Starting phenix.real_space_refine on Sun Aug 24 00:39:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7c_28902/08_2025/8f7c_28902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7c_28902/08_2025/8f7c_28902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f7c_28902/08_2025/8f7c_28902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7c_28902/08_2025/8f7c_28902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f7c_28902/08_2025/8f7c_28902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7c_28902/08_2025/8f7c_28902.map" } resolution = 3.92 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= 0.019 sd= 0.154 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 77 5.16 5 C 10423 2.51 5 N 2716 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 15925 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2275 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 15925 At special positions: 0 Unit cell: (119.7, 118.8, 113.4, 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 77 16.00 O 2709 8.00 N 2716 7.00 C 10423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.04 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.04 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.04 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.04 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.04 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 897.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3892 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 7 sheets defined 75.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 59 through 74 removed outlier: 3.770A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.505A pdb=" N LEU A 114 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 119 through 147 Proline residue: A 125 - end of helix removed outlier: 3.669A pdb=" N LEU A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 3.932A pdb=" N GLU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 4.070A pdb=" N ASP A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 removed outlier: 4.260A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 238 removed outlier: 4.008A pdb=" N ALA A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.798A pdb=" N ILE A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 250 " --> pdb=" O CYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 314 removed outlier: 3.963A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 339 removed outlier: 4.124A pdb=" N ARG A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.874A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 removed outlier: 3.560A pdb=" N ILE A 358 " --> pdb=" O ARG A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 360 through 368 removed outlier: 3.529A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.781A pdb=" N ILE B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.502A pdb=" N LEU B 114 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 118 through 147 removed outlier: 4.071A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.686A pdb=" N LEU B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 3.960A pdb=" N GLU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 removed outlier: 4.186A pdb=" N ASP B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 4.187A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.923A pdb=" N ALA B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.786A pdb=" N ILE B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 removed outlier: 3.987A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.355A pdb=" N ARG B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.914A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 358 removed outlier: 3.531A pdb=" N ILE B 358 " --> pdb=" O ARG B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 360 through 368 removed outlier: 3.542A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 59 through 74 removed outlier: 3.770A pdb=" N ILE C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.507A pdb=" N LEU C 114 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP C 115 " --> pdb=" O ALA C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 115' Processing helix chain 'C' and resid 119 through 147 Proline residue: C 125 - end of helix removed outlier: 3.680A pdb=" N LEU C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 3.899A pdb=" N GLU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 removed outlier: 4.092A pdb=" N ASP C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 removed outlier: 4.056A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 238 removed outlier: 4.089A pdb=" N ALA C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 250 removed outlier: 3.785A pdb=" N ILE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 250 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 removed outlier: 4.032A pdb=" N ILE C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 329 through 339 removed outlier: 4.042A pdb=" N ARG C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.870A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 removed outlier: 3.569A pdb=" N ILE C 358 " --> pdb=" O ARG C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 360 through 368 removed outlier: 3.536A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 59 through 74 removed outlier: 3.771A pdb=" N ILE D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.503A pdb=" N LEU D 114 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 115 " --> pdb=" O ALA D 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 115' Processing helix chain 'D' and resid 118 through 147 removed outlier: 4.095A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 3.687A pdb=" N LEU D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.946A pdb=" N GLU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 removed outlier: 4.008A pdb=" N ASP D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 