Starting phenix.real_space_refine on Tue Nov 18 20:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uvn_8608/11_2025/5uvn_8608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uvn_8608/11_2025/5uvn_8608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5uvn_8608/11_2025/5uvn_8608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uvn_8608/11_2025/5uvn_8608.map" model { file = "/net/cci-nas-00/data/ceres_data/5uvn_8608/11_2025/5uvn_8608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uvn_8608/11_2025/5uvn_8608_neut.cif" } resolution = 3.96 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= 0.001 sd= 0.010 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 18 5.16 5 C 10770 2.51 5 N 2886 2.21 5 O 3228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16902 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASP:plan': 11, 'GLN:plan1': 10, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASP:plan': 11, 'GLN:plan1': 10, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASP:plan': 11, 'GLN:plan1': 10, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASP:plan': 11, 'GLN:plan1': 10, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASP:plan': 11, 'GLN:plan1': 10, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 162 Chain: "E" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "F" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 9, 'ASP:plan': 11, 'GLN:plan1': 10, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 162 Chain: "F" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 4.35, per 1000 atoms: 0.26 Number of scatterers: 16902 At special positions: 0 Unit cell: (106.11, 111.35, 168.99, 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 18 16.00 O 3228 8.00 N 2886 7.00 C 10770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 913.8 milliseconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 30.4% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU A 95 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 98 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 436 through 467 Processing helix chain 'B' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU B 95 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 430 Processing helix chain 'B' and resid 436 through 467 Processing helix chain 'C' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU C 95 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 98 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 238 through 245 removed outlier: 4.035A pdb=" N THR C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 281 Processing helix chain 'C' and resid 322 through 333 removed outlier: 3.630A pdb=" N GLN C 327 " --> pdb=" O PRO C 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 346 Processing helix chain 'C' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 436 through 467 Processing helix chain 'D' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU D 95 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 98 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 238 through 245 removed outlier: 4.035A pdb=" N THR D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN D 327 " --> pdb=" O PRO D 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 430 Processing helix chain 'D' and resid 436 through 467 Processing helix chain 'E' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU E 95 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 281 Processing helix chain 'E' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN E 327 " --> pdb=" O PRO E 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 430 Processing helix chain 'E' and resid 436 through 467 Processing helix chain 'F' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU F 95 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 98 " --> pdb=" O GLU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 281 Processing helix chain 'F' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN F 327 " --> pdb=" O PRO F 323 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 430 Processing helix chain 'F' and resid 436 through 467 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU A 85 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 75 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS A 87 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 62 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE A 104 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE A 178 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 186 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE A 203 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE A 268 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 161 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 236 Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU A 386 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 306 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 313 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 307 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE A 407 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 289 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.839A pdb=" N GLU B 85 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 75 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS B 87 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 62 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE B 104 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE B 178 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 186 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 203 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE B 268 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 161 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 236 Processing sheet with id=AB2, first strand: chain 'B' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU B 386 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B 306 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 313 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE B 307 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE B 407 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 