Starting phenix.real_space_refine on Sat Aug 23 10:23:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm2_50547/08_2025/9fm2_50547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm2_50547/08_2025/9fm2_50547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fm2_50547/08_2025/9fm2_50547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm2_50547/08_2025/9fm2_50547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fm2_50547/08_2025/9fm2_50547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm2_50547/08_2025/9fm2_50547.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 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 116 5.16 5 C 7260 2.51 5 N 2005 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11567 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain breaks: 2 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 331} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2674 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 331} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 331} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.27 Number of scatterers: 11567 At special positions: 0 Unit cell: (115.2, 115.2, 92.16, 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 116 16.00 O 2186 8.00 N 2005 7.00 C 7260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.06 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.06 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.05 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.08 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.10 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.00 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.06 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=1.97 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.07 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.00 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.00 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.05 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.05 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.02 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.04 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.00 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 420 " distance=2.05 Simple disulfide: pdb=" SG CYS E 122 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 229 " distance=1.99 Simple disulfide: pdb=" SG CYS E 231 " - pdb=" SG CYS E 236 " distance=2.08 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.04 Simple disulfide: pdb=" SG CYS E 424 " - pdb=" SG CYS E 447 " distance=1.99 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=0, symmetry=0 Links applied NAG-ASN " NAG B 500 " - " ASN B 284 " " NAG C 500 " - " ASN C 284 " " NAG D 500 " - " ASN D 284 " " NAG E 500 " - " ASN E 284 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 596.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 30 sheets defined 1.2% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.721A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.504A pdb=" N THR A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 196 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.937A pdb=" N THR A 68 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.620A pdb=" N LEU A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 38 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 89 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 98 removed outlier: 6.930A pdb=" N ILE B 445 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 97 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 443 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 122 removed outlier: 5.840A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 121 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 128 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 131 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 155 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET B 174 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER B 158 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 172 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 179 through 183 removed outlier: 4.324A pdb=" N ASP B 212 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 206 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.739A pdb=" N ASN B 230 " --> pdb=" O TYR B 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.593A pdb=" N GLU B 250 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 253 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 264 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS B 255 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 269 removed outlier: 3.510A pdb=" N ILE B 314 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR B 278 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 292 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 352 through 356 removed outlier: 3.618A pdb=" N VAL B 353 " --> pdb=" O TRP B 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 380 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.137A pdb=" N LYS C 94 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N CYS C 447 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 448 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 411 " --> pdb=" O GLY C 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 115 through 122 removed outlier: 5.795A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 121 