218 removed outlier: 3.963A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 238 removed outlier: 4.017A pdb=" N ALA D 229 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 235 " --> pdb=" O HIS D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.827A pdb=" N ILE D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 removed outlier: 3.944A pdb=" N ILE D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 305 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.584A pdb=" N TRP D 336 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.997A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 removed outlier: 3.546A pdb=" N ILE D 358 " --> pdb=" O ARG D 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 360 through 368 removed outlier: 3.563A pdb=" N ILE D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 59 through 74 removed outlier: 3.751A pdb=" N ILE E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 111 through 115 removed outlier: 3.503A pdb=" N LEU E 114 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP E 115 " --> pdb=" O ALA E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 115' Processing helix chain 'E' and resid 119 through 147 Proline residue: E 125 - end of helix removed outlier: 3.680A pdb=" N LEU E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.953A pdb=" N GLU E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 209 through 218 removed outlier: 3.586A pdb=" N LEU E 214 " --> pdb=" O PHE E 210 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 238 removed outlier: 4.072A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 235 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.708A pdb=" N ILE E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA E 250 " --> pdb=" O CYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 314 removed outlier: 3.965A pdb=" N ILE E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 306 " --> pdb=" O ASN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 326 removed outlier: 4.034A pdb=" N HIS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 339 removed outlier: 4.292A pdb=" N ARG E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 4.129A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE E 350 " --> pdb=" O ILE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 removed outlier: 3.569A pdb=" N ILE E 358 " --> pdb=" O ARG E 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 360 through 368 removed outlier: 3.512A pdb=" N ILE E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 59 through 74 removed outlier: 3.768A pdb=" N ILE F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 Processing helix chain 'F' and resid 111 through 115 removed outlier: 3.563A pdb=" N TRP F 115 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 135 removed outlier: 3.652A pdb=" N PHE F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) Proline residue: F 125 - end of helix removed outlier: 3.958A pdb=" N MET F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 147 removed outlier: 3.575A pdb=" N LEU F 140 " --> pdb=" O TYR F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 160 removed outlier: 3.974A pdb=" N ASN F 155 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 157 " --> pdb=" O GLU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 166 removed outlier: 4.107A pdb=" N HIS F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 218 removed outlier: 4.297A pdb=" N GLU F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 238 removed outlier: 4.045A pdb=" N ALA F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS F 231 " --> pdb=" O TYR F 227 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 234 " --> pdb=" O ARG F 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 235 " --> pdb=" O HIS F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.771A pdb=" N ILE F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F 250 " --> pdb=" O CYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 314 removed outlier: 3.997A pdb=" N ILE F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET F 301 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 326 removed outlier: 4.217A pdb=" N HIS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 removed outlier: 4.165A pdb=" N ARG F 334 " --> pdb=" O ILE F 330 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP F 336 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG F 337 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.862A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 358 removed outlier: 3.531A pdb=" N ILE F 358 " --> pdb=" O ARG F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 360 through 368 removed outlier: 3.578A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 368 " --> pdb=" O LEU F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 48 through 59 Processing helix chain 'G' and resid 59 through 74 removed outlier: 3.780A pdb=" N ILE G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.541A pdb=" N GLY G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.628A pdb=" N TRP G 115 " --> pdb=" O ALA G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 147 removed outlier: 4.093A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 3.671A pdb=" N LEU G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA G 133 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Proline residue: G 138 - end of helix removed outlier: 3.967A pdb=" N GLU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU G 145 " --> pdb=" O GLY G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 removed outlier: 4.047A pdb=" N ASP G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN G 163 " --> pdb=" O GLN G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.606A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 238 removed outlier: 3.966A pdb=" N ALA G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS G 231 