Starting phenix.real_space_refine on Sat Jul 4 01:30:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzy_24783/07_2026/7rzy_24783.cif" } resolution = 3.5 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= 0.021 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 11032 2.51 5 N 3017 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17458 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "2" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "3" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "4" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "5" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "6" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "7" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "1" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.98, per 1000 atoms: 0.23 Number of scatterers: 17458 At special positions: 0 Unit cell: (154.057, 154.057, 68.1667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3311 8.00 N 3017 7.00 C 11032 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 614.5 milliseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 10 sheets defined 55.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain '1' and resid 5 through 14 removed outlier: 3.567A pdb=" N ILE 1 9 " --> pdb=" O ARG 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 19 through 36 removed outlier: 4.121A pdb=" N SER 1 36 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 54 through 74 removed outlier: 3.999A pdb=" N ARG 1 68 " --> pdb=" O ASN 1 64 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLU 1 69 " --> pdb=" O GLN 1 65 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER 1 70 " --> pdb=" O ASN 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 89 through 100 Processing helix chain '1' and resid 114 through 127 Proline residue: 1 124 - end of helix Processing helix chain '1' and resid 136 through 140 Processing helix chain '1' and resid 149 through 162 Processing helix chain '1' and resid 171 through 173 No H-bonds generated for 'chain '1' and resid 171 through 173' Processing helix chain '1' and resid 174 through 181 removed outlier: 4.020A pdb=" N LEU 1 178 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN 1 181 " --> pdb=" O VAL 1 177 " (cutoff:3.500A) Processing helix chain '1' and resid 181 through 188 removed outlier: 3.604A pdb=" N ARG 1 187 " --> pdb=" O GLN 1 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 1 188 " --> pdb=" O LEU 1 184 " (cutoff:3.500A) Processing helix chain '1' and resid 204 through 217 removed outlier: 4.227A pdb=" N THR 1 208 " --> pdb=" O GLY 1 204 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 238 removed outlier: 4.059A pdb=" N LYS 1 232 " --> pdb=" O GLU 1 228 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS 1 233 " --> pdb=" O SER 1 229 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 258 removed outlier: 3.541A pdb=" N LEU 1 245 " --> pdb=" O ASN 1 241 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 276 Processing helix chain '1' and resid 308 through 314 removed outlier: 4.298A pdb=" N HIS 1 314 " --> pdb=" O ASP 1 310 " (cutoff:3.500A) Processing helix chain '2' and resid 5 through 14 removed outlier: 3.606A pdb=" N ILE 2 9 " --> pdb=" O ARG 2 5 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 36 removed outlier: 3.983A pdb=" N SER 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 74 removed outlier: 3.866A pdb=" N ARG 2 68 " --> pdb=" O ASN 2 64 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU 2 69 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER 2 70 " --> pdb=" O ASN 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 89 through 101 Processing helix chain '2' and resid 114 through 127 Proline residue: 2 124 - end of helix Processing helix chain '2' and resid 149 through 162 Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 174 through 181 removed outlier: 3.970A pdb=" N LEU 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN 2 181 " --> pdb=" O VAL 2 177 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 188 removed outlier: 3.586A pdb=" N PHE 2 188 " --> pdb=" O LEU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 217 Processing helix chain '2' and resid 227 through 238 removed outlier: 4.029A pdb=" N LYS 2 232 " --> pdb=" O GLU 2 228 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS 2 233 " --> pdb=" O SER 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 258 removed outlier: 3.636A pdb=" N LEU 2 245 " --> pdb=" O ASN 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 268 through 276 Processing helix chain '2' and resid 308 through 313 Processing helix chain '3' and resid 5 through 14 removed outlier: 3.648A pdb=" N ILE 3 9 " --> pdb=" O ARG 3 5 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 36 removed outlier: 3.903A pdb=" N SER 3 36 " --> pdb=" O CYS 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 74 removed outlier: 3.951A pdb=" N ARG 3 68 " --> pdb=" O ASN 3 64 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU 3 69 " --> pdb=" O GLN 3 65 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER 3 70 " --> pdb=" O ASN 3 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY 3 74 " --> pdb=" O SER 3 70 " (cutoff:3.500A) Processing helix chain '3' and resid 89 through 101 Processing helix chain '3' and resid 114 through 127 Proline residue: 3 124 - end of helix Processing helix chain '3' and resid 149 through 162 Processing helix chain '3' and resid 171 through 173 No H-bonds generated for 'chain '3' and resid 171 through 173' Processing helix chain '3' and resid 174 through 181 removed outlier: 3.861A pdb=" N LEU 3 178 " --> pdb=" O SER 3 174 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN 3 181 " --> pdb=" O VAL 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 181 through 187 Processing helix chain '3' and resid 204 through 217 removed outlier: 3.942A pdb=" N THR 3 208 " --> pdb=" O GLY 3 204 " (cutoff:3.500A) Processing helix chain '3' and resid 227 through 238 removed outlier: 4.112A pdb=" N LYS 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS 3 233 " --> pdb=" O SER 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 241 through 258 removed outlier: 3.542A pdb=" N LEU 3 245 " --> pdb=" O ASN 3 241 " (cutoff:3.500A) Processing helix chain '3' and resid 268 through 276 Processing helix chain '3' and resid 295 through 300 removed outlier: 3.676A pdb=" N ARG 3 300 " --> pdb=" O ASP 3 297 " (cutoff:3.500A) Processing helix chain '3' and resid 308 through 314 removed outlier: 4.487A pdb=" N HIS 3 314 " --> pdb=" O ASP 3 310 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 14 removed outlier: 3.536A pdb=" N ILE 4 9 " --> pdb=" O ARG 4 5 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 36 removed outlier: 3.986A pdb=" N SER 4 36 " --> pdb=" O CYS 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 74 removed outlier: 3.946A pdb=" N ARG 4 68 " --> pdb=" O ASN 4 64 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU 4 69 " --> pdb=" O GLN 4 65 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER 4 70 " --> pdb=" O ASN 4 66 " (cutoff:3.500A) Processing helix chain '4' and resid 89 through 101 removed outlier: 3.743A pdb=" N MET 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) Processing helix chain '4' and resid 114 through 127 Proline residue: 4 124 - end of helix Processing helix chain '4' and resid 149 through 162 Processing helix chain '4' and resid 171 through 173 No H-bonds generated for 'chain '4' and resid 171 through 173' Processing helix chain '4' and resid 174 through 181 removed outlier: 3.811A