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 131 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET C 174 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER C 158 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 172 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 180 through 183 removed outlier: 4.540A pdb=" N ASP C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 206 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR C 210 " --> pdb=" O TYR C 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG C 223 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 230 " --> pdb=" O TYR C 237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG C 223 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 238 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 254 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE C 253 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU C 264 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS C 255 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.536A pdb=" N ILE C 314 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 311 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 303 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG C 292 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU C 276 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 98 removed outlier: 6.976A pdb=" N ILE D 445 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU D 97 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR D 443 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 122 removed outlier: 5.655A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 121 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 131 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU D 156 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 171 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 179 through 183 removed outlier: 4.458A pdb=" N ASP D 212 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR D 206 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.626A pdb=" N ASN D 230 " --> pdb=" O TYR D 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.510A pdb=" N PHE D 253 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU D 264 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 255 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 268 through 269 removed outlier: 3.538A pdb=" N ILE D 314 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 303 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG D 292 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU D 276 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 352 through 356 removed outlier: 3.546A pdb=" N TYR D 380 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 367 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N MET D 377 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL D 399 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU D 379 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 92 through 98 removed outlier: 6.853A pdb=" N ILE E 445 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 97 " --> pdb=" O THR E 443 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR E 443 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 448 " --> pdb=" O PRO E 423 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 115 through 122 removed outlier: 5.744A pdb=" N GLU E 117 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU E 132 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 121 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 128 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 159 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 131 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E 157 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 180 through 183 removed outlier: 3.525A pdb=" N TYR E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP E 212 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR E 206 " --> pdb=" O TYR E 210 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR E 210 " --> pdb=" O TYR E 206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG E 223 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN E 230 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.519A pdb=" N ARG E 223 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE E 253 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU E 264 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS E 255 " --> pdb=" O ILE E 262 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 268 through 269 removed outlier: 3.884A pdb=" N THR E 311 " --> pdb=" O ASN E 306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 303 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG E 292 " --> pdb=" O GLU E 276 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU E 276 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 352 through 356 removed outlier: 3.516A pdb=" N GLY E 362 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET E 377 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL E 399 " --> pdb=" O MET E 377 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU E 379 " --> pdb=" O SER E 397 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1927 1.31 - 1.45: 3340 1.45 - 1.58: 6398 1.58 - 1.71: 2 1.71 - 1.84: 162 Bond restraints: 11829 Sorted by residual: bond pdb=" C PRO D 423 " pdb=" O PRO D 423 " ideal model delta sigma weight residual 1.235 1.190 0.045 7.90e-03 1.60e+04 3.31e+01 bond