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 234 " --> pdb=" O ARG G 230 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 235 " --> pdb=" O HIS G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 250 removed outlier: 3.771A pdb=" N ILE G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA G 250 " --> pdb=" O CYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 314 removed outlier: 3.910A pdb=" N ILE G 295 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET G 301 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU G 306 " --> pdb=" O ASN G 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 324 Processing helix chain 'G' and resid 330 through 339 removed outlier: 4.244A pdb=" N ARG G 334 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG G 337 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER G 339 " --> pdb=" O GLN G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.878A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE G 350 " --> pdb=" O ILE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 358 removed outlier: 3.549A pdb=" N ILE G 358 " --> pdb=" O ARG G 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 358' Processing helix chain 'G' and resid 360 through 368 removed outlier: 3.585A pdb=" N ILE G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.505A pdb=" N PHE A 257 " --> pdb=" O CYS A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.540A pdb=" N TYR B 80 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.619A pdb=" N TYR C 80 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 257 " --> pdb=" O CYS C 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.615A pdb=" N TYR D 80 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.635A pdb=" N TYR F 80 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 820 hydrogen bonds defined for protein. 2415 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: 2.45 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5047 1.35 - 1.48: 4082 1.48 - 1.60: 7062 1.60 - 1.72: 0 1.72 - 1.85: 98 Bond restraints: 16289 Sorted by residual: bond pdb=" CB CYS D 279 " pdb=" SG CYS D 279 " ideal model delta sigma weight residual 1.808 1.846 -0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" CB CYS E 279 " pdb=" SG CYS E 279 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB CYS B 279 " pdb=" SG CYS B 279 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB CYS F 279 " pdb=" SG CYS F 279 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.15e+00 ... (remaining 16284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 21852 1.74 - 3.49: 208 3.49 - 5.23: 66 5.23 - 6.97: 14 6.97 - 8.72: 8 Bond angle restraints: 22148 Sorted by residual: angle pdb=" CA CYS B 81 " pdb=" CB CYS B 81 " pdb=" SG CYS B 81 " ideal model delta sigma weight residual 114.40 122.02 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS D 81 " pdb=" CB CYS D 81 " pdb=" SG CYS D 81 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS A 81 " pdb=" CB CYS A 81 " pdb=" SG CYS A 81 " ideal model delta sigma weight residual 114.40 121.70 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS F 81 " pdb=" CB CYS F 81 " pdb=" SG CYS F 81 " ideal model delta sigma weight residual 114.40 121.66 -7.26 2.30e+00 1.89e-01 9.97e+00 angle pdb=" CA CYS E 81 " pdb=" CB CYS E 81 " pdb=" SG CYS E 81 " ideal model delta sigma weight residual 114.40 121.58 -7.18 2.30e+00 1.89e-01 9.74e+00 ... (remaining 22143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 8638 16.63 - 33.26: 828 33.26 - 49.88: 238 49.88 - 66.51: 24 66.51 - 83.14: 9 Dihedral angle restraints: 9737 sinusoidal: 3780 harmonic: 5957 Sorted by residual: dihedral pdb=" CB CYS D 81 " pdb=" SG CYS D 81 " pdb=" SG CYS D 279 " pdb=" CB CYS D 279 " ideal model delta sinusoidal sigma weight residual 93.00 47.85 45.15 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS B 81 " pdb=" SG CYS B 81 " pdb=" SG CYS B 279 " pdb=" CB CYS B 279 " ideal model delta sinusoidal sigma weight residual 93.00 47.86 45.14 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS E 81 " pdb=" SG CYS E 81 " pdb=" SG CYS E 279 " pdb=" CB CYS E 279 " ideal model delta sinusoidal sigma weight residual 93.00 48.09 44.91 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 9734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1467 0.026 - 0.052: 803 0.052 - 0.078: 218 0.078 - 0.104: 72 0.104 - 0.130: 44 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA CYS B 81 " pdb=" N CYS B 81 " pdb=" C CYS B 81 " pdb=" CB CYS B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA CYS F 81 " pdb=" N CYS F 81 " pdb=" C CYS F 81 " pdb=" CB CYS F 81 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA CYS C 81 " pdb=" N CYS C 81 " pdb=" C CYS C 81 " pdb=" CB CYS C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2601 not shown) Planarity restraints: 2758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 264 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO F 265 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 82 " -0.009 2.00e-02 2.50e+03 8.65e-03 1.50e+00 pdb=" CG TYR A 82 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 82 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 82 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 82 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 82 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 82 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 61 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO G 62 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " -0.017 5.00e-02 4.00e+02 ... (remaining 2755 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2901 2.77 - 3.30: 14781 3.30 - 3.84: 23231 3.84 - 4.37: 24360 4.37 - 4.90: 43015 Nonbonded interactions: 108288 Sorted by model distance: nonbonded pdb=" OE2 GLU D 153 " pdb=" OH TYR D 213 " model vdw 2.239 3.040 nonbonded pdb=" O GLN B 252 " pdb=" NH2 ARG B 288 " model vdw 2.307 3.120 nonbonded pdb=" CA GLN