289 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU C 85 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA C 75 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS C 87 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 62 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE C 104 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE C 178 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 186 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 203 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE C 268 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 161 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB7, first strand: chain 'C' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU C 386 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU C 306 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 313 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE C 307 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE C 407 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 289 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU D 85 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA D 75 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 87 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 62 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE D 104 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE D 178 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL D 186 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE D 203 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE D 268 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 161 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC3, first strand: chain 'D' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU D 386 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU D 306 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 313 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 307 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE D 407 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 289 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 44 through 49 removed outlier: 6.837A pdb=" N GLU E 85 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA E 75 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS E 87 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 62 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE E 104 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE E 178 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL E 186 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE E 203 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE E 268 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 161 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU E 386 " --> pdb=" O PRO E 304 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU E 306 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 313 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 307 " --> pdb=" O ARG E 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE E 407 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 289 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 44 through 49 removed outlier: 6.839A pdb=" N GLU F 85 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA F 75 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS F 87 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE F 62 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE F 104 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.371A pdb=" N PHE F 178 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG F 182 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL F 186 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE F 203 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE F 268 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 161 " --> pdb=" O PHE F 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU F 386 " --> pdb=" O PRO F 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU F 306 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY F 313 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE F 307 " --> pdb=" O ARG F 311 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE F 407 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU F 289 " --> pdb=" O ILE F 407 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4940 1.33 - 1.45: 2492 1.45 - 1.57: 9704 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 17172 Sorted by residual: bond pdb=" C LEU F 299 " pdb=" N GLN F 300 " ideal model delta sigma weight residual 1.335 1.216 0.119 3.59e-02 7.76e+02 1.09e+01 bond pdb=" C LEU B 299 " pdb=" N GLN B 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.09e+01 bond pdb=" C LEU A 299 " pdb=" N GLN A 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.08e+01 bond pdb=" C LEU D 299 " pdb=" N GLN D 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.08e+01 bond pdb=" C LEU E 299 " pdb=" N GLN E 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.07e+01 ... (remaining 17167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21671 1.85 - 3.70: 1465 3.70 - 5.56: 277 5.56 - 7.41: 69 7.41 - 9.26: 50 Bond angle restraints: 23532 Sorted by residual: angle pdb=" C SER B 239 " pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 117.23 109.03 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" C SER E 239 " pdb=" CA SER E 239 " pdb=" CB SER E 239 " ideal model delta sigma weight residual 117.23 109.04 8.19 1.36e+00 5.41e-01 3.62e+01 angle pdb=" C SER A 239 " pdb=" CA SER A 239 " pdb=" CB SER A 239 " ideal model delta sigma weight residual 117.23 109.06 8.17 1.36e+00 5.41e-01 3.61e+01 angle pdb=" C SER D 239 " pdb=" CA SER D 239 " pdb=" CB SER D 239 " ideal model delta sigma weight residual 117.23 109.06 8.17 1.36e+00 5.41e-01 3.61e+01 angle pdb=" C SER F 239 " pdb=" CA SER F 239 " pdb=" CB SER F 239 " ideal model delta sigma weight residual 117.23 109.08 8.15 1.36e+00 5.41e-01 3.60e+01 ... (remaining 23527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.39: 8351 7.39 - 14.79: 1382 14.79 - 22.18: 293 22.18 - 29.58: 60 29.58 - 36.97: 6 Dihedral