pdb=" N LEU 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN 4 181 " --> pdb=" O VAL 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 181 through 188 Processing helix chain '4' and resid 204 through 217 Processing helix chain '4' and resid 227 through 238 removed outlier: 4.260A pdb=" N LYS 4 232 " --> pdb=" O GLU 4 228 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS 4 233 " --> pdb=" O SER 4 229 " (cutoff:3.500A) Processing helix chain '4' and resid 241 through 258 removed outlier: 3.536A pdb=" N LEU 4 245 " --> pdb=" O ASN 4 241 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 276 Processing helix chain '4' and resid 308 through 313 Processing helix chain '5' and resid 5 through 14 Processing helix chain '5' and resid 19 through 36 removed outlier: 3.946A pdb=" N SER 5 36 " --> pdb=" O CYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 74 removed outlier: 3.961A pdb=" N ARG 5 68 " --> pdb=" O ASN 5 64 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU 5 69 " --> pdb=" O GLN 5 65 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER 5 70 " --> pdb=" O ASN 5 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY 5 74 " --> pdb=" O SER 5 70 " (cutoff:3.500A) Processing helix chain '5' and resid 89 through 101 Processing helix chain '5' and resid 114 through 127 Proline residue: 5 124 - end of helix Processing helix chain '5' and resid 149 through 162 Processing helix chain '5' and resid 171 through 173 No H-bonds generated for 'chain '5' and resid 171 through 173' Processing helix chain '5' and resid 174 through 181 removed outlier: 3.885A pdb=" N LEU 5 178 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN 5 181 " --> pdb=" O VAL 5 177 " (cutoff:3.500A) Processing helix chain '5' and resid 181 through 188 Processing helix chain '5' and resid 204 through 217 removed outlier: 3.926A pdb=" N THR 5 208 " --> pdb=" O GLY 5 204 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 238 removed outlier: 4.182A pdb=" N LYS 5 232 " --> pdb=" O GLU 5 228 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS 5 233 " --> pdb=" O SER 5 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 5 234 " --> pdb=" O LEU 5 230 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 258 removed outlier: 3.580A pdb=" N LEU 5 245 " --> pdb=" O ASN 5 241 " (cutoff:3.500A) Processing helix chain '5' and resid 268 through 276 Processing helix chain '5' and resid 295 through 300 removed outlier: 3.613A pdb=" N ARG 5 300 " --> pdb=" O ASP 5 297 " (cutoff:3.500A) Processing helix chain '5' and resid 308 through 313 Processing helix chain '6' and resid 5 through 14 removed outlier: 3.595A pdb=" N ILE 6 9 " --> pdb=" O ARG 6 5 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 36 removed outlier: 4.010A pdb=" N SER 6 36 " --> pdb=" O CYS 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 74 removed outlier: 3.951A pdb=" N ARG 6 68 " --> pdb=" O ASN 6 64 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU 6 69 " --> pdb=" O GLN 6 65 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 6 70 " --> pdb=" O ASN 6 66 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY 6 74 " --> pdb=" O SER 6 70 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 101 removed outlier: 3.508A pdb=" N MET 6 101 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 114 through 127 Proline residue: 6 124 - end of helix Processing helix chain '6' and resid 149 through 162 Processing helix chain '6' and resid 171 through 173 No H-bonds generated for 'chain '6' and resid 171 through 173' Processing helix chain '6' and resid 174 through 181 removed outlier: 3.978A pdb=" N LEU 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN 6 181 " --> pdb=" O VAL 6 177 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 188 removed outlier: 3.673A pdb=" N PHE 6 188 " --> pdb=" O LEU 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 204 through 217 removed outlier: 3.969A pdb=" N THR 6 208 " --> pdb=" O GLY 6 204 " (cutoff:3.500A) Processing helix chain '6' and resid 227 through 238 removed outlier: 3.782A pdb=" N LYS 6 232 " --> pdb=" O GLU 6 228 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS 6 233 " --> pdb=" O SER 6 229 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 258 removed outlier: 3.641A pdb=" N LEU 6 245 " --> pdb=" O ASN 6 241 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 276 Processing helix chain '6' and resid 296 through 300 removed outlier: 3.743A pdb=" N ARG 6 300 " --> pdb=" O ASP 6 297 " (cutoff:3.500A) Processing helix chain '6' and resid 308 through 313 Processing helix chain '7' and resid 5 through 14 Processing helix chain '7' and resid 19 through 36 removed outlier: 4.082A pdb=" N SER 7 36 " --> pdb=" O CYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 74 removed outlier: 3.923A pdb=" N ARG 7 68 " --> pdb=" O ASN 7 64 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER 7 70 " --> pdb=" O ASN 7 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 7 74 " --> pdb=" O SER 7 70 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 101 removed outlier: 3.529A pdb=" N MET 7 101 " --> pdb=" O LEU 7 97 " (cutoff:3.500A) Processing helix chain '7' and resid 114 through 127 Proline residue: 7 124 - end of helix Processing helix chain '7' and resid 149 through 162 Processing helix chain '7' and resid 171 through 173 No H-bonds generated for 'chain '7' and resid 171 through 173' Processing helix chain '7' and resid 174 through 181 removed outlier: 3.786A pdb=" N LEU 7 178 " --> pdb=" O SER 7 174 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN 7 181 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing helix chain '7' and resid 181 through 188 Processing helix chain '7' and resid 204 through 217 removed outlier: 3.897A pdb=" N THR 7 208 " --> pdb=" O GLY 7 204 " (cutoff:3.500A) Processing helix chain '7' and resid 227 through 238 removed outlier: 3.732A pdb=" N LYS 7 232 " --> pdb=" O GLU 7 228 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS 7 233 " --> pdb=" O SER 7 229 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 258 Processing helix chain '7' and resid 268 through 276 Processing helix chain '7' and resid 295 through 300 removed outlier: 3.705A pdb=" N ARG 7 300 " --> pdb=" O ASP 7 297 " (cutoff:3.500A) Processing helix chain '7' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain '1' and resid 46 through 47 removed outlier: 6.975A pdb=" N MET 1 46 " --> pdb=" O VAL 1 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '1' and resid 79 through 82 removed outlier: 3.636A pdb=" N LEU 1 80 " --> pdb=" O LEU 1 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 46 through 47 removed outlier: 7.121A pdb=" N MET 2 46 " --> pdb=" O VAL 2 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '2' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain '3' and resid 46 through 47 removed outlier: 6.917A pdb=" N MET 3 46 " --> pdb=" O VAL 3 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '4' and resid 46 through 47 removed outlier: 7.097A pdb=" N MET 4 46 " --> pdb=" O VAL 4 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '4' and resid 79 through 82 removed outlier: 3.621A pdb=" N LEU 4 80 " --> pdb=" O LEU 4 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 46 through 47 removed outlier: 6.978A pdb=" N MET 5 46 " --> pdb=" O VAL 5 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '6' and resid 46 through 47 removed outlier: 6.917A pdb=" N MET 6 46 " --> pdb=" O VAL 6 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '7' and resid 46 through 47 removed outlier: 6.971A pdb=" N