A 335 " pdb=" NE ARG A 338 " model vdw 2.318 3.550 nonbonded pdb=" O GLY D 329 " pdb=" NH1 ARG D 333 " model vdw 2.332 3.120 nonbonded pdb=" OE2 GLU F 120 " pdb=" NE2 GLN F 252 " model vdw 2.333 3.120 ... (remaining 108283 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.200 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.245 16304 Z= 0.220 Angle : 0.525 8.718 22176 Z= 0.273 Chirality : 0.036 0.130 2604 Planarity : 0.004 0.061 2758 Dihedral : 13.947 83.140 5803 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 1967 helix: 0.63 (0.15), residues: 1183 sheet: 0.01 (0.59), residues: 70 loop : -0.92 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.022 0.001 TYR A 82 PHE 0.021 0.001 PHE G 210 TRP 0.008 0.001 TRP G 336 HIS 0.001 0.000 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00231 (16289) covalent geometry : angle 0.52155 (22148) SS BOND : bond 0.00771 ( 14) SS BOND : angle 1.71322 ( 28) hydrogen bonds : bond 0.26430 ( 820) hydrogen bonds : angle 6.70602 ( 2415) Misc. bond : bond 0.24508 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LEU cc_start: 0.9129 (tp) cc_final: 0.8911 (tp) REVERT: B 341 PHE cc_start: 0.7798 (m-80) cc_final: 0.7314 (m-80) REVERT: C 265 PRO cc_start: 0.7133 (Cg_endo) cc_final: 0.6841 (Cg_exo) REVERT: C 340 GLN cc_start: 0.7876 (mp-120) cc_final: 0.7094 (mm-40) REVERT: C 341 PHE cc_start: 0.7740 (m-80) cc_final: 0.7259 (m-80) REVERT: D 135 MET cc_start: 0.8183 (mmt) cc_final: 0.7942 (mmt) REVERT: D 210 PHE cc_start: 0.8062 (t80) cc_final: 0.7575 (t80) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1419 time to fit residues: 62.8744 Evaluate side-chains 247 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN E 231 HIS ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122943 restraints weight = 23191.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126215 restraints weight = 13992.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127552 restraints weight = 10462.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129174 restraints weight = 8177.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129645 restraints weight = 7069.668| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16304 Z= 0.148 Angle : 0.587 7.552 22176 Z= 0.309 Chirality : 0.039 0.136 2604 Planarity : 0.004 0.047 2758 Dihedral : 4.092 18.076 2191 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.09 % Allowed : 9.32 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 1967 helix: 1.08 (0.15), residues: 1246 sheet: -0.07 (0.62), residues: 70 loop : -1.15 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.019 0.001 TYR A 213 PHE 0.012 0.001 PHE E 313 TRP 0.008 0.001 TRP C 336 HIS 0.005 0.001 HIS E 311 Details of bonding type rmsd covalent geometry : bond 0.00289 (16289) covalent geometry : angle 0.58299 (22148) SS BOND : bond 0.00727 ( 14) SS BOND : angle 1.91849 ( 28) hydrogen bonds : bond 0.06869 ( 820) hydrogen bonds : angle 4.53532 ( 2415) Misc. bond : bond 0.00303 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.543 Fit side-chains REVERT: A 323 ASP cc_start: 0.8177 (t0) cc_final: 0.7879 (t0) REVERT: A 340 GLN cc_start: 0.7820 (mp10) cc_final: 0.7518 (mp10) REVERT: B 265 PRO cc_start: 0.7283 (Cg_endo) cc_final: 0.7068 (Cg_exo) REVERT: B 341 PHE cc_start: 0.7841 (m-80) cc_final: 0.7388 (m-80) REVERT: C 265 PRO cc_start: 0.7432 (Cg_endo) cc_final: 0.6892 (Cg_exo) REVERT: C 340 GLN cc_start: 0.8052 (mp-120) cc_final: 0.7210 (mm-40) REVERT: C 341 PHE cc_start: 0.7796 (m-80) cc_final: 0.7335 (m-80) REVERT: D 210 PHE cc_start: 0.7585 (t80) cc_final: 0.7022 (t80) REVERT: E 219 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8364 (mmm160) REVERT: E 334 ARG cc_start: 0.7537 (ptp90) cc_final: 0.6845 (ptp90) REVERT: E 337 ARG cc_start: 0.8242 (ptp90) cc_final: 0.7937 (ptp90) REVERT: G 265 PRO cc_start: 0.7812 (Cg_endo) cc_final: 0.7290 (Cg_exo) outliers start: 35 outliers final: 29 residues processed: 275 average time/residue: 0.1410 time to fit residues: 56.1402 Evaluate side-chains 257 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 242 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 163 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.160665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119667 restraints weight = 23458.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123214 restraints weight = 14232.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125543 restraints weight = 10113.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126777 restraints weight = 8104.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127862 restraints weight = 7127.918| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16304 Z= 0.139 Angle : 0.545 6.942 22176 Z= 0.287 Chirality : 0.038 0.126 2604 Planarity : 0.004 0.051 2758 Dihedral : 3.863 18.197 2191 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.41 % Allowed : 11.30 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1967 helix: 1.34 (0.15), residues: 1246 sheet: -0.37 (0.62), residues: 70 loop : -1.07 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.016 0.002 TYR C 213 PHE 0.019 0.001 PHE G 210 TRP 0.010 0.001 TRP E 142 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00300 (16289) covalent geometry : angle 0.54135 (22148) SS BOND : bond 0.00608 ( 14) SS BOND : angle 1.82523 ( 28) hydrogen bonds : bond 0.06495 ( 820) hydrogen bonds : angle 4.28911 ( 2415) Misc. bond : bond 0.00410 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.633 Fit side-chains REVERT: A 323 ASP cc_start: 0.8307 (t0) cc_final: 0.8038 (t0) REVERT: A 340 GLN cc_start: 0.7788 (mp10) cc_final: 0.7455 (mp10) REVERT: B 265 PRO cc_start: 0.7414 (Cg_endo) cc_final: 0.7182 (Cg_exo) REVERT: B 341 PHE cc_start: 0.7843 (m-80) cc_final: 0.7398 (m-80) REVERT: C 265 PRO cc_start: 0.7514 (Cg_endo) cc_final: 0.7138 (Cg_exo) REVERT: C 340 GLN cc_start: 0.8014 (mp-120) cc_final: 0.7161 (mm-40) REVERT: C 341 PHE cc_start: 0.7807 (m-80) cc_final: 0.7361 (m-80) REVERT: D 210 PHE cc_start: 0.7688 (t80) cc_final: 0.7128 (t80) REVERT: D 265 PRO cc_start: 0.7536 (Cg_endo) cc_final: 0.7158 (Cg_exo) REVERT: E 334 ARG cc_start: 0.7364 (ptp90) cc_final: 0.6695 (ptp90) REVERT: E 337 ARG cc_start: 0.8203 (ptp90) cc_final: 0.7852 (ptp90) REVERT: F 82 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: F 135 MET cc_start: 0.8841 (tpp) cc_final: 0.8389 (mtt) REVERT: F 153 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8050 (tm-30) REVERT: G 265 PRO cc_start: 0.7815 (Cg_endo) cc_final: 0.7444 (Cg_exo) outliers start: 57 outliers final: 40 residues processed: 280 average time/residue: 0.1319 time to fit residues: 55.0950 Evaluate side-chains 266 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 88 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125381 restraints weight = 22880.