angle restraints: 10092 sinusoidal: 3018 harmonic: 7074 Sorted by residual: dihedral pdb=" CA ASP E 294 " pdb=" C ASP E 294 " pdb=" N SER E 295 " pdb=" CA SER E 295 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP D 294 " pdb=" C ASP D 294 " pdb=" N SER D 295 " pdb=" CA SER D 295 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1891 0.052 - 0.104: 846 0.104 - 0.155: 180 0.155 - 0.207: 20 0.207 - 0.259: 9 Chirality restraints: 2946 Sorted by residual: chirality pdb=" CG LEU D 170 " pdb=" CB LEU D 170 " pdb=" CD1 LEU D 170 " pdb=" CD2 LEU D 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU F 170 " pdb=" CB LEU F 170 " pdb=" CD1 LEU F 170 " pdb=" CD2 LEU F 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2943 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK C 456 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C UNK C 456 " -0.064 2.00e-02 2.50e+03 pdb=" O UNK C 456 " 0.024 2.00e-02 2.50e+03 pdb=" N UNK C 457 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK E 456 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C UNK E 456 " -0.063 2.00e-02 2.50e+03 pdb=" O UNK E 456 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK E 457 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 456 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C UNK D 456 " -0.063 2.00e-02 2.50e+03 pdb=" O UNK D 456 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK D 457 " 0.021 2.00e-02 2.50e+03 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 244 2.59 - 3.17: 16152 3.17 - 3.75: 23691 3.75 - 4.32: 32837 4.32 - 4.90: 53502 Nonbonded interactions: 126426 Sorted by model distance: nonbonded pdb=" NH1 ARG A 65 " pdb=" O LEU F 81 " model vdw 2.013 3.120 nonbonded pdb=" O LEU D 81 " pdb=" NH1 ARG E 65 " model vdw 2.016 3.120 nonbonded pdb=" O LEU A 81 " pdb=" NH1 ARG B 65 " model vdw 2.017 3.120 nonbonded pdb=" O LEU C 81 " pdb=" NH1 ARG D 65 " model vdw 2.023 3.120 nonbonded pdb=" O LEU B 81 " pdb=" NH1 ARG C 65 " model vdw 2.024 3.120 ... (remaining 126421 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 0.012 0.119 17172 Z= 0.530 Angle : 1.132 9.262 23532 Z= 0.594 Chirality : 0.059 0.259 2946 Planarity : 0.008 0.078 3054 Dihedral : 7.901 36.971 5544 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.54 % Favored : 90.91 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -4.03 (0.14), residues: 2178 helix: -3.73 (0.20), residues: 354 sheet: -2.16 (0.14), residues: 612 loop : -2.64 (0.14), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG E 369 TYR 0.016 0.003 TYR B 181 PHE 0.032 0.003 PHE F 250 TRP 0.031 0.006 TRP E 219 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.01205 (17172) covalent geometry : angle 1.13154 (23532) hydrogen bonds : bond 0.17492 ( 762) hydrogen bonds : angle 12.07157 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 422 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8839 (t0) cc_final: 0.8589 (t0) REVERT: A 63 LYS cc_start: 0.8672 (pttt) cc_final: 0.8268 (pttp) REVERT: A 71 VAL cc_start: 0.9024 (t) cc_final: 0.8773 (p) REVERT: A 87 LYS cc_start: 0.7161 (mttt) cc_final: 0.6653 (mttm) REVERT: A 105 TRP cc_start: 0.8495 (p90) cc_final: 0.7310 (p90) REVERT: A 143 ASP cc_start: 0.9040 (p0) cc_final: 0.8820 (p0) REVERT: A 342 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7221 (pt0) REVERT: A 373 LYS cc_start: 0.7229 (mttt) cc_final: 0.6893 (mttm) REVERT: B 51 ASN cc_start: 0.8929 (t0) cc_final: 0.8665 (t0) REVERT: B 63 LYS cc_start: 0.8813 (pttt) cc_final: 0.8268 (pttp) REVERT: B 87 LYS cc_start: 0.7162 (mttt) cc_final: 0.6768 (mttm) REVERT: B 127 TYR cc_start: 0.8969 (p90) cc_final: 0.8736 (p90) REVERT: B 143 ASP cc_start: 0.9066 (p0) cc_final: 0.8811 (p0) REVERT: B 215 ASN cc_start: 0.6255 (m-40) cc_final: 0.6038 (m110) REVERT: B 274 GLN cc_start: 0.7409 (mt0) cc_final: 0.7197 (mt0) REVERT: B 342 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8351 (mt-10) REVERT: B 373 LYS cc_start: 0.7480 (mttt) cc_final: 0.6864 (mttm) REVERT: C 61 THR cc_start: 0.8315 (p) cc_final: 0.8092 (p) REVERT: C 63 LYS cc_start: 0.8518 (pttt) cc_final: 0.8161 (pttp) REVERT: C 71 VAL cc_start: 0.8914 (t) cc_final: 0.8498 (p) REVERT: C 143 ASP cc_start: 0.9095 (p0) cc_final: 0.8783 (p0) REVERT: C 145 LEU cc_start: 0.7938 (mt) cc_final: 0.7663 (mt) REVERT: C 161 ILE cc_start: 0.8579 (mt) cc_final: 0.8335 (mt) REVERT: C 226 VAL cc_start: 0.8931 (t) cc_final: 0.8696 (p) REVERT: C 363 LEU cc_start: 0.9243 (mt) cc_final: 0.8965 (mt) REVERT: C 373 LYS cc_start: 0.7272 (mttt) cc_final: 0.6783 (mttm) REVERT: D 51 ASN cc_start: 0.8854 (t0) cc_final: 0.8612 (t0) REVERT: D 63 LYS cc_start: 0.8671 (pttt) cc_final: 0.8248 (pttp) REVERT: D 71 VAL cc_start: 0.9023 (t) cc_final: 0.8772 (p) REVERT: D 87 LYS cc_start: 0.7157 (mttt) cc_final: 0.6652 (mttm) REVERT: D 105 TRP cc_start: 0.8467 (p90) cc_final: 0.7239 (p90) REVERT: D 143 ASP cc_start: 0.9058 (p0) cc_final: 0.8846 (p0) REVERT: D 342 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7221 (pt0) REVERT: D 373 LYS cc_start: 0.7262 (mttt) cc_final: 0.6918 (mttm) REVERT: E 51 ASN cc_start: 0.8932 (t0) cc_final: 0.8658 (t0) REVERT: E 63 LYS cc_start: 0.8813 (pttt) cc_final: 0.8256 (pttp) REVERT: E 87 LYS cc_start: 0.7164 (mttt) cc_final: 0.6770 (mttm) REVERT: E 127 TYR cc_start: 0.8971 (p90) cc_final: 0.8736 (p90) REVERT: E 143 ASP cc_start: 0.9064 (p0) cc_final: 0.8819 (p0) REVERT: E 215 ASN cc_start: 0.6252 (m-40) cc_final: 0.6031 (m110) REVERT: E 274 GLN cc_start: 0.7398 (mt0) cc_final: 0.7187 (mt0) REVERT: E 342 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8351 (mt-10) REVERT: E 373 LYS cc_start: 0.7451 (mttt) cc_final: 0.6850 (mttm) REVERT: F 61 THR cc_start: 0.8329 (p) cc_final: 0.8105 (p) REVERT: F 63 LYS cc_start: 0.8494 (pttt) cc_final: 0.8173 (pttp) REVERT: F 71 VAL cc_start: 0.8868 (t) cc_final: 0.8470 (p) REVERT: F 143 ASP cc_start: 0.9103 (p0) cc_final: 0.8783 (p0) REVERT: F 145 LEU cc_start: 0.7996 (mt) cc_final: 0.7677 (mt) REVERT: F 161 ILE cc_start: 0.8582 (mt) cc_final: 0.8337 (mt) REVERT: F 226 VAL cc_start: 0.8947 (t) cc_final: 0.8709 (p) REVERT: F 274 GLN cc_start: 0.7193 (mt0) cc_final: 0.6900 (mt0) REVERT: F 363 LEU cc_start: 0.9152 (mt) cc_final: 0.8900 (mt) REVERT: F 373 LYS cc_start: 0.7335 (mttt) cc_final: 0.6887 (mttm) outliers start: 6 outliers final: 0 residues processed: 422 average time/residue: 0.1375 time to fit residues: 86.2829 Evaluate side-chains 269 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 215 ASN A 285 HIS A 359 HIS A 376 ASN B 285 HIS B 359 HIS B 376 ASN C 215 ASN C 285 HIS C 359 HIS C 376 ASN D 201 GLN D 215 ASN D 285 HIS D 359 HIS D 376 ASN E 285 HIS E 359 HIS E 376 ASN F 215 ASN F 285 HIS F 359 HIS F 376 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110118 restraints weight = 29526.