pdb=" C PRO E 423 " pdb=" O PRO E 423 " ideal model delta sigma weight residual 1.235 1.195 0.040 7.90e-03 1.60e+04 2.53e+01 bond pdb=" C ILE D 191 " pdb=" O ILE D 191 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.01e-02 9.80e+03 1.97e+01 bond pdb=" C ILE B 191 " pdb=" O ILE B 191 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.01e-02 9.80e+03 1.85e+01 bond pdb=" C ARG B 363 " pdb=" O ARG B 363 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.14e-02 7.69e+03 1.66e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14724 1.95 - 3.89: 1078 3.89 - 5.84: 147 5.84 - 7.78: 20 7.78 - 9.73: 6 Bond angle restraints: 15975 Sorted by residual: angle pdb=" N CYS B 277 " pdb=" CA CYS B 277 " pdb=" C CYS B 277 " ideal model delta sigma weight residual 108.75 118.45 -9.70 1.71e+00 3.42e-01 3.22e+01 angle pdb=" CG MET C 449 " pdb=" SD MET C 449 " pdb=" CE MET C 449 " ideal model delta sigma weight residual 100.90 110.63 -9.73 2.20e+00 2.07e-01 1.95e+01 angle pdb=" CA ASP D 197 " pdb=" CB ASP D 197 " pdb=" CG ASP D 197 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CA CYS C 229 " pdb=" CB CYS C 229 " pdb=" SG CYS C 229 " ideal model delta sigma weight residual 114.40 123.39 -8.99 2.30e+00 1.89e-01 1.53e+01 angle pdb=" CA CYS D 229 " pdb=" CB CYS D 229 " pdb=" SG CYS D 229 " ideal model delta sigma weight residual 114.40 123.17 -8.77 2.30e+00 1.89e-01 1.45e+01 ... (remaining 15970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 6440 16.81 - 33.61: 576 33.61 - 50.42: 106 50.42 - 67.22: 25 67.22 - 84.03: 7 Dihedral angle restraints: 7154 sinusoidal: 2919 harmonic: 4235 Sorted by residual: dihedral pdb=" CB CYS B 277 " pdb=" SG CYS B 277 " pdb=" SG CYS B 291 " pdb=" CB CYS B 291 " ideal model delta sinusoidal sigma weight residual 93.00 48.89 44.11 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS E 318 " pdb=" SG CYS E 318 " pdb=" SG CYS E 337 " pdb=" CB CYS E 337 " ideal model delta sinusoidal sigma weight residual 93.00 129.87 -36.87 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA ALA C 290 " pdb=" C ALA C 290 " pdb=" N CYS C 291 " pdb=" CA CYS C 291 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 994 0.062 - 0.124: 534 0.124 - 0.186: 150 0.186 - 0.248: 41 0.248 - 0.310: 7 Chirality restraints: 1726 Sorted by residual: chirality pdb=" C1 NAG E 500 " pdb=" ND2 ASN E 284 " pdb=" C2 NAG E 500 " pdb=" O5 NAG E 500 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG C 500 " pdb=" ND2 ASN C 284 " pdb=" C2 NAG C 500 " pdb=" O5 NAG C 500 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLU E 258 " pdb=" N GLU E 258 " pdb=" C GLU E 258 " pdb=" CB GLU E 258 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1723 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 446 " 0.055 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR C 446 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR C 446 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 446 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR C 446 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR C 446 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR C 446 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR C 446 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 177 " 0.023 2.00e-02 2.50e+03 3.20e-02 2.56e+01 pdb=" CG TRP D 177 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP D 177 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP D 177 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP D 177 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 177 " -0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP D 177 " -0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 177 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 177 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP D 177 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 210 " -0.018 2.00e-02 2.50e+03 2.93e-02 1.72e+01 pdb=" CG TYR B 210 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 210 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 210 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 210 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 210 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 210 " 0.035 2.00e-02 2.50e+03 pdb=" OH TYR B 210 " -0.041 2.00e-02 2.50e+03 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3004 2.81 - 3.33: 9590 3.33 - 3.85: 18820 3.85 - 4.38: 21225 4.38 - 4.90: 37276 Nonbonded interactions: 89915 Sorted by model distance: nonbonded pdb=" OD2 ASP A 52 " pdb=" OG SER A 56 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR D 278 " pdb=" NZ LYS D 349 " model vdw 2.290 3.120 nonbonded pdb=" OD1 ASP B 194 " pdb=" NZ LYS B 203 " model vdw 2.291 3.120 nonbonded pdb=" OD2 ASP E 194 " pdb=" NZ LYS E 203 " model vdw 2.292 3.120 nonbonded pdb=" OG1 THR E 319 " pdb=" O ASP E 392 " model vdw 2.297 3.040 ... (remaining 89910 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 'B' and (resid 79 through 134 or resid 151 through 500)) selection = chain 'C' selection = (chain 'D' and (resid 79 through 134 or resid 151 through 500)) selection = (chain 'E' and (resid 79 through 134 or resid 151 through 500)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.440 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.010 0.078 11866 Z= 0.627 Angle : 1.155 9.726 16053 Z= 0.678 Chirality : 0.080 0.310 1726 Planarity : 0.008 0.101 2046 Dihedral : 13.319 84.028 4357 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.20), residues: 