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128816 restraints weight = 13958.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131080 restraints weight = 9980.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132405 restraints weight = 8022.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133371 restraints weight = 7021.642| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16304 Z= 0.131 Angle : 0.554 12.492 22176 Z= 0.288 Chirality : 0.037 0.165 2604 Planarity : 0.004 0.054 2758 Dihedral : 3.900 21.394 2191 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.45 % Allowed : 14.05 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 1967 helix: 1.49 (0.15), residues: 1239 sheet: -0.39 (0.62), residues: 70 loop : -1.07 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 334 TYR 0.022 0.002 TYR E 94 PHE 0.019 0.001 PHE G 210 TRP 0.008 0.001 TRP E 142 HIS 0.002 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00285 (16289) covalent geometry : angle 0.54533 (22148) SS BOND : bond 0.00967 ( 14) SS BOND : angle 2.82658 ( 28) hydrogen bonds : bond 0.05576 ( 820) hydrogen bonds : angle 4.15140 ( 2415) Misc. bond : bond 0.00334 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8094 (pp) REVERT: A 323 ASP cc_start: 0.8307 (t0) cc_final: 0.8041 (t0) REVERT: A 340 GLN cc_start: 0.7722 (mp10) cc_final: 0.7428 (mp10) REVERT: B 82 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: B 265 PRO cc_start: 0.7505 (Cg_endo) cc_final: 0.7190 (Cg_exo) REVERT: B 341 PHE cc_start: 0.7967 (m-80) cc_final: 0.7552 (m-80) REVERT: C 265 PRO cc_start: 0.7730 (Cg_endo) cc_final: 0.7097 (Cg_exo) REVERT: C 340 GLN cc_start: 0.7979 (mp-120) cc_final: 0.7143 (mm-40) REVERT: C 341 PHE cc_start: 0.7789 (m-80) cc_final: 0.7349 (m-80) REVERT: D 210 PHE cc_start: 0.7691 (t80) cc_final: 0.7223 (t80) REVERT: D 265 PRO cc_start: 0.7600 (Cg_endo) cc_final: 0.7198 (Cg_exo) REVERT: E 265 PRO cc_start: 0.7501 (Cg_endo) cc_final: 0.6839 (Cg_exo) REVERT: E 337 ARG cc_start: 0.8181 (ptp90) cc_final: 0.7839 (ptp90) REVERT: F 82 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: F 135 MET cc_start: 0.8866 (tpp) cc_final: 0.8468 (mtt) REVERT: F 153 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 265 PRO cc_start: 0.7913 (Cg_endo) cc_final: 0.7503 (Cg_exo) outliers start: 41 outliers final: 31 residues processed: 270 average time/residue: 0.1264 time to fit residues: 51.1018 Evaluate side-chains 269 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 77 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 193 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 84 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126484 restraints weight = 22766.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129898 restraints weight = 13985.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132120 restraints weight = 9995.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133566 restraints weight = 8053.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134288 restraints weight = 7023.998| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 16304 Z= 0.122 Angle : 0.544 11.598 22176 Z= 0.280 Chirality : 0.037 0.169 2604 Planarity : 0.004 0.057 2758 Dihedral : 3.784 20.419 2191 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.87 % Allowed : 14.52 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 1967 helix: 1.59 (0.15), residues: 1239 sheet: -0.45 (0.62), residues: 70 loop : -1.04 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 334 TYR 0.028 0.001 TYR G 213 PHE 0.020 0.001 PHE G 210 TRP 0.007 0.001 TRP E 142 HIS 0.002 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00264 (16289) covalent geometry : angle 0.53497 (22148) SS BOND : bond 0.00772 ( 14) SS BOND : angle 2.77171 ( 28) hydrogen bonds : bond 0.05155 ( 820) hydrogen bonds : angle 4.00484 ( 2415) Misc. bond : bond 0.00299 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8119 (pp) REVERT: A 323 ASP cc_start: 0.8305 (t0) cc_final: 0.8031 (t0) REVERT: A 340 GLN cc_start: 0.7746 (mp10) cc_final: 0.7419 (mp10) REVERT: B 82 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: B 265 PRO cc_start: 0.7489 (Cg_endo) cc_final: 0.7212 (Cg_exo) REVERT: B 341 PHE cc_start: 0.7979 (m-80) cc_final: 0.7550 (m-80) REVERT: C 265 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7045 (Cg_exo) REVERT: C 340 GLN cc_start: 0.7961 (mp-120) cc_final: 0.7133 (mm-40) REVERT: C 341 PHE cc_start: 0.7883 (m-80) cc_final: 0.7421 (m-80) REVERT: D 210 PHE cc_start: 0.7679 (t80) cc_final: 0.7224 (t80) REVERT: D 265 PRO cc_start: 0.7599 (Cg_endo) cc_final: 0.7270 (Cg_exo) REVERT: D 304 ILE cc_start: 0.8136 (tt) cc_final: 0.7748 (tt) REVERT: D 334 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7193 (ptt-90) REVERT: E 265 PRO cc_start: 0.7439 (Cg_endo) cc_final: 0.6778 (Cg_exo) REVERT: E 334 ARG cc_start: 0.7319 (ptp90) cc_final: 0.6925 (ptp90) REVERT: E 337 ARG cc_start: 0.8251 (ptp90) cc_final: 0.7885 (ptp90) REVERT: F 82 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: F 135 MET cc_start: 0.8855 (tpp) cc_final: 0.8494 (mtt) REVERT: F 153 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8148 (tm-30) REVERT: G 261 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8381 (pp) REVERT: G 265 PRO cc_start: 0.7964 (Cg_endo) cc_final: 0.7450 (Cg_exo) outliers start: 48 outliers final: 32 residues processed: 273 average time/residue: 0.1331 time to fit residues: 53.8923 Evaluate side-chains 267 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 122 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.160141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119613 restraints weight = 23622.