MET 7 46 " --> pdb=" O VAL 7 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 697 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3535 1.34 - 1.46: 3843 1.46 - 1.58: 10262 1.58 - 1.70: 35 1.70 - 1.81: 133 Bond restraints: 17808 Sorted by residual: bond pdb=" N LYS 1 89 " pdb=" CA LYS 1 89 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.78e+01 bond pdb=" N VAL 5 79 " pdb=" CA VAL 5 79 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL 7 79 " pdb=" CA VAL 7 79 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N VAL 2 17 " pdb=" CA VAL 2 17 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.21e+01 bond pdb=" N ILE 1 131 " pdb=" CA ILE 1 131 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.14e-02 7.69e+03 1.21e+01 ... (remaining 17803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 15504 1.57 - 3.15: 6490 3.15 - 4.72: 1689 4.72 - 6.29: 444 6.29 - 7.87: 2 Bond angle restraints: 24129 Sorted by residual: angle pdb=" PB ATP 1 402 " pdb=" O3B ATP 1 402 " pdb=" PG ATP 1 402 " ideal model delta sigma weight residual 139.87 132.00 7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" PA ATP 6 401 " pdb=" O3A ATP 6 401 " pdb=" PB ATP 6 401 " ideal model delta sigma weight residual 136.83 131.12 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" PB ATP 1 401 " pdb=" O3B ATP 1 401 " pdb=" PG ATP 1 401 " ideal model delta sigma weight residual 139.87 134.43 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" PA ATP 2 401 " pdb=" O3A ATP 2 401 " pdb=" PB ATP 2 401 " ideal model delta sigma weight residual 136.83 131.52 5.31 1.00e+00 1.00e+00 2.81e+01 angle pdb=" C ASN 2 200 " pdb=" N GLY 2 201 " pdb=" CA GLY 2 201 " ideal model delta sigma weight residual 119.99 125.93 -5.94 1.13e+00 7.83e-01 2.76e+01 ... (remaining 24124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9745 17.95 - 35.90: 848 35.90 - 53.85: 190 53.85 - 71.79: 25 71.79 - 89.74: 14 Dihedral angle restraints: 10822 sinusoidal: 4480 harmonic: 6342 Sorted by residual: dihedral pdb=" CA MET 4 171 " pdb=" C MET 4 171 " pdb=" N PRO 4 172 " pdb=" CA PRO 4 172 " ideal model delta harmonic sigma weight residual -180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLN 4 191 " pdb=" C GLN 4 191 " pdb=" N VAL 4 192 " pdb=" CA VAL 4 192 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN 1 191 " pdb=" C GLN 1 191 " pdb=" N VAL 1 192 " pdb=" CA VAL 1 192 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 10819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 805 0.041 - 0.081: 796 0.081 - 0.121: 738 0.121 - 0.162: 261 0.162 - 0.202: 95 Chirality restraints: 2695 Sorted by residual: chirality pdb=" CA ILE 1 82 " pdb=" N ILE 1 82 " pdb=" C ILE 1 82 " pdb=" CB ILE 1 82 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE 6 82 " pdb=" N ILE 6 82 " pdb=" C ILE 6 82 " pdb=" CB ILE 6 82 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL 6 292 " pdb=" N VAL 6 292 " pdb=" C VAL 6 292 " pdb=" CB VAL 6 292 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 2692 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN 7 191 " 0.024 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C GLN 7 191 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN 7 191 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL 7 192 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 6 191 " 0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C GLN 6 191 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN 6 191 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL 6 192 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 5 191 " 0.024 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C GLN 5 191 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN 5 191 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL 5 192 " 0.029 2.00e-02 2.50e+03 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 6862 2.97 - 3.45: 18411 3.45 - 3.94: 27711 3.94 - 4.42: 29585 4.42 - 4.90: 51630 Nonbonded interactions: 134199 Sorted by model distance: nonbonded pdb=" O ILE 1 133 " pdb=" N PHE 1 169 " model vdw 2.491 3.120 nonbonded pdb=" NH1 ARG 4 14 " pdb=" OG SER 5 40 " model vdw 2.501 3.120 nonbonded pdb=" O ILE 3 133 " pdb=" N PHE 3 169 " model vdw 2.550 3.120 nonbonded pdb=" O MET 4 171 " pdb=" OG SER 4 174 " model vdw 2.558 3.040 nonbonded pdb=" O MET 7 101 " pdb=" N ASP 7 103 " model vdw 2.559 3.120 ... (remaining 134194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and resid 4 through 314) selection = (chain '2' and resid 4 through 314) selection = (chain '3' and resid 4 through 314) selection = (chain '4' and resid 4 through 314) selection = (chain '5' and resid 4 through 314) selection = (chain '6' and resid 4 through 314) selection = chain '7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.170 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4012 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 : 0.014 0.125 17828 Z= 1.143 Angle : 1.827 7.866 24129 Z= 1.373 Chirality : 0.083 0.202 2695 Planarity : 0.003 0.050 3080 Dihedral : 14.402 89.743 6720 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 1.43 % Allowed : 10.17 % Favored : 88.40 % Rotamer: Outliers : 0.80 % Allowed : 4.83 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.15), residues: 2163 helix: -1.28 (0.13), residues: 1113 sheet: -4.06 (0.36), residues: 70 loop : -2.47 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 6 187 TYR 0.019 0.001 TYR 4 173 PHE 0.014 0.001 PHE 5 136 TRP 0.008 0.001 TRP 4 308 HIS 0.004 0.001 HIS 7 185 Details of bonding type rmsd/Z covalent geometry : bond 0.01393 / 1.08 (17808) covalent geometry : angle 1.82720 / 1.37 (24129) hydrogen bonds : bond 0.15773 / 10.80 ( 697) hydrogen bonds : angle 6.48604 / 4.75 ( 2064) Misc. bond : bond 0.11440 / 7.49 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 400 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 36 SER cc_start: 0.6845 (m) cc_final: 0.6412 (p) REVERT: 1 89 LYS cc_start: 0.6656 (mtmm) cc_final: 0.6249 (mtmm) REVERT: 1 132 ILE cc_start: 0.5961 (mt) cc_final: 0.5152 (mt) REVERT: 1 192 VAL cc_start: 0.3705 (OUTLIER) cc_final: 0.2872 (m) REVERT: 2 44 CYS cc_start: 0.7151 (m) cc_final: 0.6803 (p) REVERT: 2 58 VAL cc_start: 0.2919 (t) cc_final: 0.2636 (t) REVERT: 2 147 VAL cc_start: 0.5963 (p) cc_final: 0.5742 (p) REVERT: 3 192 VAL cc_start: 0.6004 (OUTLIER) cc_final: 0.5636 (t) REVERT: 4 211 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5998 (mm-30) REVERT: 6 190 ILE cc_start: 0.2581 (mt) cc_final: 0.2361 (mt) REVERT: 7 89 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7604 (mtmm) REVERT: 7 190 ILE cc_start: 0.4252 (mt) cc_final: 0.3755 (pt) REVERT: 7 253 SER cc_start: 0.6332 (t) cc_final: 0.5461 (p) outliers start: 15 outliers final: 3 residues processed: 411 average time/residue: 0.1341 time to fit residues: 79.9181 Evaluate side-chains 311 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 306 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 259 ASN Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 7 residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 65 GLN 2 138 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 153 ASN 6 261 HIS 7 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.178440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159081 restraints weight = 27163.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163461 restraints weight = 14873.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.166416 restraints weight = 9618.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.168312 restraints weight = 6996.