1454 helix: None (None), residues: 0 sheet: -0.57 (0.22), residues: 535 loop : -1.55 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 295 TYR 0.055 0.008 TYR C 446 PHE 0.057 0.009 PHE B 172 TRP 0.054 0.010 TRP D 177 HIS 0.022 0.005 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.01014 (11829) covalent geometry : angle 1.15149 (15975) SS BOND : bond 0.02875 ( 33) SS BOND : angle 1.80835 ( 66) hydrogen bonds : bond 0.30513 ( 324) hydrogen bonds : angle 10.97479 ( 882) link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 0.84110 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.4263 (tt) cc_final: 0.3866 (tp) REVERT: A 64 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7745 (mmmt) REVERT: A 66 ARG cc_start: 0.7424 (ttp80) cc_final: 0.6768 (tpt90) REVERT: A 82 MET cc_start: 0.7236 (mpp) cc_final: 0.6857 (mmt) REVERT: A 90 TYR cc_start: 0.8379 (m-80) cc_final: 0.8088 (m-80) REVERT: B 206 TYR cc_start: 0.9175 (t80) cc_final: 0.8095 (t80) REVERT: B 357 MET cc_start: 0.8421 (mpp) cc_final: 0.7982 (mpp) REVERT: C 220 ASN cc_start: 0.8316 (t0) cc_final: 0.7919 (t0) REVERT: C 239 MET cc_start: 0.7504 (ttp) cc_final: 0.6930 (ttp) REVERT: C 337 CYS cc_start: 0.8542 (m) cc_final: 0.7906 (t) REVERT: C 427 ILE cc_start: 0.8991 (mt) cc_final: 0.8787 (mt) REVERT: C 449 MET cc_start: 0.7107 (mtm) cc_final: 0.6524 (mtm) REVERT: D 119 PHE cc_start: 0.6797 (p90) cc_final: 0.6400 (p90) REVERT: D 208 GLU cc_start: 0.8758 (mp0) cc_final: 0.8384 (tp30) REVERT: D 222 LEU cc_start: 0.8426 (tp) cc_final: 0.8169 (tp) REVERT: D 239 MET cc_start: 0.6508 (ttp) cc_final: 0.6260 (ttp) REVERT: D 305 LEU cc_start: 0.6658 (tt) cc_final: 0.6356 (tt) REVERT: D 357 MET cc_start: 0.7562 (mpp) cc_final: 0.7069 (mpp) REVERT: D 429 MET cc_start: 0.7076 (mtt) cc_final: 0.6706 (mtt) REVERT: D 449 MET cc_start: 0.7122 (ttm) cc_final: 0.6898 (ttm) REVERT: D 453 GLN cc_start: 0.8365 (pp30) cc_final: 0.8127 (pp30) REVERT: E 168 GLU cc_start: 0.5420 (tt0) cc_final: 0.4861 (tt0) REVERT: E 239 MET cc_start: 0.4977 (ttm) cc_final: 0.4217 (ttm) REVERT: E 254 LEU cc_start: 0.7145 (mm) cc_final: 0.6877 (mm) REVERT: E 285 LYS cc_start: 0.7806 (mppt) cc_final: 0.7372 (tttp) REVERT: E 305 LEU cc_start: 0.7958 (tt) cc_final: 0.7681 (tt) REVERT: E 403 MET cc_start: 0.9183 (mpp) cc_final: 0.8965 (mtt) REVERT: E 449 MET cc_start: 0.7576 (mtm) cc_final: 0.7114 (mtm) REVERT: E 453 GLN cc_start: 0.8360 (pp30) cc_final: 0.7857 (pp30) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.0925 time to fit residues: 30.1225 Evaluate side-chains 163 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 169 ASN C 199 ASN C 431 HIS D 230 ASN D 306 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.176005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.139739 restraints weight = 18393.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.144766 restraints weight = 10471.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.148017 restraints weight = 7478.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.149991 restraints weight = 6028.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.151673 restraints weight = 5233.797| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11866 Z= 0.140 Angle : 0.644 9.048 16053 Z= 0.333 Chirality : 0.046 0.156 1726 Planarity : 0.004 0.042 2046 Dihedral : 6.093 54.040 1700 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.22 % Allowed : 8.43 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.35 (0.21), residues: 599 loop : -1.31 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.019 0.002 TYR E 365 PHE 0.015 0.001 PHE B 281 TRP 0.019 0.002 TRP A 36 HIS 0.008 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00315 (11829) covalent geometry : angle 0.64018 (15975) SS BOND : bond 0.00448 ( 33) SS BOND : angle 1.17294 ( 66) hydrogen bonds : bond 0.04980 ( 324) hydrogen bonds : angle 7.65631 ( 882) link_NAG-ASN : bond 0.00161 ( 4) link_NAG-ASN : angle 0.92261 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7125 (m-30) cc_final: 0.6784 (m-30) REVERT: A 82 MET cc_start: 0.6794 (mpp) cc_final: 0.6276 (mmp) REVERT: C 225 GLN cc_start: 0.7996 (mp10) cc_final: 0.7538 (mp10) REVERT: C 239 MET cc_start: 0.4510 (ttp) cc_final: 0.4237 (ttp) REVERT: C 287 ILE cc_start: 0.8885 (mt) cc_final: 0.8604 (mm) REVERT: D 197 ASP cc_start: 0.7691 (p0) cc_final: 0.7485 (t70) REVERT: D 239 MET cc_start: 0.5284 (ttp) cc_final: 0.4874 (ttp) REVERT: D 292 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7243 (tmm-80) REVERT: D 429 MET cc_start: 0.7448 (mtt) cc_final: 0.6840 (mtt) REVERT: E 453 GLN cc_start: 0.7618 (pp30) cc_final: 0.7255 (pp30) outliers start: 15 outliers final: 11 residues processed: 192 average time/residue: 0.0901 time to fit residues: 25.4865 Evaluate side-chains 172 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 409 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 133 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 306 ASN E 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.174945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.138740 restraints weight = 18589.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.143728 restraints weight = 10495.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.146989 restraints weight = 7502.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.149177 restraints weight = 6045.