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122693 restraints weight = 15192.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124664 restraints weight = 11258.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125633 restraints weight = 9309.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126680 restraints weight = 8312.958| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16304 Z= 0.183 Angle : 0.637 10.933 22176 Z= 0.328 Chirality : 0.040 0.177 2604 Planarity : 0.004 0.060 2758 Dihedral : 3.849 21.604 2191 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.42 % Allowed : 15.36 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 1967 helix: 1.52 (0.15), residues: 1239 sheet: -0.63 (0.64), residues: 70 loop : -0.98 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 219 TYR 0.026 0.002 TYR E 213 PHE 0.020 0.001 PHE G 210 TRP 0.015 0.002 TRP E 142 HIS 0.003 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00431 (16289) covalent geometry : angle 0.62728 (22148) SS BOND : bond 0.01051 ( 14) SS BOND : angle 3.10267 ( 28) hydrogen bonds : bond 0.06909 ( 820) hydrogen bonds : angle 4.25998 ( 2415) Misc. bond : bond 0.00291 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 234 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8876 (mmm160) cc_final: 0.8185 (mmm160) REVERT: A 261 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8235 (pp) REVERT: A 323 ASP cc_start: 0.8334 (t0) cc_final: 0.8051 (t0) REVERT: A 340 GLN cc_start: 0.7678 (mp10) cc_final: 0.7415 (mp10) REVERT: B 82 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: B 265 PRO cc_start: 0.7543 (Cg_endo) cc_final: 0.7295 (Cg_exo) REVERT: B 341 PHE cc_start: 0.8063 (m-80) cc_final: 0.7652 (m-80) REVERT: C 261 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7804 (pp) REVERT: C 265 PRO cc_start: 0.7747 (Cg_endo) cc_final: 0.7325 (Cg_exo) REVERT: C 334 ARG cc_start: 0.7818 (ptp90) cc_final: 0.7540 (ptp90) REVERT: C 337 ARG cc_start: 0.8011 (ptt-90) cc_final: 0.7477 (ptp-170) REVERT: C 340 GLN cc_start: 0.7950 (mp-120) cc_final: 0.7067 (mm-40) REVERT: C 341 PHE cc_start: 0.7966 (m-80) cc_final: 0.7456 (m-80) REVERT: D 265 PRO cc_start: 0.7703 (Cg_endo) cc_final: 0.7455 (Cg_exo) REVERT: D 334 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7275 (ptt-90) REVERT: E 261 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8405 (pp) REVERT: E 265 PRO cc_start: 0.7712 (Cg_endo) cc_final: 0.7081 (Cg_exo) REVERT: E 334 ARG cc_start: 0.7478 (ptp90) cc_final: 0.6992 (ptt-90) REVERT: E 337 ARG cc_start: 0.8280 (ptp90) cc_final: 0.7901 (ptp90) REVERT: F 82 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: F 135 MET cc_start: 0.8929 (tpp) cc_final: 0.8615 (mtt) REVERT: F 153 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8098 (tm-30) REVERT: G 261 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8439 (pp) REVERT: G 265 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7543 (Cg_exo) outliers start: 74 outliers final: 56 residues processed: 284 average time/residue: 0.1325 time to fit residues: 55.9841 Evaluate side-chains 291 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123186 restraints weight = 22842.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126561 restraints weight = 14193.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128751 restraints weight = 10243.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130018 restraints weight = 8305.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130956 restraints weight = 7299.423| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16304 Z= 0.134 Angle : 0.573 10.691 22176 Z= 0.296 Chirality : 0.038 0.165 2604 Planarity : 0.004 0.060 2758 Dihedral : 3.858 20.921 2191 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.17 % Allowed : 16.68 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1967 helix: 1.60 (0.15), residues: 1239 sheet: -0.50 (0.64), residues: 70 loop : -1.01 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 334 TYR 0.025 0.002 TYR G 213 PHE 0.020 0.001 PHE G 210 TRP 0.008 0.001 TRP E 142 HIS 0.002 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00298 (16289) covalent geometry : angle 0.56526 (22148) SS BOND : bond 0.01012 ( 14) SS BOND : angle 2.72864 ( 28) hydrogen bonds : bond 0.05559 ( 820) hydrogen bonds : angle 4.05391 ( 2415) Misc. bond : bond 0.00279 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8876 (mmm160) cc_final: 0.8199 (mmm160) REVERT: A 261 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8233 (pp) REVERT: A 337 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7245 (pmt170) REVERT: A 340 GLN cc_start: 0.7659 (mp10) cc_final: 0.7424 (mp10) REVERT: B 82 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: B 265 PRO cc_start: 0.7501 (Cg_endo) cc_final: 0.7270 (Cg_exo) REVERT: B 341 PHE cc_start: 0.8029 (m-80) cc_final: 0.7605 (m-80) REVERT: C 261 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7800 (pp) REVERT: C 334 ARG cc_start: 0.7770 (ptp90) cc_final: 0.7542 (ptp90) REVERT: C 337 ARG cc_start: 0.7932 (ptt-90) cc_final: 0.7465 (ptp-170) REVERT: C 340 GLN cc_start: 0.7964 (mp-120) cc_final: 0.7090 (mm-40) REVERT: C 341 PHE cc_start: 0.7924 (m-80) cc_final: 0.7405 (m-10) REVERT: D 265 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7421 (Cg_exo) REVERT: D 334 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.7143 (ptt-90) REVERT: E 261 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8394 (pp) REVERT: F 82 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: F 135 MET cc_start: 0.8903 (tpp) cc_final: 0.8579 (mtt) REVERT: F 153 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8144 (tm-30) REVERT: G 219 ARG cc_start: 0.8660 (mmp-170) cc_final: 0.8429 (mmm160) REVERT: G 261 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8403 (pp) REVERT: G 265 PRO cc_start: 0.7975 (Cg_endo) cc_final: 0.7502 (Cg_exo) outliers start: 53 outliers final: 42 residues processed: 253 average time/residue: 0.1380 time to fit residues: 51.3791 Evaluate side-chains 265 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 137 optimal weight: 0.0770 chunk 161 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121953 restraints weight = 22986.