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169777 restraints weight = 5510.389| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4688 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 17828 Z= 0.199 Angle : 0.755 13.502 24129 Z= 0.383 Chirality : 0.044 0.224 2695 Planarity : 0.005 0.050 3080 Dihedral : 7.025 89.873 2400 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.52 % Favored : 92.97 % Rotamer: Outliers : 2.12 % Allowed : 11.63 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2163 helix: 0.39 (0.15), residues: 1134 sheet: -4.04 (0.40), residues: 84 loop : -2.00 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 7 187 TYR 0.018 0.002 TYR 4 173 PHE 0.019 0.002 PHE 3 237 TRP 0.017 0.002 TRP 4 284 HIS 0.009 0.002 HIS 4 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (17808) covalent geometry : angle 0.75544 / 0.38 (24129) hydrogen bonds : bond 0.03690 / 2.56 ( 697) hydrogen bonds : angle 3.98470 / 2.94 ( 2064) Misc. bond : bond 0.00191 / 0.15 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 377 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 14 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6568 (ptp90) REVERT: 1 24 LYS cc_start: 0.6584 (ttmm) cc_final: 0.6290 (tttp) REVERT: 1 89 LYS cc_start: 0.6643 (mtmm) cc_final: 0.6281 (mtmm) REVERT: 1 132 ILE cc_start: 0.6410 (mt) cc_final: 0.5587 (mt) REVERT: 1 182 SER cc_start: 0.7099 (t) cc_final: 0.6485 (p) REVERT: 1 192 VAL cc_start: 0.5403 (OUTLIER) cc_final: 0.5011 (m) REVERT: 1 207 LYS cc_start: 0.7093 (tttm) cc_final: 0.6870 (ttmt) REVERT: 2 23 ARG cc_start: 0.7211 (ttm-80) cc_final: 0.7008 (ttp-110) REVERT: 2 43 THR cc_start: 0.6963 (p) cc_final: 0.6675 (m) REVERT: 2 192 VAL cc_start: 0.6396 (OUTLIER) cc_final: 0.5960 (t) REVERT: 2 254 ILE cc_start: 0.6039 (mm) cc_final: 0.5790 (mm) REVERT: 2 266 GLU cc_start: 0.6041 (mm-30) cc_final: 0.5807 (mm-30) REVERT: 3 192 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7358 (m) REVERT: 3 235 TYR cc_start: 0.4985 (t80) cc_final: 0.4473 (t80) REVERT: 4 169 PHE cc_start: 0.5436 (m-80) cc_final: 0.4872 (m-80) REVERT: 4 305 ASP cc_start: 0.5562 (p0) cc_final: 0.5196 (p0) REVERT: 5 169 PHE cc_start: 0.5399 (m-80) cc_final: 0.4435 (m-80) REVERT: 5 249 ILE cc_start: 0.7197 (mm) cc_final: 0.6987 (mm) REVERT: 6 79 VAL cc_start: 0.3362 (m) cc_final: 0.2997 (p) REVERT: 6 141 GLU cc_start: 0.4630 (mm-30) cc_final: 0.3441 (mp0) REVERT: 7 41 GLU cc_start: 0.6274 (tt0) cc_final: 0.6029 (tt0) REVERT: 7 59 ILE cc_start: 0.6723 (mt) cc_final: 0.6391 (mt) REVERT: 7 100 GLU cc_start: 0.6850 (tp30) cc_final: 0.6609 (mm-30) REVERT: 7 101 MET cc_start: 0.5499 (tpt) cc_final: 0.5181 (tpt) REVERT: 7 153 ASN cc_start: 0.6938 (m110) cc_final: 0.6670 (m110) REVERT: 7 253 SER cc_start: 0.6862 (t) cc_final: 0.5901 (p) outliers start: 40 outliers final: 14 residues processed: 396 average time/residue: 0.1383 time to fit residues: 79.0804 Evaluate side-chains 339 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 174 SER Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 112 LEU Chi-restraints excluded: chain 5 residue 174 SER Chi-restraints excluded: chain 6 residue 29 MET Chi-restraints excluded: chain 6 residue 45 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 170 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 192 optimal weight: 0.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 81 HIS ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 1 183 GLN ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 261 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 153 ASN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 261 HIS 6 181 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.181262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.161997 restraints weight = 27109.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.166510 restraints weight = 14641.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.169650 restraints weight = 9336.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.171541 restraints weight = 6625.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173104 restraints weight = 5158.513| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5135 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17828 Z= 0.166 Angle : 0.710 10.702 24129 Z= 0.354 Chirality : 0.042 0.171 2695 Planarity : 0.006 0.121 3080 Dihedral : 6.839 87.488 2397 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.44 % Favored : 92.00 % Rotamer: Outliers : 3.29 % Allowed : 13.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2163 helix: 0.60 (0.15), residues: 1141 sheet: -3.34 (0.35), residues: 154 loop : -1.82 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG 6 187 TYR 0.021 0.002 TYR 3 173 PHE 0.031 0.002 PHE 1 188 TRP 0.017 0.002 TRP 4 284 HIS 0.008 0.002 HIS 6 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (17808) covalent geometry : angle 0.71050 / 0.35 (24129) hydrogen bonds : bond 0.03443 / 2.41 ( 697) hydrogen bonds : angle 3.93475 / 2.91 ( 2064) Misc. bond : bond 0.00824 / 0.45 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 365 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 13 LYS cc_start: 0.8013 (tppt) cc_final: 0.6251 (tppt) REVERT: 1 14 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.6851 (ptp90) REVERT: 1 36 SER cc_start: 0.7572 (m) cc_final: 0.7225 (p) REVERT: 1 79 VAL cc_start: 0.5955 (m) cc_final: 0.5754 (t) REVERT: 1 83 GLU cc_start: 0.4286 (tt0) cc_final: 0.4086 (tt0) REVERT: 1 89 LYS cc_start: 0.6638 (mtmm) cc_final: 0.6281 (mtmm) REVERT: 1 132 ILE cc_start: 0.6240 (mt) cc_final: 0.5935 (mt) REVERT: 2 13 LYS cc_start: 0.7736 (tppt) cc_final: 0.6491 (tppt) REVERT: 2 43 THR cc_start: 0.6997 (p) cc_final: 0.6788 (m) REVERT: 2 157 MET cc_start: 0.5475 (tpp) cc_final: 0.5246 (tpp) REVERT: 2 191 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: 2 195 ARG cc_start: 0.6069 (ptp-110) cc_final: 0.5820 (mtm110) REVERT: 3 105 LEU cc_start: 0.5315 (mm) cc_final: 0.5100 (mp) REVERT: 3 195 ARG cc_start: 0.6967 (mtp85) cc_final: 0.6521 (mtp85) REVERT: 4 43 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.5115 (p) REVERT: 4 61 LYS cc_start: 0.8104 (tptp) cc_final: 0.7794 (tptp) REVERT: 4 169 PHE cc_start: 0.6619 (m-80) cc_final: 0.6084 (m-10) REVERT: 4 305 ASP cc_start: 0.5897 (p0) cc_final: 0.5461 (p0) REVERT: 5 168 ILE cc_start: 0.6792 (pt) cc_final: 0.6583 (pt) REVERT: 5 249 ILE cc_start: 0.7356 (mm) cc_final: 0.7137 (mm) REVERT: 6 14 ARG cc_start: 0.6882 (mpp80) cc_final: 0.6521 (mtm180) REVERT: 6 16 PHE cc_start: 0.7410 (t80) cc_final: 0.7096 (t80) REVERT: 6 29 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5730 (mtm) REVERT: 6 62 TYR cc_start: 0.5904 (t80) cc_final: 0.5546 (t80) REVERT: 6 79 VAL cc_start: 0.5076 (m) cc_final: 0.4725 (m) REVERT: 6 141 GLU cc_start: 0.4644 (mm-30) cc_final: 0.3522 (mp0) REVERT: 6 267 GLU cc_start: 0.5737 (tp30) cc_final: 0.4878 (pt0) REVERT: 6 289 GLU cc_start: 0.6244 (tp30) cc_final: 0.6015 (tp30) REVERT: 7 59 ILE cc_start: 0.7117 (mt) cc_final: 0.6560 (mt) REVERT: 7 100 GLU cc_start: 0.6874 (tp30) cc_final: 0.6631 (mm-30) REVERT: 7 101 MET cc_start: 0.5672 (tpt) cc_final: 0.5336 (tpt) REVERT: 7 166 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6765 (mt) REVERT: 7 193 GLU cc_start: 0.5316 (mm-30) cc_final: 0.4987 (tm-30) outliers start: 62 outliers final: 24 residues processed: 401 average time/residue: 0.1446 time to fit residues: 84.2992 Evaluate side-chains 363 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 335 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 171 MET Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 146 ARG Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 112 LEU Chi-restraints excluded: chain 5 residue 132 ILE Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 174 SER Chi-restraints excluded: chain 5 residue 234 LEU Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 6 residue 29 MET Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 192 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 180 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 81 HIS ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 ASN ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 153 ASN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 153 ASN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.178544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.158861 restraints weight = 27522.