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112225 restraints weight = 20788.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113734 restraints weight = 16177.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114566 restraints weight = 13456.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115606 restraints weight = 11910.989| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17172 Z= 0.155 Angle : 0.734 8.551 23532 Z= 0.378 Chirality : 0.048 0.153 2946 Planarity : 0.006 0.062 3054 Dihedral : 6.472 22.779 2592 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.54 % Favored : 90.63 % Rotamer: Outliers : 1.08 % Allowed : 9.24 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -3.02 (0.16), residues: 2178 helix: -2.83 (0.20), residues: 396 sheet: -1.48 (0.16), residues: 702 loop : -1.96 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.011 0.001 TYR E 288 PHE 0.016 0.002 PHE B 292 TRP 0.022 0.004 TRP A 105 HIS 0.005 0.002 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00320 (17172) covalent geometry : angle 0.73439 (23532) hydrogen bonds : bond 0.04132 ( 762) hydrogen bonds : angle 7.33871 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 365 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8728 (mttt) cc_final: 0.8185 (mttm) REVERT: A 293 LYS cc_start: 0.8108 (pttp) cc_final: 0.7719 (ptmt) REVERT: A 342 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7278 (pt0) REVERT: A 373 LYS cc_start: 0.8636 (mttt) cc_final: 0.8306 (mttm) REVERT: B 87 LYS cc_start: 0.8786 (mttt) cc_final: 0.8307 (mttm) REVERT: B 215 ASN cc_start: 0.8287 (m-40) cc_final: 0.8055 (m-40) REVERT: B 342 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7360 (pt0) REVERT: B 373 LYS cc_start: 0.8804 (mttt) cc_final: 0.8468 (mttm) REVERT: C 265 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8428 (mmtt) REVERT: C 363 LEU cc_start: 0.9015 (mt) cc_final: 0.8804 (mt) REVERT: C 373 LYS cc_start: 0.8763 (mttt) cc_final: 0.8474 (mttm) REVERT: D 87 LYS cc_start: 0.8728 (mttt) cc_final: 0.8181 (mttm) REVERT: D 342 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7281 (pt0) REVERT: D 373 LYS cc_start: 0.8642 (mttt) cc_final: 0.8306 (mttm) REVERT: E 87 LYS cc_start: 0.8786 (mttt) cc_final: 0.8303 (mttm) REVERT: E 215 ASN cc_start: 0.8285 (m-40) cc_final: 0.8057 (m-40) REVERT: E 342 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7360 (pt0) REVERT: E 373 LYS cc_start: 0.8810 (mttt) cc_final: 0.8474 (mttm) REVERT: F 265 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8425 (mmtt) REVERT: F 373 LYS cc_start: 0.8768 (mttt) cc_final: 0.8474 (mttm) outliers start: 16 outliers final: 12 residues processed: 373 average time/residue: 0.1331 time to fit residues: 75.5101 Evaluate side-chains 282 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN D 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103249 restraints weight = 30650.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104779 restraints weight = 22730.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107234 restraints weight = 18121.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106954 restraints weight = 15738.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106898 restraints weight = 13307.104| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 17172 Z= 0.341 Angle : 0.878 12.314 23532 Z= 0.442 Chirality : 0.052 0.151 2946 Planarity : 0.006 0.066 3054 Dihedral : 6.542 23.319 2592 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 1.10 % Allowed : 7.94 % Favored : 90.96 % Rotamer: Outliers : 4.79 % Allowed : 10.05 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -3.23 (0.16), residues: 2178 helix: -2.22 (0.21), residues: 402 sheet: -1.86 (0.15), residues: 762 loop : -2.23 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 196 TYR 0.010 0.002 TYR D 383 PHE 0.028 0.003 PHE E 250 TRP 0.020 0.004 TRP F 219 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00791 (17172) covalent geometry : angle 0.87820 (23532) hydrogen bonds : bond 0.04656 ( 762) hydrogen bonds : angle 6.94862 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8106 (p0) cc_final: 0.7839 (p0) REVERT: A 87 LYS cc_start: 0.8732 (mttt) cc_final: 0.8507 (mttm) REVERT: A 293 LYS cc_start: 0.8305 (pttp) cc_final: 0.7870 (ptmt) REVERT: A 342 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7430 (pt0) REVERT: A 373 LYS cc_start: 0.8625 (mttt) cc_final: 0.8317 (mttm) REVERT: B 80 ASP cc_start: 0.7589 (p0) cc_final: 0.7199 (p0) REVERT: B 87 LYS cc_start: 0.8755 (mttt) cc_final: 0.8386 (mttm) REVERT: B 373 LYS cc_start: 0.8964 (mttt) cc_final: 0.8559 (mttm) REVERT: C 80 ASP cc_start: 0.7862 (p0) cc_final: 0.7530 (p0) REVERT: C 265 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8626 (mmtt) REVERT: C 360 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8400 (mm) REVERT: C 373 LYS cc_start: 0.8841 (mttt) cc_final: 0.8539 (mttm) REVERT: D 80 ASP cc_start: 0.8099 (p0) cc_final: 0.7840 (p0) REVERT: D 87 LYS cc_start: 0.8726 (mttt) cc_final: 0.8505 (mttm) REVERT: D 342 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7427 (pt0) REVERT: D 373 LYS cc_start: 0.8636 (mttt) cc_final: 0.8326 (mttm) REVERT: E 80 ASP cc_start: 0.7593 (p0) cc_final: 0.7209 (p0) REVERT: E 87 LYS cc_start: 0.8752 (mttt) cc_final: 0.8387 (mttm) REVERT: E 373 LYS cc_start: 0.8961 (mttt) cc_final: 0.8558 (mttm) REVERT: F 80 ASP cc_start: 0.7871 (p0) cc_final: 0.7567 (p0) REVERT: F 265 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8622 (mmtt) REVERT: F 373 LYS cc_start: 0.8834 (mttt) cc_final: 0.8558 (mttm) outliers start: 71 outliers final: 40 residues processed: 320 average time/residue: 0.1217 time to fit residues: 61.0164 Evaluate side-chains 285 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106290 restraints weight = 29834.