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.150311 restraints weight = 5214.831| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11866 Z= 0.141 Angle : 0.636 11.138 16053 Z= 0.325 Chirality : 0.046 0.193 1726 Planarity : 0.004 0.039 2046 Dihedral : 5.989 56.326 1700 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.76 % Allowed : 11.18 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.19 (0.21), residues: 592 loop : -1.34 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.019 0.001 TYR C 217 PHE 0.026 0.001 PHE D 119 TRP 0.018 0.001 TRP A 36 HIS 0.007 0.001 HIS C 431 Details of bonding type rmsd covalent geometry : bond 0.00326 (11829) covalent geometry : angle 0.63042 (15975) SS BOND : bond 0.00393 ( 33) SS BOND : angle 1.41831 ( 66) hydrogen bonds : bond 0.04195 ( 324) hydrogen bonds : angle 7.06397 ( 882) link_NAG-ASN : bond 0.00069 ( 4) link_NAG-ASN : angle 0.79670 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7715 (pp) REVERT: C 225 GLN cc_start: 0.8419 (mp10) cc_final: 0.7855 (mp10) REVERT: C 287 ILE cc_start: 0.9065 (mt) cc_final: 0.8747 (mm) REVERT: C 375 MET cc_start: 0.7162 (tpp) cc_final: 0.6597 (tmm) REVERT: C 377 MET cc_start: 0.7987 (mmm) cc_final: 0.7662 (mmm) REVERT: C 409 TYR cc_start: 0.7068 (m-80) cc_final: 0.6768 (m-80) REVERT: D 197 ASP cc_start: 0.7583 (p0) cc_final: 0.7336 (t70) REVERT: D 203 LYS cc_start: 0.8284 (pttm) cc_final: 0.7573 (ptpt) REVERT: D 225 GLN cc_start: 0.7406 (mp10) cc_final: 0.6697 (mp10) REVERT: D 239 MET cc_start: 0.5428 (ttp) cc_final: 0.5117 (ttp) REVERT: D 285 LYS cc_start: 0.7899 (tptt) cc_final: 0.7311 (tppt) REVERT: D 429 MET cc_start: 0.7472 (mtt) cc_final: 0.6912 (mtt) REVERT: E 453 GLN cc_start: 0.7638 (pp30) cc_final: 0.7329 (pp30) outliers start: 34 outliers final: 24 residues processed: 187 average time/residue: 0.0851 time to fit residues: 23.7752 Evaluate side-chains 184 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 409 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN D 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.173853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.137603 restraints weight = 18610.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.142365 restraints weight = 10609.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145587 restraints weight = 7692.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.147751 restraints weight = 6209.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.149033 restraints weight = 5370.701| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11866 Z= 0.147 Angle : 0.631 10.650 16053 Z= 0.323 Chirality : 0.045 0.166 1726 Planarity : 0.003 0.031 2046 Dihedral : 5.919 55.774 1700 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.76 % Allowed : 12.56 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.20 (0.21), residues: 592 loop : -1.34 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.020 0.001 TYR C 217 PHE 0.014 0.001 PHE B 130 TRP 0.019 0.001 TRP A 36 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00344 (11829) covalent geometry : angle 0.62466 (15975) SS BOND : bond 0.00568 ( 33) SS BOND : angle 1.55609 ( 66) hydrogen bonds : bond 0.03930 ( 324) hydrogen bonds : angle 6.82313 ( 882) link_NAG-ASN : bond 0.00053 ( 4) link_NAG-ASN : angle 0.82885 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8417 (mm) cc_final: 0.7953 (tt) REVERT: B 97 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7679 (pp) REVERT: C 217 TYR cc_start: 0.7278 (p90) cc_final: 0.6995 (p90) REVERT: C 287 ILE cc_start: 0.8945 (mt) cc_final: 0.8636 (mm) REVERT: C 377 MET cc_start: 0.7999 (mmm) cc_final: 0.7407 (mmm) REVERT: C 409 TYR cc_start: 0.6887 (m-80) cc_final: 0.6570 (m-80) REVERT: D 197 ASP cc_start: 0.7533 (p0) cc_final: 0.7306 (t70) REVERT: D 285 LYS cc_start: 0.7984 (tptt) cc_final: 0.7385 (tppt) REVERT: D 429 MET cc_start: 0.7539 (mtt) cc_final: 0.6976 (mtt) REVERT: E 453 GLN cc_start: 0.7619 (pp30) cc_final: 0.7335 (pp30) outliers start: 34 outliers final: 24 residues processed: 184 average time/residue: 0.0869 time to fit residues: 24.0407 Evaluate side-chains 176 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 409 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 132 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN C 431 HIS E 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.172434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.134865 restraints weight = 18655.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.139652 restraints weight = 10863.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.142766 restraints weight = 7938.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.144811 restraints weight = 6498.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.145906 restraints weight = 5682.751| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11866 Z= 0.181 Angle : 0.668 11.415 16053 Z= 0.340 Chirality : 0.046 0.193 1726 Planarity : 0.004 0.032 2046 Dihedral : 5.973 55.673 1700 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.32 % Allowed : 13.70 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.21 (0.22), residues: 574 loop : -1.48 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.017 0.002 TYR C 217 PHE 0.016 0.002 PHE B 130 TRP 0.022 0.002 TRP A 36 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00422 (11829) covalent geometry : angle 0.66173 (15975) SS BOND : bond 0.00507 ( 33) SS BOND : angle 1.55969 ( 66) hydrogen bonds : bond 0.04057 ( 324) hydrogen bonds : angle 6.74362 ( 882) link_NAG-ASN : bond 0.00074 ( 4) link_NAG-ASN : angle 0.97651 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8543 (mm) cc_final: 0.8115 (tt) REVERT: A 52 ASP cc_start: 0.7292 (m-30) cc_final: 0.7036 (m-30) REVERT: B 97 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7723 (pp) REVERT: B 171 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (pt) REVERT: B 201 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7108 (tt) REVERT: B 227 SER cc_start: 0.8518 (t) cc_final: 0.7965 (m) REVERT: B 237 TYR cc_start: 0.7476 (m-80) cc_final: 0.7201 (m-10) REVERT: C 225 GLN cc_start: 0.8487 (mp10) cc_final: 0.8198 (mp10) REVERT: C 287 ILE cc_start: 0.8941 (mt) cc_final: 0.8644 (mm) REVERT: C 409 TYR cc_start: 0.6987 (m-80) cc_final: 0.6703 (m-80) REVERT: D 285 LYS cc_start: 0.8030 (tptt) cc_final: 0.7376 (tppt) REVERT: D 403 MET cc_start: 0.7543 (tpp) cc_final: 0.7317 (tpp) REVERT: D 429 MET cc_start: 0.7524 (mtt) cc_final: 0.7032 (mtt) REVERT: E 225 GLN cc_start: 0.7486 (mp10) cc_final: 0.7071 (mp10) outliers start: 41 outliers final: 33 residues processed: 184 average time/residue: 0.0869 time to fit residues: 24.2349 Evaluate side-chains 187 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.172907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.135253 restraints weight = 18828.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.140016 restraints weight = 10934.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.143231 restraints weight = 8009.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.145111 restraints weight = 6518.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.146577 restraints weight = 5725.647| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11866 Z= 0.159 Angle : 0.642 9.524 16053 Z= 0.327 Chirality : 0.045 0.155 1726 Planarity : 0.004 0.040 2046 Dihedral : 5.906 54.921 1700 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.48 % Allowed : 14.99 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.18 (0.22), residues: 574 loop : -1.48 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 223 TYR 0.023 0.002 TYR C 217 PHE 0.020 0.001 PHE D 119 TRP 0.023 0.001 TRP A 36 HIS 0.009 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00370 (11829) covalent geometry : angle 0.63802 (15975) SS BOND : bond 0.00453 ( 33) SS BOND : angle 1.29897 ( 66) hydrogen bonds : bond 0.03826 ( 324) hydrogen bonds : angle 6.62605 ( 882) link_NAG-ASN : bond 0.00046 ( 4) link_NAG-ASN : angle 1.01125 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7624 (m-30) cc_final: 0.7290 (m-30) REVERT: A 64 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7361 (mmtt) REVERT: A 75 LYS cc_start: 0.8472 (pptt) cc_final: 0.8124 (pttp) REVERT: B 97 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7687 (pp) REVERT: B 171 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8046 (pt) REVERT: B 227 SER cc_start: 0.8510 (t) cc_final: 0.7961 (m) REVERT: B 237 TYR cc_start: 0.7603 (m-80) cc_final: 0.7342 (m-10) REVERT: C 197 ASP cc_start: 0.8311 (t70) cc_final: 0.8074 (t70) REVERT: C 225 GLN cc_start: 0.8537 (mp10) cc_final: 0.8324 (mp10) REVERT: C 287 ILE cc_start: 0.8916 (mt) cc_final: 0.8640 (mm) REVERT: C 377 MET cc_start: 0.7983 (mmm) cc_final: 0.7747 (mmm) REVERT: C 409 TYR cc_start: 0.7092 (m-80) cc_final: 0.6798 (m-80) REVERT: D 197 ASP cc_start: 0.7526 (t70) cc_final: 0.7176 (t70) REVERT: D 429 MET cc_start: 0.7533 (mtt) cc_final: 0.7034 (mtt) REVERT: D 454 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7486 (tt) REVERT: E 201 LEU cc_start: 0.7998 (pt) cc_final: 0.7560 (pp) REVERT: E 225 GLN cc_start: 0.7649 (mp10) cc_final: 0.7170 (mp10) REVERT: E 305 LEU cc_start: 0.7565 (tt) cc_final: 0.7237 (tp) outliers start: 43 outliers final: 32 residues processed: 191 average time/residue: 0.0871 time to fit residues: 24.8408 Evaluate side-chains 188 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.172853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.135174 restraints weight = 18784.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.139980 restraints weight = 10922.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.142831 restraints weight = 7978.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.145044 restraints weight = 6598.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.146185 restraints weight = 5740.903| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 11866 Z= 0.158 Angle : 0.664 9.512 16053 Z= 0.336 Chirality : 0.046 0.256 1726 Planarity : 0.004 0.035 2046 Dihedral : 5.895 54.651 1700 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.48 % Allowed : 15.88 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.16 (0.22), residues: 574 loop : -1.49 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.018 0.002 TYR C 217 PHE 0.013 0.001 PHE B 130 TRP 0.024 0.001 TRP A 36 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00376 (11829) covalent geometry : angle 0.65199 (15975) SS BOND : bond 0.00669 ( 33) SS BOND : angle 2.03009 ( 66) hydrogen bonds : bond 0.03851 ( 324) hydrogen bonds : angle 6.54404 ( 882) link_NAG-ASN : bond 0.00046 ( 4) link_NAG-ASN : angle 1.02390 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8515 (mm) cc_final: 0.8209 (tp) REVERT: A 52 ASP cc_start: 0.7191 (m-30) cc_final: 0.6960 (m-30) REVERT: A 64 LYS cc_start: 0.7906 (mmpt) cc_final: 0.7384 (mmtt) REVERT: A 75 LYS cc_start: 0.8520 (pptt) cc_final: 0.8196 (pttp) REVERT: B 97 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7693 (pp) REVERT: B 171 