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.163561 restraints weight = 14687.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.166776 restraints weight = 9301.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.168831 restraints weight = 6625.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.170222 restraints weight = 5083.856| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 17828 Z= 0.235 Angle : 0.855 20.868 24129 Z= 0.429 Chirality : 0.046 0.268 2695 Planarity : 0.006 0.125 3080 Dihedral : 8.111 170.132 2395 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.00 % Favored : 91.45 % Rotamer: Outliers : 4.73 % Allowed : 13.81 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2163 helix: 0.39 (0.15), residues: 1085 sheet: -3.66 (0.34), residues: 168 loop : -2.03 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 3 23 TYR 0.024 0.003 TYR 2 28 PHE 0.036 0.003 PHE 6 288 TRP 0.020 0.003 TRP 4 284 HIS 0.007 0.002 HIS 7 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (17808) covalent geometry : angle 0.85545 / 0.43 (24129) hydrogen bonds : bond 0.04181 / 2.86 ( 697) hydrogen bonds : angle 4.26837 / 3.14 ( 2064) Misc. bond : bond 0.00355 / 0.19 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 458 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 13 LYS cc_start: 0.8640 (tppt) cc_final: 0.7580 (tppt) REVERT: 1 36 SER cc_start: 0.7452 (m) cc_final: 0.7106 (p) REVERT: 1 37 ASP cc_start: 0.6578 (t70) cc_final: 0.5475 (t70) REVERT: 1 89 LYS cc_start: 0.6544 (mtmm) cc_final: 0.6307 (mtmm) REVERT: 1 135 GLU cc_start: 0.4667 (tp30) cc_final: 0.4388 (tp30) REVERT: 1 207 LYS cc_start: 0.7806 (tttm) cc_final: 0.7459 (tttp) REVERT: 1 208 THR cc_start: 0.6960 (t) cc_final: 0.6617 (t) REVERT: 1 239 GLN cc_start: 0.7580 (mp10) cc_final: 0.7008 (mp10) REVERT: 2 298 MET cc_start: 0.2966 (ptm) cc_final: 0.2405 (ptp) REVERT: 3 43 THR cc_start: 0.7159 (p) cc_final: 0.6906 (p) REVERT: 3 45 MET cc_start: 0.7270 (ptm) cc_final: 0.7027 (ptp) REVERT: 3 58 VAL cc_start: 0.5961 (OUTLIER) cc_final: 0.5475 (t) REVERT: 3 61 LYS cc_start: 0.8143 (tptt) cc_final: 0.7608 (tptp) REVERT: 3 135 GLU cc_start: 0.5997 (tp30) cc_final: 0.5672 (tp30) REVERT: 3 195 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7077 (ttm-80) REVERT: 3 255 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6664 (mm-30) REVERT: 4 11 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7337 (ttp80) REVERT: 4 43 THR cc_start: 0.6569 (OUTLIER) cc_final: 0.6287 (p) REVERT: 4 168 ILE cc_start: 0.8093 (pt) cc_final: 0.7874 (mt) REVERT: 4 273 SER cc_start: 0.8048 (t) cc_final: 0.7505 (t) REVERT: 5 101 MET cc_start: 0.6408 (tmm) cc_final: 0.5487 (tmm) REVERT: 5 136 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: 5 185 HIS cc_start: 0.7304 (t70) cc_final: 0.7031 (t-90) REVERT: 5 211 GLU cc_start: 0.6319 (tt0) cc_final: 0.6032 (tt0) REVERT: 5 230 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4506 (tt) REVERT: 5 249 ILE cc_start: 0.8045 (mm) cc_final: 0.7842 (mm) REVERT: 6 14 ARG cc_start: 0.7531 (mpp80) cc_final: 0.7283 (mtm180) REVERT: 6 16 PHE cc_start: 0.8059 (t80) cc_final: 0.7733 (t80) REVERT: 6 141 GLU cc_start: 0.5641 (mm-30) cc_final: 0.4096 (mp0) REVERT: 6 156 LYS cc_start: 0.6869 (ttpp) cc_final: 0.6373 (tppt) REVERT: 6 171 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.3555 (mtt) REVERT: 6 250 TYR cc_start: 0.7724 (t80) cc_final: 0.7327 (t80) REVERT: 6 253 SER cc_start: 0.7460 (t) cc_final: 0.7158 (p) REVERT: 6 267 GLU cc_start: 0.7007 (tp30) cc_final: 0.5828 (pt0) REVERT: 7 41 GLU cc_start: 0.7199 (tt0) cc_final: 0.6778 (tt0) REVERT: 7 60 LYS cc_start: 0.7639 (tptp) cc_final: 0.7088 (tppt) REVERT: 7 96 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5973 (tt0) REVERT: 7 166 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7437 (mp) REVERT: 7 181 ASN cc_start: 0.7216 (p0) cc_final: 0.6931 (p0) REVERT: 7 193 GLU cc_start: 0.6460 (mm-30) cc_final: 0.6042 (tm-30) REVERT: 7 241 ASN cc_start: 0.7097 (m110) cc_final: 0.6842 (m-40) outliers start: 89 outliers final: 38 residues processed: 509 average time/residue: 0.1538 time to fit residues: 111.2843 Evaluate side-chains 451 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 407 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 116 THR Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 133 ILE Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 200 ASN Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 238 SER Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 107 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 153 ASN Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 132 ILE Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 147 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 171 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 181 ASN 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 191 GLN ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 153 ASN 4 231 GLN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153956 restraints weight = 27010.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158776 restraints weight = 14314.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162073 restraints weight = 9113.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164252 restraints weight = 6480.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.165702 restraints weight = 4986.587| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.9265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 17828 Z= 0.215 Angle : 0.790 13.955 24129 Z= 0.395 Chirality : 0.045 0.376 2695 Planarity : 0.007 0.187 3080 Dihedral : 7.980 168.162 2394 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.81 % Favored : 91.59 % Rotamer: Outliers : 3.56 % Allowed : 17.63 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2163 helix: 0.29 (0.16), residues: 1099 sheet: -3.23 (0.40), residues: 140 loop : -2.07 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG 2 187 TYR 0.023 0.002 TYR 3 173 PHE 0.040 0.003 PHE 5 269 TRP 0.020 0.002 TRP 4 154 HIS 0.005 0.001 HIS 3 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (17808) covalent geometry : angle 0.79040 / 0.39 (24129) hydrogen bonds : bond 0.03775 / 2.65 ( 697) hydrogen bonds : angle 4.15822 / 3.02 ( 2064) Misc. bond : bond 0.00419 / 0.20 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 485 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 13 LYS cc_start: 0.8609 (tppt) cc_final: 0.7887 (tppt) REVERT: 1 41 GLU cc_start: 0.7595 (tt0) cc_final: 0.7321 (tt0) REVERT: 1 60 LYS cc_start: 0.7327 (tptt) cc_final: 0.6957 (ttmm) REVERT: 1 215 LYS cc_start: 0.7829 (tppp) cc_final: 0.7584 (tppp) REVERT: 1 239 GLN cc_start: 0.7628 (mp10) cc_final: 0.7136 (mp10) REVERT: 1 255 GLU cc_start: 0.5489 (mt-10) cc_final: 0.5135 (mt-10) REVERT: 2 