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108350 restraints weight = 20605.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109914 restraints weight = 15948.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110900 restraints weight = 13245.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111723 restraints weight = 11627.848| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17172 Z= 0.157 Angle : 0.687 10.123 23532 Z= 0.348 Chirality : 0.047 0.144 2946 Planarity : 0.005 0.065 3054 Dihedral : 5.739 23.528 2592 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.91 % Favored : 90.27 % Rotamer: Outliers : 2.83 % Allowed : 13.97 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.17), residues: 2178 helix: -0.56 (0.27), residues: 360 sheet: -1.00 (0.18), residues: 654 loop : -2.14 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 297 TYR 0.009 0.001 TYR B 333 PHE 0.014 0.002 PHE B 250 TRP 0.020 0.003 TRP C 105 HIS 0.002 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00347 (17172) covalent geometry : angle 0.68705 (23532) hydrogen bonds : bond 0.03662 ( 762) hydrogen bonds : angle 6.22573 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8146 (p0) cc_final: 0.7740 (p0) REVERT: A 87 LYS cc_start: 0.8726 (mttt) cc_final: 0.8334 (mttm) REVERT: A 215 ASN cc_start: 0.8316 (m-40) cc_final: 0.8001 (m-40) REVERT: A 293 LYS cc_start: 0.7823 (pttp) cc_final: 0.7435 (ptmt) REVERT: A 342 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7320 (pt0) REVERT: A 363 LEU cc_start: 0.8979 (mt) cc_final: 0.8744 (mt) REVERT: A 373 LYS cc_start: 0.8592 (mttt) cc_final: 0.8284 (mttm) REVERT: B 80 ASP cc_start: 0.7817 (p0) cc_final: 0.7220 (p0) REVERT: B 87 LYS cc_start: 0.8729 (mttt) cc_final: 0.8289 (mttm) REVERT: B 108 LYS cc_start: 0.8662 (tppp) cc_final: 0.8341 (tptm) REVERT: B 293 LYS cc_start: 0.8097 (pttm) cc_final: 0.7609 (ptmt) REVERT: B 373 LYS cc_start: 0.8915 (mttt) cc_final: 0.8476 (mttm) REVERT: C 80 ASP cc_start: 0.8010 (p0) cc_final: 0.7512 (p0) REVERT: C 265 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8412 (mmtt) REVERT: C 360 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8330 (mm) REVERT: C 373 LYS cc_start: 0.8807 (mttt) cc_final: 0.8488 (mttm) REVERT: D 80 ASP cc_start: 0.8160 (p0) cc_final: 0.7760 (p0) REVERT: D 87 LYS cc_start: 0.8737 (mttt) cc_final: 0.8332 (mttm) REVERT: D 215 ASN cc_start: 0.8308 (m-40) cc_final: 0.7976 (m-40) REVERT: D 342 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7323 (pt0) REVERT: D 363 LEU cc_start: 0.9002 (mt) cc_final: 0.8751 (mt) REVERT: D 373 LYS cc_start: 0.8595 (mttt) cc_final: 0.8275 (mttm) REVERT: E 80 ASP cc_start: 0.7862 (p0) cc_final: 0.7304 (p0) REVERT: E 87 LYS cc_start: 0.8737 (mttt) cc_final: 0.8290 (mttm) REVERT: E 108 LYS cc_start: 0.8676 (tppp) cc_final: 0.8359 (tptm) REVERT: E 293 LYS cc_start: 0.8123 (pttm) cc_final: 0.7624 (ptmt) REVERT: E 373 LYS cc_start: 0.8919 (mttt) cc_final: 0.8474 (mttm) REVERT: F 80 ASP cc_start: 0.8029 (p0) cc_final: 0.7547 (p0) REVERT: F 108 LYS cc_start: 0.8267 (ttpp) cc_final: 0.8043 (tttm) REVERT: F 265 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8405 (mmtt) REVERT: F 373 LYS cc_start: 0.8808 (mttt) cc_final: 0.8477 (mttm) outliers start: 42 outliers final: 21 residues processed: 331 average time/residue: 0.1269 time to fit residues: 64.7190 Evaluate side-chains 290 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 18 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101851 restraints weight = 30234.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104712 restraints weight = 23058.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104692 restraints weight = 17996.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105947 restraints weight = 15188.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106431 restraints weight = 13612.289| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17172 Z= 0.263 Angle : 0.780 14.975 23532 Z= 0.391 Chirality : 0.049 0.145 2946 Planarity : 0.006 0.067 3054 Dihedral : 5.875 24.530 2592 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.46 % Favored : 89.72 % Rotamer: Outliers : 4.59 % Allowed : 14.44 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -2.49 (0.17), residues: 2178 helix: -0.29 (0.28), residues: 342 sheet: -1.57 (0.16), residues: 774 loop : -2.14 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 308 TYR 0.008 0.002 TYR B 282 PHE 0.016 0.002 PHE E 250 TRP 0.017 0.003 TRP C 219 HIS 0.003 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00610 (17172) covalent geometry : angle 0.78026 (23532) hydrogen bonds : bond 0.04102 ( 762) hydrogen bonds : angle 6.37971 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 267 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8241 (p0) cc_final: 0.7804 (p0) REVERT: A 87 LYS cc_start: 0.8777 (mttt) cc_final: 0.8506 (mttm) REVERT: A 215 ASN cc_start: 0.8337 (m-40) cc_final: 0.8085 (m-40) REVERT: A 293 LYS cc_start: 0.8156 (pttp) cc_final: 0.7728 (ptmt) REVERT: A 342 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7271 (pt0) REVERT: A 363 LEU cc_start: 0.8932 (mt) cc_final: 0.8638 (mt) REVERT: A 373 LYS cc_start: 0.8622 (mttt) cc_final: 0.8358 (mttm) REVERT: B 80 ASP cc_start: 0.8070 (p0) cc_final: 0.7576 (p0) REVERT: B 87 LYS cc_start: 0.8734 (mttt) cc_final: 0.8320 (mttm) REVERT: B 187 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: B 265 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8691 (mmmm) REVERT: B 373 LYS cc_start: 0.8915 (mttt) cc_final: 0.8494 (mttm) REVERT: C 80 ASP cc_start: 0.8102 (p0) cc_final: 0.7578 (p0) REVERT: C 265 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8442 (mmtt) REVERT: C 360 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8126 (mm) REVERT: C 373 LYS cc_start: 0.8850 (mttt) cc_final: 0.8540 (mttm) REVERT: D 80 ASP cc_start: 0.8302 (p0) cc_final: 0.7827 (p0) REVERT: D 87 LYS cc_start: 0.8789 (mttt) cc_final: 0.8505 (mttm) REVERT: D 215 ASN cc_start: 0.8338 (m-40) cc_final: 0.8077 (m-40) REVERT: D 293 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7817 (ptpp) REVERT: D 342 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7300 (pt0) REVERT: D 363 LEU cc_start: 0.8932 (mt) cc_final: 0.8642 (mt) REVERT: D 373 LYS cc_start: 0.8637 (mttt) cc_final: 0.8379 (mttm) REVERT: E 80 ASP cc_start: 0.8063 (p0) cc_final: 0.7565 (p0) REVERT: E 87 LYS cc_start: 0.8737 (mttt) cc_final: 0.8322 (mttm) REVERT: E 265 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8695 (mmmm) REVERT: E 373 LYS cc_start: 0.8916 (mttt) cc_final: 0.8504 (mttm) REVERT: F 80 ASP cc_start: 0.8114 (p0) cc_final: 0.7552 (p0) REVERT: F 131 GLN cc_start: 0.8829 (tt0) cc_final: 0.8521 (tt0) REVERT: F 265 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8442 (mmtt) REVERT: F 373 LYS cc_start: 0.8836 (mttt) cc_final: 0.8521 (mttm) outliers start: 68 outliers final: 42 residues processed: 320 average time/residue: 0.1253 time to fit residues: 62.0798 Evaluate side-chains 288 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 106 optimal weight: 0.0050 chunk 139 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106506 restraints weight = 29506.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109306 restraints weight = 22213.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109498 restraints weight = 16849.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110701 restraints weight = 15285.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111616 restraints weight = 12794.727| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17172 Z= 0.140 Angle : 0.693 16.687 23532 Z= 0.346 Chirality : 0.046 0.142 2946 Planarity : 0.005 0.064 3054 Dihedral : 5.327 24.717 2592 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.00 % Favored : 90.17 % Rotamer: Outliers : 3.58 % Allowed : 16.40 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -1.73 (0.18), residues: 2178 helix: 0.48 (0.30), residues: 342 sheet: -0.73 (0.18), residues: 654 loop : -1.93 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.008 0.001 TYR E 288 PHE 0.023 0.002 PHE D 250 TRP 0.018 0.003 TRP C 105 HIS 0.001 0.000 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00308 (17172) covalent geometry : angle 0.69346 (23532) hydrogen bonds : bond 0.03475 ( 762) hydrogen bonds : angle 5.88770 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8238 (p0) cc_final: 0.7755 (p0) REVERT: A 87 LYS cc_start: 0.8745 (mttt) cc_final: 0.8481 (mttm) REVERT: A 215 ASN cc_start: 0.8224 (m-40) cc_final: 0.7884 (m-40) REVERT: A 265 LYS cc_start: 0.8628 (mmmt) cc_final: 0.7714 (tppt) REVERT: A 342 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7313 (pt0) REVERT: A 363 LEU cc_start: 0.8880 (mt) cc_final: 0.8586 (mt) REVERT: B 80 ASP cc_start: 0.8006 (p0) cc_final: 0.7520 (p0) REVERT: B 87 LYS cc_start: 0.8677 (mttt) cc_final: 0.8306 (mttm) REVERT: B 220 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: B 373 LYS cc_start: 0.8889 (mttt) cc_final: 0.8470 (mttm) REVERT: C 80 ASP cc_start: 0.8012 (p0) cc_final: 0.7377 (p0) REVERT: C 265 LYS cc_start: 0.8758 (mmmt) cc_final: 0.7729 (tppt) REVERT: C 360 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 373 LYS cc_start: 0.8731 (mttt) cc_final: 0.8424 (mttm) REVERT: D 80 ASP cc_start: 0.8247 (p0) cc_final: 0.7772 (p0) REVERT: D 87 LYS cc_start: 0.8752 (mttt) cc_final: 0.8484 (mttm) REVERT: D 215 ASN cc_start: 0.8224 (m-40) cc_final: 0.7858 (m-40) REVERT: D 265 LYS cc_start: 0.8635 (mmmt) cc_final: 0.7718 (tppt) REVERT: D 342 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7270 (pt0) REVERT: D 363 LEU cc_start: 0.8899 (mt) cc_final: 0.8599 (mt) REVERT: E 80 ASP cc_start: 0.8034 (p0) cc_final: 0.7551 (p0) REVERT: E 87 LYS cc_start: 0.8696 (mttt) cc_final: 0.8309 (mttm) REVERT: E 220 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7786 (tttm) REVERT: E 373 LYS cc_start: 0.8892 (mttt) cc_final: 0.8473 (mttm) REVERT: F 80 ASP cc_start: 0.8019 (p0) cc_final: 0.7389 (p0) REVERT: F 265 LYS cc_start: 0.8760 (mmmt) cc_final: 0.7736 (tppt) REVERT: F 373 LYS cc_start: 0.8730 (mttt) cc_final: 0.8425 (mttm) outliers start: 53 outliers final: 27 residues processed: 326 average time/residue: 0.1244 time to fit residues: 62.5067 Evaluate side-chains 291 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105825 restraints weight = 29716.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107791 restraints weight = 22396.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107589 restraints weight = 19583.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108723 restraints weight = 17277.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109728 restraints weight = 14463.955| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17172 Z= 0.203 Angle : 0.761 18.070 23532 Z= 0.374 Chirality : 0.047 0.142 2946 Planarity : 0.005 0.066 3054 Dihedral : 5.421 24.208 2592 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.92 % Favored : 89.26 % Rotamer: Outliers : 3.58 % Allowed : 18.02 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -1.83 (0.18), residues: 2178 helix: 0.49 (0.30), residues: 342 sheet: -0.97 (0.17), residues: 726 loop : -1.95 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 65 TYR 0.010 0.001 TYR C 127 PHE 0.023 0.002 PHE A 218 TRP 0.017 0.003 TRP C 219 HIS 0.002 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00469 (17172) covalent geometry : angle 0.76116 (23532) hydrogen bonds : bond 0.03754 ( 762) hydrogen bonds : angle 5.95963 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8253 (p0) cc_final: 0.7754 (p0) REVERT: A 87 LYS cc_start: 0.8757 (mttt) cc_final: 0.8509 (mttm) REVERT: A 265 LYS cc_start: 0.8670 (mmmt) cc_final: 0.7695 (tppt) REVERT: A 342 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7313 (pt0) REVERT: A 363 LEU cc_start: 0.9030 (mt) cc_final: 0.8697 (mt) REVERT: B 80 ASP cc_start: 0.8063 (p0) cc_final: 0.7577 (p0) REVERT: B 87 LYS cc_start: 0.8704 (mttt) cc_final: 0.8340 (mttm) REVERT: B 265 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8348 (tptt) REVERT: B 373 LYS cc_start: 0.8909 (mttt) cc_final: 0.8521 (mttm) REVERT: C 80 ASP cc_start: 0.8120 (p0) cc_final: 0.7574 (p0) REVERT: C 265 LYS cc_start: 0.8788 (mmmt) cc_final: 0.7754 (tppt) REVERT: C 360 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7877 (mm) REVERT: C 373 LYS cc_start: 0.8697 (mttt) cc_final: 0.8400 (mttm) REVERT: D 80 ASP cc_start: 0.8258 (p0) cc_final: 0.7757 (p0) REVERT: D 87 LYS cc_start: 0.8756 (mttt) cc_final: 0.8508 (mttm) REVERT: D 215 ASN cc_start: 0.8353 (m-40) cc_final: 0.7915 (m-40) REVERT: D 265 LYS cc_start: 0.8671 (mmmt) cc_final: 0.7716 (tppt) REVERT: D 293 LYS cc_start: 0.7765 (ptpp) cc_final: 0.7333 (mtpt) REVERT: D 342 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7305 (pt0) REVERT: D 363 LEU cc_start: 0.9030 (mt) cc_final: 0.8668 (mt) REVERT: E 80 ASP cc_start: 0.8070 (p0) cc_final: 0.7573 (p0) REVERT: E 87 LYS cc_start: 0.8709 (mttt) cc_final: 0.8344 (mttm) REVERT: E 265 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8363 (tptt) REVERT: E 373 LYS cc_start: 0.8897 (mttt) cc_final: 0.8498 (mttm) REVERT: F 80 ASP cc_start: 0.8123 (p0) cc_final: 0.7585 (p0) REVERT: F 265 LYS cc_start: 0.8789 (mmmt) cc_final: 0.7762 (tppt) REVERT: F 373 LYS cc_start: 0.8689 (mttt) cc_final: 0.8393 (mttm) outliers start: 53 outliers final: 39 residues processed: 304 average time/residue: 0.1236 time to fit residues: 58.8143 Evaluate side-chains 296 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 227 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104389 restraints weight = 29977.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106277 restraints weight = 21881.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107637 restraints weight = 17354.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108468 restraints weight = 14717.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109249 restraints weight = 13187.443| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17172 Z= 0.227 Angle : 0.775 17.687 23532 Z= 0.384 Chirality : 0.048 0.141 2946 Planarity : 0.006 0.067 3054 Dihedral : 5.494 23.473 2592 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.15 % Favored : 89.03 % Rotamer: Outliers : 3.98 % Allowed : 17.95 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -1.98 (0.18), residues: 2178 helix: 0.16 (0.29), residues: 360 sheet: -1.06 (0.17), residues: 726 loop : -2.01 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.017 0.002 TYR D 271 PHE 0.022 0.002 PHE D 218 TRP 0.020 0.003 TRP F 219 HIS 0.002 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00529 (17172) covalent geometry : angle 0.77463 (23532) hydrogen bonds : bond 0.03861 ( 762) hydrogen bonds : angle 5.99400 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8321 (p0) cc_final: 0.7774 (p0) REVERT: A 87 LYS cc_start: 0.8751 (mttt) cc_final: 0.8502 (mttm) REVERT: A 342 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7366 (pt0) REVERT: A 363 LEU cc_start: 0.9034 (mt) cc_final: 0.8677 (mt) REVERT: B 80 ASP cc_start: 0.8049 (p0) cc_final: 0.7572 (p0) REVERT: B 87 LYS cc_start: 0.8687 (mttt) cc_final: 0.8304 (mttm) REVERT: B 265 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8863 (tppt) REVERT: B 373 LYS cc_start: 0.8899 (mttt) cc_final: 0.8508 (mttm) REVERT: C 80 ASP cc_start: 0.8164 (p0) cc_final: 0.7624 (p0) REVERT: C 265 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8430 (mmtt) REVERT: C 360 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7826 (mm) REVERT: C 373 LYS cc_start: 0.8663 (mttt) cc_final: 0.8373 (mttm) REVERT: D 80 ASP cc_start: 0.8330 (p0) cc_final: 0.7781 (p0) REVERT: D 87 LYS cc_start: 0.8760 (mttt) cc_final: 0.8505 (mttm) REVERT: D 265 LYS cc_start: 0.8749 (mmmt) cc_final: 0.7800 (tppt) REVERT: D 342 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7264 (pt0) REVERT: D 363 LEU cc_start: 0.9033 (mt) cc_final: 0.8671 (mt) REVERT: E 80 ASP cc_start: 0.8056 (p0) cc_final: 0.7575 (p0) REVERT: E 87 LYS cc_start: 0.8692 (mttt) cc_final: 0.8304 (mttm) REVERT: E 265 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8859 (tppt) REVERT: E 373 LYS cc_start: 0.8898 (mttt) cc_final: 0.8499 (mttm) REVERT: F 80 ASP cc_start: 0.8171 (p0) cc_final: 0.7646 (p0) REVERT: F 220 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7706 (tttm) REVERT: F 265 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8436 (mmtt) REVERT: F 373 LYS cc_start: 0.8678 (mttt) cc_final: 0.8341 (mttm) outliers start: 59 outliers final: 44 residues processed: 307 average time/residue: 0.1241 time to fit residues: 59.0843 Evaluate side-chains 296 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 235 optimal weight: 40.0000 chunk 134 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107166 restraints weight = 29722.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108732 restraints weight = 22113.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109130 restraints weight = 17714.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109627 restraints weight = 16933.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110140 restraints weight = 14511.116| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17172 Z= 0.189 Angle : 0.747 17.027 23532 Z= 0.372 Chirality : 0.047 0.150 2946 Planarity : 0.005 0.065 3054 Dihedral : 5.312 23.056 2592 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.38 % Favored : 88.80 % Rotamer: Outliers : 3.58 % Allowed : 18.56 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -1.81 (0.18), residues: 2178 helix: 0.33 (0.30), residues: 360 sheet: -0.89 (0.18), residues: 714 loop : -1.95 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 65 TYR 0.018 0.001 TYR A 127 PHE 0.020 0.002 PHE A 218 TRP 0.018 0.003 TRP B 219 HIS 0.002 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00437 (17172) covalent geometry : angle 0.74720 (23532) hydrogen bonds : bond 0.03644 ( 762) hydrogen bonds : angle 5.83783 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8297 (p0) cc_final: 0.7724 (p0) REVERT: A 87 LYS cc_start: 0.8737 (mttt) cc_final: 0.8494 (mttm) REVERT: A 342 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7313 (pt0) REVERT: A 363 LEU cc_start: 0.9089 (mt) cc_final: 0.8783 (mt) REVERT: B 80 ASP cc_start: 0.8063 (p0) cc_final: 0.7571 (p0) REVERT: B 87 LYS cc_start: 0.8682 (mttt) cc_final: 0.8295 (mttm) REVERT: B 373 LYS cc_start: 0.8848 (mttt) cc_final: 0.8475 (mttm) REVERT: C 80 ASP cc_start: 0.8174 (p0) cc_final: 0.7652 (p0) REVERT: C 265 LYS cc_start: 0.8819 (mmmt) cc_final: 0.7741 (tppt) REVERT: C 360 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7738 (mm) REVERT: C 368 LEU cc_start: 0.8766 (mt) cc_final: 0.8563 (mt) REVERT: C 373 LYS cc_start: 0.8637 (mttt) cc_final: 0.8333 (mttm) REVERT: D 80 ASP cc_start: 0.8304 (p0) cc_final: 0.7731 (p0) REVERT: D 87 LYS cc_start: 0.8743 (mttt) cc_final: 0.8486 (mttm) REVERT: D 265 LYS cc_start: 0.8538 (mmmt) cc_final: 0.7615 (tppt) REVERT: D 342 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7304 (pt0) REVERT: D 363 LEU cc_start: 0.9094 (mt) cc_final: 0.8774 (mt) REVERT: E 80 ASP cc_start: 0.8073 (p0) cc_final: 0.7581 (p0) REVERT: E 87 LYS cc_start: 0.8688 (mttt) cc_final: 0.8295 (mttm) REVERT: E 373 LYS cc_start: 0.8904 (mttt) cc_final: 0.8547 (mttm) REVERT: F 80 ASP cc_start: 0.8175 (p0) cc_final: 0.7651 (p0) REVERT: F 220 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7577 (tttm) REVERT: F 265 LYS cc_start: 0.8809 (mmmt) cc_final: 0.7753 (tppt) REVERT: F 373 LYS cc_start: 0.8687 (mttt) cc_final: 0.8364 (mttm) outliers start: 53 outliers final: 44 residues processed: 302 average time/residue: 0.1193 time to fit residues: 56.3215 Evaluate side-chains 301 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 151 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN E 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102108 restraints weight = 30196.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104039 restraints weight = 21329.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105393 restraints weight = 16779.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106433 restraints weight = 14191.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107215 restraints weight = 12559.860| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17172 Z= 0.157 Angle : 0.707 16.659 23532 Z= 0.352 Chirality : 0.046 0.144 2946 Planarity : 0.005 0.064 3054 Dihedral : 5.045 22.851 2592 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.28 % Favored : 88.89 % Rotamer: Outliers : 2.63 % Allowed : 18.96 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -1.61 (0.18), residues: 2178 helix: 0.55 (0.30), residues: 360 sheet: -0.72 (0.18), residues: 714 loop : -1.88 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 65 TYR 0.024 0.001 TYR A 271 PHE 0.016 0.001 PHE D 218 TRP 0.017 0.003 TRP C 105 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00360 (17172) covalent geometry : angle 0.70747 (23532) hydrogen bonds : bond 0.03430 ( 762) hydrogen bonds : angle 5.61368 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8235 (p0) cc_final: 0.7636 (p0) REVERT: A 87 LYS cc_start: 0.8747 (mttt) cc_final: 0.8475 (mttm) REVERT: A 265 LYS cc_start: 0.8619 (mmmt) cc_final: 0.7837 (tppt) REVERT: A 342 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7286 (pt0) REVERT: A 363 LEU cc_start: 0.8994 (mt) cc_final: 0.8694 (mt) REVERT: B 80 ASP cc_start: 0.8040 (p0) cc_final: 0.7527 (p0) REVERT: B 87 LYS cc_start: 0.8722 (mttt) cc_final: 0.8267 (mttm) REVERT: B 373 LYS cc_start: 0.8894 (mttt) cc_final: 0.8565 (mttm) REVERT: C 80 ASP cc_start: 0.8185 (p0) cc_final: 0.7651 (p0) REVERT: C 265 LYS cc_start: 0.8777 (mmmt) cc_final: 0.7715 (tppt) REVERT: C 360 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7736 (mm) REVERT: C 373 LYS cc_start: 0.8695 (mttt) cc_final: 0.8380 (mttm) REVERT: D 80 ASP cc_start: 0.8230 (p0) cc_final: 0.7636 (p0) REVERT: D 87 LYS cc_start: 0.8758 (mttt) cc_final: 0.8449 (mttm) REVERT: D 265 LYS cc_start: 0.8659 (mmmt) cc_final: 0.7726 (tppt) REVERT: D 342 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7293 (pt0) REVERT: D 363 LEU cc_start: 0.8999 (mt) cc_final: 0.8695 (mt) REVERT: E 80 ASP cc_start: 0.8032 (p0) cc_final: 0.7525 (p0) REVERT: E 87 LYS cc_start: 0.8722 (mttt) cc_final: 0.8259 (mttm) REVERT: E 373 LYS cc_start: 0.8895 (mttt) cc_final: 0.8596 (mttm) REVERT: F 80 ASP cc_start: 0.8180 (p0) cc_final: 0.7652 (p0) REVERT: F 265 LYS cc_start: 0.8779 (mmmt) cc_final: 0.7731 (tppt) REVERT: F 373 LYS cc_start: 0.8699 (mttt) cc_final: 0.8389 (mttm) outliers start: 39 outliers final: 36 residues processed: 300 average time/residue: 0.1195 time to fit residues: 56.0422 Evaluate side-chains 287 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 108 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 188 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN B 215 ASN C 376 ASN D 376 ASN E 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108383 restraints weight = 29236.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110396 restraints weight = 20718.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111917 restraints weight = 16225.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112995 restraints weight = 13563.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113514 restraints weight = 11933.950| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17172 Z= 0.142 Angle : 0.709 16.520 23532 Z= 0.352 Chirality : 0.046 0.145 2946 Planarity : 0.005 0.065 3054 Dihedral : 4.901 22.442 2592 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.10 % Favored : 89.03 % Rotamer: Outliers : 2.63 % Allowed : 19.50 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 are not related in a simple way. whole: -1.53 (0.18), residues: 2178 helix: 0.69 (0.31), residues: 360 sheet: -0.72 (0.18), residues: 732 loop : -1.82 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 65 TYR 0.014 0.001 TYR D 127 PHE 0.012 0.001 PHE A 250 TRP 0.018 0.003 TRP F 219 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00326 (17172) covalent geometry : angle 0.70898 (23532) hydrogen bonds : bond 0.03326 ( 762) hydrogen bonds : angle 5.54411 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.52 seconds wall clock time: 45 minutes 1.12 seconds (2701.12 seconds total)