) hydrogen bonds : bond 0.03830 ( 654) hydrogen bonds : angle 4.37769 ( 2061) SS BOND : bond 0.00355 ( 10) SS BOND : angle 2.08646 ( 20) covalent geometry : bond 0.00293 (14412) covalent geometry : angle 0.75486 (19420) Misc. bond : bond 0.00028 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4351.18 seconds wall clock time: 77 minutes 4.81 seconds (4624.81 seconds total)