29 MET cc_start: 0.7391 (tpp) cc_final: 0.7102 (ttm) REVERT: 2 130 LEU cc_start: 0.8012 (tt) cc_final: 0.7760 (mt) REVERT: 2 157 MET cc_start: 0.6575 (tpt) cc_final: 0.6216 (tpt) REVERT: 2 191 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6295 (mp10) REVERT: 2 212 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.5323 (t80) REVERT: 2 239 GLN cc_start: 0.7528 (mt0) cc_final: 0.7247 (mt0) REVERT: 2 298 MET cc_start: 0.2507 (ptm) cc_final: 0.1955 (ptp) REVERT: 3 45 MET cc_start: 0.7640 (ptm) cc_final: 0.7176 (ptp) REVERT: 3 62 TYR cc_start: 0.7924 (t80) cc_final: 0.7633 (t80) REVERT: 3 134 ASP cc_start: 0.5426 (t0) cc_final: 0.5218 (t0) REVERT: 3 181 ASN cc_start: 0.7796 (t0) cc_final: 0.7537 (t0) REVERT: 3 193 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6868 (mm-30) REVERT: 3 195 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7139 (mtp85) REVERT: 4 27 SER cc_start: 0.7853 (t) cc_final: 0.7620 (t) REVERT: 4 29 MET cc_start: 0.7331 (tpp) cc_final: 0.7074 (mmm) REVERT: 4 41 GLU cc_start: 0.6432 (tp30) cc_final: 0.6052 (tp30) REVERT: 4 135 GLU cc_start: 0.5361 (mm-30) cc_final: 0.4887 (mm-30) REVERT: 4 168 ILE cc_start: 0.8094 (pt) cc_final: 0.7872 (mt) REVERT: 4 212 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6300 (t80) REVERT: 4 242 MET cc_start: 0.7182 (ppp) cc_final: 0.6861 (ppp) REVERT: 4 255 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7440 (mm-30) REVERT: 4 273 SER cc_start: 0.8245 (t) cc_final: 0.7809 (t) REVERT: 4 280 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6830 (mmtt) REVERT: 4 284 TRP cc_start: 0.7622 (t60) cc_final: 0.7086 (t60) REVERT: 4 305 ASP cc_start: 0.7137 (p0) cc_final: 0.6585 (p0) REVERT: 5 31 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.6672 (ttm-80) REVERT: 5 45 MET cc_start: 0.7646 (ttp) cc_final: 0.7370 (ttt) REVERT: 5 86 ASP cc_start: 0.5405 (t70) cc_final: 0.5152 (t70) REVERT: 5 101 MET cc_start: 0.6550 (tmm) cc_final: 0.5415 (tmm) REVERT: 5 136 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: 5 207 LYS cc_start: 0.7797 (tmtt) cc_final: 0.7576 (tptp) REVERT: 5 211 GLU cc_start: 0.6716 (tt0) cc_final: 0.6352 (tt0) REVERT: 5 227 ASN cc_start: 0.6161 (p0) cc_final: 0.5415 (m-40) REVERT: 5 288 PHE cc_start: 0.6078 (m-10) cc_final: 0.5752 (m-80) REVERT: 6 14 ARG cc_start: 0.7497 (mpp80) cc_final: 0.7190 (mtm180) REVERT: 6 23 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7304 (mtm-85) REVERT: 6 48 TYR cc_start: 0.6189 (m-10) cc_final: 0.5884 (m-10) REVERT: 6 129 LYS cc_start: 0.7525 (mtmt) cc_final: 0.7209 (mmmt) REVERT: 6 156 LYS cc_start: 0.7253 (ttpp) cc_final: 0.7022 (ttmm) REVERT: 6 253 SER cc_start: 0.7421 (t) cc_final: 0.6983 (p) REVERT: 7 33 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8281 (ptm-80) REVERT: 7 39 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6863 (mt-10) REVERT: 7 45 MET cc_start: 0.7016 (ttm) cc_final: 0.6340 (ttm) REVERT: 7 60 LYS cc_start: 0.7574 (tptp) cc_final: 0.7151 (ttmm) REVERT: 7 83 GLU cc_start: 0.6000 (tp30) cc_final: 0.4854 (tp30) REVERT: 7 116 THR cc_start: 0.6431 (m) cc_final: 0.6197 (p) REVERT: 7 129 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7618 (mtmt) REVERT: 7 166 ILE cc_start: 0.7852 (mt) cc_final: 0.7598 (mp) REVERT: 7 181 ASN cc_start: 0.7605 (p0) cc_final: 0.7282 (p0) REVERT: 7 193 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6446 (tm-30) REVERT: 7 231 GLN cc_start: 0.6520 (tt0) cc_final: 0.6052 (tt0) REVERT: 7 242 MET cc_start: 0.7848 (tpp) cc_final: 0.7506 (tpp) REVERT: 7 255 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6246 (tp30) outliers start: 67 outliers final: 36 residues processed: 522 average time/residue: 0.1559 time to fit residues: 114.2959 Evaluate side-chains 469 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 429 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 200 ASN Chi-restraints excluded: chain 2 residue 212 TYR Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 132 ILE Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 275 LEU Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 147 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 162 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 ASN ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 191 GLN ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 282 ASN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 138 HIS ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN 7 65 GLN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152309 restraints weight = 26895.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157120 restraints weight = 14457.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160393 restraints weight = 9251.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.162653 restraints weight = 6626.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.163685 restraints weight = 5119.241| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 1.0240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17828 Z= 0.187 Angle : 0.763 13.362 24129 Z= 0.376 Chirality : 0.044 0.228 2695 Planarity : 0.009 0.391 3080 Dihedral : 8.052 175.790 2394 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.30 % Favored : 92.14 % Rotamer: Outliers : 4.30 % Allowed : 19.28 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2163 helix: 0.40 (0.16), residues: 1106 sheet: -3.02 (0.53), residues: 84 loop : -2.11 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG 6 187 TYR 0.021 0.002 TYR 3 173 PHE 0.036 0.003 PHE 6 288 TRP 0.013 0.002 TRP 2 154 HIS 0.007 0.001 HIS 7 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (17808) covalent geometry : angle 0.76291 / 0.38 (24129) hydrogen bonds : bond 0.03678 / 2.58 ( 697) hydrogen bonds : angle 4.10283 / 3.01 ( 2064) Misc. bond : bond 0.00318 / 0.23 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 466 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 14 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7282 (ptp90) REVERT: 1 135 GLU cc_start: 0.4851 (tp30) cc_final: 0.4612 (tp30) REVERT: 1 215 LYS cc_start: 0.7815 (tppp) cc_final: 0.7572 (tppp) REVERT: 1 239 GLN cc_start: 0.7579 (mp10) cc_final: 0.7050 (mp10) REVERT: 1 255 GLU cc_start: 0.5609 (mt-10) cc_final: 0.5326 (mt-10) REVERT: 1 273 SER cc_start: 0.5410 (t) cc_final: 0.5135 (t) REVERT: 1 279 ASP cc_start: 0.6887 (p0) cc_final: 0.6563 (p0) REVERT: 2 29 MET cc_start: 0.7713 (tpp) cc_final: 0.7492 (ttp) REVERT: 2 30 ASP cc_start: 0.6994 (t0) cc_final: 0.6624 (t0) REVERT: 2 156 LYS cc_start: 0.7980 (tmmt) cc_final: 0.7594 (tmmt) REVERT: 2 157 MET cc_start: 0.6650 (tpt) cc_final: 0.6366 (tpt) REVERT: 2 182 SER cc_start: 0.7720 (t) cc_final: 0.7226 (m) REVERT: 2 191 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: 2 298 MET cc_start: 0.2789 (ptm) cc_final: 0.2584 (ptp) REVERT: 3 45 MET cc_start: 0.7727 (ptm) cc_final: 0.7296 (ptp) REVERT: 3 64 ASN cc_start: 0.6163 (m-40) cc_final: 0.5898 (t0) REVERT: 3 134 ASP cc_start: 0.5307 (t0) cc_final: 0.4659 (t0) REVERT: 3 135 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: 3 136 PHE cc_start: 0.7176 (m-80) cc_final: 0.6659 (m-80) REVERT: 3 181 ASN cc_start: 0.7957 (t0) cc_final: 0.7692 (t0) REVERT: 3 193 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6992 (mm-30) REVERT: 3 255 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6932 (mm-30) REVERT: 3 299 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5655 (mt) REVERT: 4 27 SER cc_start: 0.7980 (t) cc_final: 0.7710 (t) REVERT: 4 40 SER cc_start: 0.7758 (t) cc_final: 0.7348 (m) REVERT: 4 41 GLU cc_start: 0.6870 (tp30) cc_final: 0.6442 (tp30) REVERT: 4 