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8049 (pt) REVERT: B 201 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6996 (tt) REVERT: B 227 SER cc_start: 0.8502 (t) cc_final: 0.8001 (m) REVERT: B 237 TYR cc_start: 0.7549 (m-80) cc_final: 0.7314 (m-10) REVERT: C 197 ASP cc_start: 0.8359 (t70) cc_final: 0.8142 (t70) REVERT: C 225 GLN cc_start: 0.8523 (mp10) cc_final: 0.8315 (mp10) REVERT: C 239 MET cc_start: 0.5320 (ttp) cc_final: 0.4946 (ttm) REVERT: C 287 ILE cc_start: 0.8911 (mt) cc_final: 0.8629 (mm) REVERT: C 377 MET cc_start: 0.7920 (mmm) cc_final: 0.7226 (mmm) REVERT: C 409 TYR cc_start: 0.7107 (m-80) cc_final: 0.6813 (m-80) REVERT: D 126 GLU cc_start: 0.7238 (pt0) cc_final: 0.7028 (pt0) REVERT: D 197 ASP cc_start: 0.7634 (t70) cc_final: 0.7291 (t70) REVERT: D 403 MET cc_start: 0.7679 (tpp) cc_final: 0.7413 (tpp) REVERT: D 429 MET cc_start: 0.7673 (mtt) cc_final: 0.7189 (mtt) REVERT: D 454 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7515 (tt) REVERT: E 201 LEU cc_start: 0.7898 (pt) cc_final: 0.7433 (pp) REVERT: E 225 GLN cc_start: 0.7696 (mp10) cc_final: 0.7217 (mp10) outliers start: 43 outliers final: 33 residues processed: 181 average time/residue: 0.0923 time to fit residues: 25.2047 Evaluate side-chains 191 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.170285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.132841 restraints weight = 18974.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.137459 restraints weight = 11212.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140442 restraints weight = 8254.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.142171 restraints weight = 6812.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143627 restraints weight = 6031.976| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 11866 Z= 0.217 Angle : 0.716 11.968 16053 Z= 0.363 Chirality : 0.047 0.252 1726 Planarity : 0.004 0.037 2046 Dihedral : 6.047 54.606 1700 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.48 % Allowed : 16.37 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.22 (0.22), residues: 575 loop : -1.58 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.020 0.002 TYR B 206 PHE 0.016 0.002 PHE B 130 TRP 0.027 0.002 TRP A 36 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00510 (11829) covalent geometry : angle 0.70495 (15975) SS BOND : bond 0.00753 ( 33) SS BOND : angle 2.07608 ( 66) hydrogen bonds : bond 0.04195 ( 324) hydrogen bonds : angle 6.68860 ( 882) link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 1.16096 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8612 (mm) cc_final: 0.8303 (tp) REVERT: A 64 LYS cc_start: 0.7952 (mmpt) cc_final: 0.7373 (mmtt) REVERT: A 75 LYS cc_start: 0.8576 (pptt) cc_final: 0.8279 (pttp) REVERT: B 97 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7717 (pp) REVERT: B 171 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8079 (pt) REVERT: B 201 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6955 (tt) REVERT: B 227 SER cc_start: 0.8528 (t) cc_final: 0.8036 (m) REVERT: B 237 TYR cc_start: 0.7664 (m-80) cc_final: 0.7420 (m-10) REVERT: C 197 ASP cc_start: 0.8330 (t70) cc_final: 0.8104 (t70) REVERT: C 225 GLN cc_start: 0.8579 (mp10) cc_final: 0.8328 (mp10) REVERT: C 239 MET cc_start: 0.5534 (ttp) cc_final: 0.5279 (ttm) REVERT: C 287 ILE cc_start: 0.8961 (mt) cc_final: 0.8678 (mm) REVERT: C 377 MET cc_start: 0.7869 (mmm) cc_final: 0.7196 (mmm) REVERT: D 197 ASP cc_start: 0.7638 (t70) cc_final: 0.7305 (t70) REVERT: D 429 MET cc_start: 0.7691 (mtt) cc_final: 0.7186 (mtt) REVERT: D 454 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7389 (tt) REVERT: E 201 LEU cc_start: 0.7784 (pt) cc_final: 0.7444 (pp) outliers start: 43 outliers final: 34 residues processed: 179 average time/residue: 0.0888 time to fit residues: 23.9050 Evaluate side-chains 187 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 210 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.174005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.137858 restraints weight = 18362.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.142656 restraints weight = 10540.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145762 restraints weight = 7622.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.147626 restraints weight = 6195.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.148788 restraints weight = 5422.960| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 11866 Z= 0.117 Angle : 0.651 12.055 16053 Z= 0.325 Chirality : 0.045 0.212 1726 Planarity : 0.003 0.036 2046 Dihedral : 5.795 54.675 1700 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.08 % Allowed : 17.50 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.09 (0.22), residues: 568 loop : -1.50 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.020 0.001 TYR B 206 PHE 0.011 0.001 PHE B 130 TRP 0.027 0.002 TRP A 36 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00274 (11829) covalent geometry : angle 0.64421 (15975) SS BOND : bond 0.00531 ( 33) SS BOND : angle 1.60330 ( 66) hydrogen bonds : bond 0.03560 ( 324) hydrogen bonds : angle 6.33213 ( 882) link_NAG-ASN : bond 0.00078 ( 4) link_NAG-ASN : angle 1.01716 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8574 (mm) cc_final: 0.8278 (tp) REVERT: A 75 LYS cc_start: 0.8545 (pptt) cc_final: 0.8256 (pttp) REVERT: B 97 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7626 (pp) REVERT: B 171 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8060 (pt) REVERT: B 237 TYR cc_start: 0.7385 (m-80) cc_final: 0.7155 (m-10) REVERT: C 197 ASP cc_start: 0.8306 (t70) cc_final: 0.8084 (t70) REVERT: C 225 GLN cc_start: 0.8548 (mp10) cc_final: 0.8338 (mp10) REVERT: C 239 MET cc_start: 0.5355 (ttp) cc_final: 0.4978 (ttm) REVERT: C 287 ILE cc_start: 0.8919 (mt) cc_final: 0.8650 (mm) REVERT: C 377 MET cc_start: 0.7963 (mmm) cc_final: 0.7323 (mmm) REVERT: C 409 TYR cc_start: 0.7041 (m-80) cc_final: 0.6731 (m-80) REVERT: D 197 ASP cc_start: 0.7699 (t70) cc_final: 0.7399 (t70) REVERT: D 208 GLU cc_start: 0.7783 (tt0) cc_final: 0.7473 (tt0) REVERT: D 225 GLN cc_start: 0.8065 (mp10) cc_final: 0.7643 (mp10) REVERT: D 278 THR cc_start: 0.6481 (OUTLIER) cc_final: 0.6269 (m) REVERT: D 429 MET cc_start: 0.7703 (mtt) cc_final: 0.7237 (mtt) REVERT: E 201 LEU cc_start: 0.7878 (pt) cc_final: 0.7384 (pp) REVERT: E 225 GLN cc_start: 0.8185 (mp10) cc_final: 0.7735 (mp10) REVERT: E 408 TRP cc_start: 0.8858 (m100) cc_final: 0.8267 (m-10) outliers start: 38 outliers final: 29 residues processed: 189 average time/residue: 0.0879 time to fit residues: 24.9855 Evaluate side-chains 195 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.2980 chunk 0 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 0.0050 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 overall best weight: 2.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 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 = 0.4495 r_free = 0.4495 target = 0.171915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.135660 restraints weight = 18706.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.140338 restraints weight = 10759.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.143361 restraints weight = 7816.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.145391 restraints weight = 6392.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.146588 restraints weight = 5575.970| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11866 Z= 0.153 Angle : 0.677 11.450 16053 Z= 0.338 Chirality : 0.046 0.211 1726 Planarity : 0.004 0.037 2046 Dihedral : 5.826 54.480 1700 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.84 % Allowed : 17.34 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.12 (0.22), residues: 568 loop : -1.52 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.015 0.002 TYR C 217 PHE 0.017 0.001 PHE D 119 TRP 0.031 0.001 TRP A 36 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00362 (11829) covalent geometry : angle 0.67002 (15975) SS BOND : bond 0.00588 ( 33) SS BOND : angle 1.61295 ( 66) hydrogen bonds : bond 0.03739 ( 324) hydrogen bonds : angle 6.35325 ( 882) link_NAG-ASN : bond 0.00051 ( 4) link_NAG-ASN : angle 1.04339 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8537 (mm) cc_final: 0.8237 (tp) REVERT: A 75 LYS cc_start: 0.8548 (pptt) cc_final: 0.8254 (pttp) REVERT: B 97 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7751 (pp) REVERT: B 171 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8075 (pt) REVERT: B 237 TYR cc_start: 0.7439 (m-80) cc_final: 0.7181 (m-10) REVERT: C 225 GLN cc_start: 0.8333 (mp10) cc_final: 0.8072 (mp10) REVERT: C 239 MET cc_start: 0.5364 (ttp) cc_final: 0.4903 (ttm) REVERT: C 287 ILE cc_start: 0.8914 (mt) cc_final: 0.8618 (mm) REVERT: C 377 MET cc_start: 0.7967 (mmm) cc_final: 0.7320 (mmm) REVERT: D 168 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7629 (tm-30) REVERT: D 197 ASP cc_start: 0.7723 (t70) cc_final: 0.7425 (t70) REVERT: D 208 GLU cc_start: 0.7872 (tt0) cc_final: 0.7560 (tt0) REVERT: D 429 MET cc_start: 0.7721 (mtt) cc_final: 0.7247 (mtt) REVERT: E 201 LEU cc_start: 0.7941 (pt) cc_final: 0.7493 (pp) outliers start: 35 outliers final: 30 residues processed: 181 average time/residue: 0.0929 time to fit residues: 25.6060 Evaluate side-chains 187 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 256 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 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 = 0.4477 r_free = 0.4477 target = 0.171365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.133901 restraints weight = 18904.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.138550 restraints weight = 11123.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.141558 restraints weight = 8177.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143508 restraints weight = 6739.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.144603 restraints weight = 5923.852| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11866 Z= 0.187 Angle : 0.710 11.100 16053 Z= 0.355 Chirality : 0.048 0.249 1726 Planarity : 0.004 0.038 2046 Dihedral : 5.955 54.505 1700 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.92 % Allowed : 17.50 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.21), residues: 1454 helix: None (None), residues: 0 sheet: -0.18 (0.22), residues: 568 loop : -1.55 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 292 TYR 0.017 0.002 TYR E 365 PHE 0.016 0.001 PHE D 119 TRP 0.032 0.002 TRP A 36 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00439 (11829) covalent geometry : angle 0.70279 (15975) SS BOND : bond 0.00621 ( 33) SS BOND : angle 1.66657 ( 66) hydrogen bonds : bond 0.03948 ( 324) hydrogen bonds : angle 6.49257 ( 882) link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 1.15703 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.02 seconds wall clock time: 31 minutes 26.11 seconds (1886.11 seconds total)