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125304 restraints weight = 14240.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127481 restraints weight = 10272.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128740 restraints weight = 8334.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129472 restraints weight = 7337.609| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16304 Z= 0.143 Angle : 0.590 10.879 22176 Z= 0.304 Chirality : 0.038 0.164 2604 Planarity : 0.004 0.063 2758 Dihedral : 3.826 20.832 2191 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.71 % Allowed : 16.50 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.19), residues: 1967 helix: 1.63 (0.15), residues: 1239 sheet: -0.48 (0.64), residues: 70 loop : -1.00 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 334 TYR 0.026 0.002 TYR E 213 PHE 0.020 0.001 PHE G 210 TRP 0.010 0.001 TRP E 142 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00331 (16289) covalent geometry : angle 0.58153 (22148) SS BOND : bond 0.00969 ( 14) SS BOND : angle 2.88018 ( 28) hydrogen bonds : bond 0.05789 ( 820) hydrogen bonds : angle 4.06675 ( 2415) Misc. bond : bond 0.00262 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8329 (tptp) cc_final: 0.8025 (tppt) REVERT: A 219 ARG cc_start: 0.8902 (mmm160) cc_final: 0.8285 (mmm160) REVERT: A 261 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8257 (pp) REVERT: A 265 PRO cc_start: 0.7463 (Cg_endo) cc_final: 0.7205 (Cg_exo) REVERT: A 334 ARG cc_start: 0.6980 (ptp90) cc_final: 0.6723 (ptp90) REVERT: A 337 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7291 (pmt170) REVERT: A 340 GLN cc_start: 0.7706 (mp10) cc_final: 0.7469 (mp10) REVERT: B 82 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: B 265 PRO cc_start: 0.7568 (Cg_endo) cc_final: 0.7307 (Cg_exo) REVERT: B 341 PHE cc_start: 0.8038 (m-80) cc_final: 0.7631 (m-80) REVERT: C 261 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7767 (pp) REVERT: C 337 ARG cc_start: 0.7964 (ptt-90) cc_final: 0.7547 (ptp-170) REVERT: C 340 GLN cc_start: 0.7932 (mp-120) cc_final: 0.7055 (mm-40) REVERT: C 341 PHE cc_start: 0.7994 (m-80) cc_final: 0.7488 (m-10) REVERT: D 82 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8555 (m-80) REVERT: D 232 VAL cc_start: 0.9168 (p) cc_final: 0.8961 (p) REVERT: D 265 PRO cc_start: 0.7717 (Cg_endo) cc_final: 0.7443 (Cg_exo) REVERT: D 334 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7213 (ptt-90) REVERT: E 261 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8338 (pp) REVERT: F 82 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: F 135 MET cc_start: 0.8921 (tpp) cc_final: 0.8614 (mtt) REVERT: F 153 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8177 (tm-30) REVERT: G 261 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8401 (pp) REVERT: G 265 PRO cc_start: 0.7991 (Cg_endo) cc_final: 0.7536 (Cg_exo) REVERT: G 304 ILE cc_start: 0.8359 (tt) cc_final: 0.8028 (tt) outliers start: 62 outliers final: 51 residues processed: 264 average time/residue: 0.1378 time to fit residues: 53.7261 Evaluate side-chains 276 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 144 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 184 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126917 restraints weight = 22784.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130313 restraints weight = 14041.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132544 restraints weight = 10077.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133940 restraints weight = 8142.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134518 restraints weight = 7120.031| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16304 Z= 0.121 Angle : 0.561 10.528 22176 Z= 0.286 Chirality : 0.037 0.152 2604 Planarity : 0.004 0.064 2758 Dihedral : 3.802 18.868 2191 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.15 % Allowed : 18.29 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.19), residues: 1967 helix: 1.72 (0.14), residues: 1246 sheet: -0.58 (0.60), residues: 70 loop : -0.96 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 334 TYR 0.027 0.001 TYR G 213 PHE 0.020 0.001 PHE G 210 TRP 0.004 0.000 TRP E 142 HIS 0.002 0.000 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00262 (16289) covalent geometry : angle 0.55389 (22148) SS BOND : bond 0.00960 ( 14) SS BOND : angle 2.55700 ( 28) hydrogen bonds : bond 0.04634 ( 820) hydrogen bonds : angle 3.90111 ( 2415) Misc. bond : bond 0.00264 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8244 (pp) REVERT: A 265 PRO cc_start: 0.7506 (Cg_endo) cc_final: 0.7229 (Cg_exo) REVERT: A 334 ARG cc_start: 0.6905 (ptp90) cc_final: 0.6679 (ptp90) REVERT: A 337 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7252 (pmt170) REVERT: A 340 GLN cc_start: 0.7752 (mp10) cc_final: 0.7512 (mp10) REVERT: B 82 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: B 265 PRO cc_start: 0.7454 (Cg_endo) cc_final: 0.7192 (Cg_exo) REVERT: B 341 PHE cc_start: 0.8007 (m-80) cc_final: 0.7593 (m-80) REVERT: C 261 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7770 (pp) REVERT: C 337 ARG cc_start: 0.7873 (ptt-90) cc_final: 0.7460 (ptp-170) REVERT: C 340 GLN cc_start: 0.7909 (mp-120) cc_final: 0.7037 (mm-40) REVERT: C 341 PHE cc_start: 0.7933 (m-80) cc_final: 0.7450 (m-10) REVERT: D 82 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: D 232 VAL cc_start: 0.9129 (p) cc_final: 0.8924 (p) REVERT: D 265 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7390 (Cg_exo) REVERT: E 219 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8392 (mmm160) REVERT: E 261 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8234 (pp) REVERT: F 82 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: F 135 MET cc_start: 0.8884 (tpp) cc_final: 0.8560 (mtt) REVERT: F 153 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8098 (tm-30) REVERT: G 261 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8355 (pp) REVERT: G 265 PRO cc_start: 0.7947 (Cg_endo) cc_final: 0.7494 (Cg_exo) outliers start: 36 outliers final: 25 residues processed: 242 average time/residue: 0.1288 time to fit residues: 46.2501 Evaluate side-chains 252 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126111 restraints weight = 22818.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129434 restraints weight = 14034.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131634 restraints weight = 10090.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132809 restraints weight = 8151.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133817 restraints weight = 7187.289| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16304 Z= 0.124 Angle : 0.577 10.514 22176 Z= 0.293 Chirality : 0.037 0.150 2604 Planarity : 0.004 0.064 2758 Dihedral : 3.774 19.419 2191 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.21 % Allowed : 18.71 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.19), residues: 1967 helix: 1.78 (0.14), residues: 1246 sheet: -0.64 (0.59), residues: 70 loop : -0.93 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 219 TYR 0.026 0.002 TYR G 213 PHE 0.032 0.001 PHE C 210 TRP 0.006 0.000 TRP E 142 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00275 (16289) covalent geometry : angle 0.57083 (22148) SS BOND : bond 0.00943 ( 14) SS BOND : angle 2.50755 ( 28) hydrogen bonds : bond 0.04770 ( 820) hydrogen bonds : angle 3.89702 ( 2415) Misc. bond : bond 0.00260 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 261 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8262 (pp) REVERT: A 265 PRO cc_start: 0.7543 (Cg_endo) cc_final: 0.7268 (Cg_exo) REVERT: A 334 ARG cc_start: 0.6856 (ptp90) cc_final: 0.6633 (ptp90) REVERT: A 337 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7250 (pmt170) REVERT: A 340 GLN cc_start: 0.7732 (mp10) cc_final: 0.7491 (mp10) REVERT: B 82 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 265 PRO cc_start: 0.7465 (Cg_endo) cc_final: 0.7218 (Cg_exo) REVERT: B 341 PHE cc_start: 0.8012 (m-80) cc_final: 0.7590 (m-80) REVERT: C 261 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7827 (pp) REVERT: C 337 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7390 (ptp-170) REVERT: C 340 GLN cc_start: 0.7908 (mp-120) cc_final: 0.7047 (mm-40) REVERT: C 341 PHE cc_start: 0.7929 (m-80) cc_final: 0.7475 (m-80) REVERT: D 82 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: D 232 VAL cc_start: 0.9132 (p) cc_final: 0.8927 (p) REVERT: D 265 PRO cc_start: 0.7663 (Cg_endo) cc_final: 0.7409 (Cg_exo) REVERT: E 261 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8225 (pp) REVERT: E 334 ARG cc_start: 0.7045 (mtm-85) cc_final: 0.6292 (mtm-85) REVERT: E 337 ARG cc_start: 0.8173 (ptp90) cc_final: 0.7650 (ptp90) REVERT: F 82 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: F 135 MET cc_start: 0.8889 (tpp) cc_final: 0.8553 (mtt) REVERT: F 153 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8105 (tm-30) REVERT: G 261 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8346 (pp) REVERT: G 265 PRO cc_start: 0.7947 (Cg_endo) cc_final: 0.7514 (Cg_exo) REVERT: G 304 ILE cc_start: 0.8321 (tt) cc_final: 0.7983 (tt) outliers start: 37 outliers final: 26 residues processed: 239 average time/residue: 0.1313 time to fit residues: 46.0981 Evaluate side-chains 244 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 82 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 82 TYR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 62 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 187 optimal weight: 0.0270 chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126367 restraints weight = 22808.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129619 restraints weight = 14346.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131733 restraints weight = 10454.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132941 restraints weight = 8514.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133865 restraints weight = 7544.978| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16304 Z= 0.123 Angle : 0.577 10.446 22176 Z= 0.294 Chirality : 0.037 0.149 2604 Planarity : 0.004 0.070 2758 Dihedral : 3.764 19.280 2191 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.91 % Allowed : 19.55 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 1967 helix: 1.84 (0.14), residues: 1246 sheet: -0.64 (0.58), residues: 70 loop : -0.91 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 219 TYR 0.025 0.002 TYR G 213 PHE 0.017 0.001 PHE G 210 TRP 0.005 0.000 TRP E 142 HIS 0.002 0.000 HIS E 121 Details of bonding type rmsd covalent geometry : bond 0.00272 (16289) covalent geometry : angle 0.57080 (22148) SS BOND : bond 0.00923 ( 14) SS BOND : angle 2.43219 ( 28) hydrogen bonds : bond 0.04619 ( 820) hydrogen bonds : angle 3.85918 ( 2415) Misc. bond : bond 0.00258 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.58 seconds wall clock time: 44 minutes 30.19 seconds (2670.19 seconds total)