135 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5722 (mm-30) REVERT: 4 168 ILE cc_start: 0.8213 (pt) cc_final: 0.7947 (mt) REVERT: 4 182 SER cc_start: 0.6981 (p) cc_final: 0.6735 (m) REVERT: 4 184 LEU cc_start: 0.7652 (mm) cc_final: 0.7438 (mt) REVERT: 4 212 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6245 (t80) REVERT: 4 242 MET cc_start: 0.6553 (ppp) cc_final: 0.5930 (ppp) REVERT: 4 250 TYR cc_start: 0.6802 (t80) cc_final: 0.6577 (t80) REVERT: 4 255 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7369 (mm-30) REVERT: 4 273 SER cc_start: 0.8285 (t) cc_final: 0.7951 (t) REVERT: 4 305 ASP cc_start: 0.7379 (p0) cc_final: 0.6821 (p0) REVERT: 5 31 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6938 (ttm-80) REVERT: 5 101 MET cc_start: 0.6003 (tmm) cc_final: 0.5127 (tmm) REVERT: 5 137 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5964 (mp-120) REVERT: 5 171 MET cc_start: 0.6785 (mtp) cc_final: 0.6216 (mtp) REVERT: 5 227 ASN cc_start: 0.5877 (p0) cc_final: 0.5444 (m110) REVERT: 5 288 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: 5 309 GLU cc_start: 0.5153 (mm-30) cc_final: 0.4731 (mm-30) REVERT: 6 14 ARG cc_start: 0.7657 (mpp80) cc_final: 0.7266 (mtm180) REVERT: 6 19 THR cc_start: 0.7125 (m) cc_final: 0.6663 (p) REVERT: 6 32 CYS cc_start: 0.7291 (t) cc_final: 0.7087 (m) REVERT: 6 207 LYS cc_start: 0.8074 (tmtt) cc_final: 0.7266 (tptp) REVERT: 6 211 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6177 (mt-10) REVERT: 6 253 SER cc_start: 0.7522 (t) cc_final: 0.7115 (p) REVERT: 6 255 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6888 (mm-30) REVERT: 7 33 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8021 (ptm-80) REVERT: 7 60 LYS cc_start: 0.7659 (tptp) cc_final: 0.7317 (tppt) REVERT: 7 81 HIS cc_start: 0.6311 (t-90) cc_final: 0.5944 (t70) REVERT: 7 116 THR cc_start: 0.6573 (m) cc_final: 0.6287 (p) REVERT: 7 129 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7690 (mtmt) REVERT: 7 134 ASP cc_start: 0.7446 (m-30) cc_final: 0.6997 (m-30) REVERT: 7 166 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (mp) REVERT: 7 181 ASN cc_start: 0.7797 (p0) cc_final: 0.7350 (p0) REVERT: 7 193 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6654 (tm-30) REVERT: 7 231 GLN cc_start: 0.6467 (tt0) cc_final: 0.5887 (tt0) REVERT: 7 242 MET cc_start: 0.7723 (tpp) cc_final: 0.7401 (tpp) REVERT: 7 255 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6440 (tp30) outliers start: 81 outliers final: 47 residues processed: 511 average time/residue: 0.1537 time to fit residues: 111.6083 Evaluate side-chains 500 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 446 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 60 LYS Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 200 ASN Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 135 GLU Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 265 THR Chi-restraints excluded: chain 3 residue 299 LEU Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 83 GLU Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 267 GLU Chi-restraints excluded: chain 5 residue 288 PHE Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 288 PHE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 137 GLN Chi-restraints excluded: chain 7 residue 147 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 97 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 141 optimal weight: 2.9990 chunk 189 optimal weight: 0.0070 chunk 201 optimal weight: 1.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 153 ASN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.153950 restraints weight = 26906.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158799 restraints weight = 14383.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162103 restraints weight = 9170.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164182 restraints weight = 6557.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165862 restraints weight = 5136.555| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 1.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17828 Z= 0.145 Angle : 0.729 14.761 24129 Z= 0.359 Chirality : 0.043 0.233 2695 Planarity : 0.008 0.310 3080 Dihedral : 7.943 179.604 2394 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.26 % Favored : 92.19 % Rotamer: Outliers : 4.04 % Allowed : 20.87 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2163 helix: 0.62 (0.16), residues: 1099 sheet: -3.00 (0.42), residues: 140 loop : -1.99 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG 6 187 TYR 0.028 0.001 TYR 3 173 PHE 0.034 0.002 PHE 6 288 TRP 0.009 0.001 TRP 2 154 HIS 0.005 0.001 HIS 3 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (17808) covalent geometry : angle 0.72919 / 0.36 (24129) hydrogen bonds : bond 0.03160 / 2.20 ( 697) hydrogen bonds : angle 3.88056 / 2.86 ( 2064) Misc. bond : bond 0.00351 / 0.20 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 456 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 60 LYS cc_start: 0.7480 (tptp) cc_final: 0.7206 (tppt) REVERT: 1 83 GLU cc_start: 0.5566 (tt0) cc_final: 0.5361 (tt0) REVERT: 1 215 LYS cc_start: 0.7784 (tppp) cc_final: 0.7481 (tppp) REVERT: 1 261 HIS cc_start: 0.4673 (m90) cc_final: 0.4428 (m90) REVERT: 1 279 ASP cc_start: 0.6908 (p0) cc_final: 0.6640 (p0) REVERT: 2 29 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: 2 136 PHE cc_start: 0.6412 (m-10) cc_final: 0.6034 (m-10) REVERT: 2 157 MET cc_start: 0.6585 (tpt) cc_final: 0.6239 (tpt) REVERT: 2 182 SER cc_start: 0.7964 (t) cc_final: 0.7504 (m) REVERT: 2 212 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5579 (t80) REVERT: 2 239 GLN cc_start: 0.7666 (mt0) cc_final: 0.7350 (mt0) REVERT: 2 298 MET cc_start: 0.2720 (ptm) cc_final: 0.2454 (ptp) REVERT: 3 41 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6920 (mm-30) REVERT: 3 45 MET cc_start: 0.7654 (ptm) cc_final: 0.7371 (ptp) REVERT: 3 58 VAL cc_start: 0.6937 (OUTLIER) cc_final: 0.6565 (t) REVERT: 3 61 LYS cc_start: 0.8612 (tptt) cc_final: 0.8300 (tptm) REVERT: 3 134 ASP cc_start: 0.5284 (t0) cc_final: 0.4613 (t0) REVERT: 3 135 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: 3 136 PHE cc_start: 0.6990 (m-80) cc_final: 0.6482 (m-80) REVERT: 3 181 ASN cc_start: 0.8033 (t0) cc_final: 0.7759 (t0) REVERT: 3 193 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6972 (mm-30) REVERT: 3 255 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6997 (mm-30) REVERT: 3 299 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5732 (mt) REVERT: 4 27 SER cc_start: 0.7976 (t) cc_final: 0.7716 (t) REVERT: 4 40 SER cc_start: 0.7849 (t) cc_final: 0.7473 (m) REVERT: 4 41 GLU cc_start: 0.6937 (tp30) cc_final: 0.6443 (tp30) REVERT: 4 135 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5622 (mm-30) REVERT: 4 182 SER cc_start: 0.7272 (p) cc_final: 0.7019 (m) REVERT: 4 212 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6219 (t80) REVERT: 4 242 MET cc_start: 0.6527 (ppp) cc_final: 0.5795 (ppp) REVERT: 4 305 ASP cc_start: 0.7433 (p0) cc_final: 0.6881 (p0) REVERT: 5 31 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.6892 (ttm-80) REVERT: 5 101 MET cc_start: 0.5896 (tmm) cc_final: 0.4990 (tmm) REVERT: 5 118 ARG cc_start: 0.4410 (OUTLIER) cc_final: 0.3499 (ptm160) REVERT: 5 137 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5950 (mp-120) REVERT: 5 171 MET cc_start: 0.6814 (mtp) cc_final: 0.6278 (mtp) REVERT: 5 220 GLU cc_start: 0.6014 (pm20) cc_final: 0.5032 (mt-10) REVERT: 5 271 PHE cc_start: 0.8106 (t80) cc_final: 0.7772 (t80) REVERT: 5 273 SER cc_start: 0.8337 (t) cc_final: 0.7926 (t) REVERT: 5 288 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6227 (m-80) REVERT: 5 309 GLU cc_start: 0.5369 (mm-30) cc_final: 0.4927 (mm-30) REVERT: 6 14 ARG cc_start: 0.7567 (mpp80) cc_final: 0.7254 (mtm180) REVERT: 6 96 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5955 (mm-30) REVERT: 6 101 MET cc_start: 0.6055 (tpt) cc_final: 0.5501 (tmm) REVERT: 6 137 GLN cc_start: 0.6274 (mp10) cc_final: 0.5860 (mp10) REVERT: 6 153 ASN cc_start: 0.7387 (m-40) cc_final: 0.6454 (m110) REVERT: 6 253 SER cc_start: 0.7561 (t) cc_final: 0.7069 (p) REVERT: 7 33 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.8081 (ttp80) REVERT: 7 60 LYS cc_start: 0.7719 (tptp) cc_final: 0.7351 (tppt) REVERT: 7 81 HIS cc_start: 0.6337 (t-90) cc_final: 0.5949 (t70) REVERT: 7 116 THR cc_start: 0.6664 (m) cc_final: 0.6404 (p) REVERT: 7 134 ASP cc_start: 0.7142 (m-30) cc_final: 0.6716 (m-30) REVERT: 7 166 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7683 (mp) REVERT: 7 181 ASN cc_start: 0.7748 (p0) cc_final: 0.7499 (p0) REVERT: 7 193 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6662 (tm-30) REVERT: 7 231 GLN cc_start: 0.6532 (tt0) cc_final: 0.5914 (tt0) REVERT: 7 242 MET cc_start: 0.7671 (tpp) cc_final: 0.7447 (tpp) REVERT: 7 255 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6682 (tp30) outliers start: 76 outliers final: 45 residues processed: 496 average time/residue: 0.1504 time to fit residues: 106.2488 Evaluate side-chains 498 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 443 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 29 MET Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 130 LEU Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 173 TYR Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 212 TYR Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 135 GLU Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 265 THR Chi-restraints excluded: chain 3 residue 299 LEU Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 174 SER Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 118 ARG Chi-restraints excluded: chain 5 residue 132 ILE Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 267 GLU Chi-restraints excluded: chain 5 residue 288 PHE Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 306 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 147 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 208 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS 4 179 GLN ** 4 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.150770 restraints weight = 26629.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155590 restraints weight = 14202.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.158924 restraints weight = 9074.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.160783 restraints weight = 6509.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162671 restraints weight = 5197.670| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 1.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17828 Z= 0.192 Angle : 0.780 12.675 24129 Z= 0.390 Chirality : 0.045 0.202 2695 Planarity : 0.008 0.312 3080 Dihedral : 7.964 178.915 2394 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.86 % Favored : 91.59 % Rotamer: Outliers : 4.35 % Allowed : 20.55 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.25 (0.18), residues: 2163 helix: 0.48 (0.16), residues: 1106 sheet: -3.16 (0.37), residues: 189 loop : -1.98 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG 6 187 TYR 0.024 0.002 TYR 5 48 PHE 0.037 0.003 PHE 6 288 TRP 0.016 0.002 TRP 5 154 HIS 0.008 0.001 HIS 3 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (17808) covalent geometry : angle 0.78036 / 0.39 (24129) hydrogen bonds : bond 0.03676 / 2.55 ( 697) hydrogen bonds : angle 4.14255 / 3.02 ( 2064) Misc. bond : bond 0.00297 / 0.19 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 448 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 48 TYR cc_start: 0.7763 (m-80) cc_final: 0.7191 (m-10) REVERT: 1 60 LYS cc_start: 0.7818 (tptp) cc_final: 0.7382 (tppt) REVERT: 1 130 LEU cc_start: 0.8210 (mt) cc_final: 0.7992 (mt) REVERT: 1 157 MET cc_start: 0.6761 (mtt) cc_final: 0.6523 (mtt) REVERT: 1 182 SER cc_start: 0.8263 (t) cc_final: 0.8048 (p) REVERT: 1 215 LYS cc_start: 0.7703 (tppp) cc_final: 0.7477 (tppp) REVERT: 1 279 ASP cc_start: 0.6869 (p0) cc_final: 0.6566 (p0) REVERT: 2 30 ASP cc_start: 0.7018 (t70) cc_final: 0.6518 (t0) REVERT: 2 135 GLU cc_start: 0.4145 (tm-30) cc_final: 0.3895 (tm-30) REVERT: 2 136 PHE cc_start: 0.6567 (m-10) cc_final: 0.6221 (m-10) REVERT: 2 182 SER cc_start: 0.7967 (t) cc_final: 0.7738 (m) REVERT: 2 266 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6828 (mm-30) REVERT: 3 45 MET cc_start: 0.7593 (ptm) cc_final: 0.7376 (ptp) REVERT: 3 61 LYS cc_start: 0.8671 (tptt) cc_final: 0.8391 (tptm) REVERT: 3 136 PHE cc_start: 0.7119 (m-80) cc_final: 0.6526 (m-80) REVERT: 3 146 ARG cc_start: 0.6542 (mmm160) cc_final: 0.6329 (mtm180) REVERT: 3 181 ASN cc_start: 0.8317 (t0) cc_final: 0.8031 (t0) REVERT: 3 193 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7062 (mm-30) REVERT: 3 299 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6046 (mt) REVERT: 4 27 SER cc_start: 0.8112 (t) cc_final: 0.7846 (t) REVERT: 4 29 MET cc_start: 0.7424 (tpp) cc_final: 0.6707 (mtm) REVERT: 4 40 SER cc_start: 0.8231 (t) cc_final: 0.7832 (m) REVERT: 4 41 GLU cc_start: 0.7183 (tp30) cc_final: 0.6657 (tp30) REVERT: 4 135 GLU cc_start: 0.6536 (mm-30) cc_final: 0.5923 (mm-30) REVERT: 4 157 MET cc_start: 0.7646 (tmm) cc_final: 0.7424 (tmm) REVERT: 4 171 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6610 (ptp) REVERT: 4 182 SER cc_start: 0.7617 (p) cc_final: 0.7417 (m) REVERT: 4 195 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7562 (ttm-80) REVERT: 4 212 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6299 (t80) REVERT: 4 242 MET cc_start: 0.6808 (ppp) cc_final: 0.6175 (ppp) REVERT: 4 250 TYR cc_start: 0.7019 (t80) cc_final: 0.6604 (t80) REVERT: 4 284 TRP cc_start: 0.7746 (t60) cc_final: 0.7089 (t60) REVERT: 4 305 ASP cc_start: 0.7603 (p0) cc_final: 0.7070 (p0) REVERT: 5 11 ARG cc_start: 0.8098 (tmm-80) cc_final: 0.7853 (tmm-80) REVERT: 5 31 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: 5 48 TYR cc_start: 0.7639 (m-80) cc_final: 0.7183 (m-80) REVERT: 5 101 MET cc_start: 0.6067 (tmm) cc_final: 0.5037 (tmm) REVERT: 5 118 ARG cc_start: 0.4505 (OUTLIER) cc_final: 0.3456 (ptm160) REVERT: 5 161 LYS cc_start: 0.7629 (mttt) cc_final: 0.7061 (mptt) REVERT: 5 220 GLU cc_start: 0.6466 (pm20) cc_final: 0.5500 (mt-10) REVERT: 5 225 LEU cc_start: 0.3909 (OUTLIER) cc_final: 0.3654 (mt) REVERT: 5 227 ASN cc_start: 0.5834 (OUTLIER) cc_final: 0.5295 (p0) REVERT: 5 284 TRP cc_start: 0.7955 (t60) cc_final: 0.7265 (t60) REVERT: 5 288 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: 5 309 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5336 (mm-30) REVERT: 6 14 ARG cc_start: 0.7654 (mpp80) cc_final: 0.7345 (mtm180) REVERT: 6 101 MET cc_start: 0.6394 (tpt) cc_final: 0.5899 (tmm) REVERT: 6 136 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: 6 153 ASN cc_start: 0.7695 (m-40) cc_final: 0.6968 (m110) REVERT: 6 156 LYS cc_start: 0.7461 (ttpp) cc_final: 0.7139 (ttmt) REVERT: 6 242 MET cc_start: 0.7655 (tpp) cc_final: 0.7428 (tpp) REVERT: 7 33 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8089 (ttp80) REVERT: 7 60 LYS cc_start: 0.7587 (tptp) cc_final: 0.7214 (ttmm) REVERT: 7 116 THR cc_start: 0.6744 (m) cc_final: 0.6524 (p) REVERT: 7 166 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7781 (mp) REVERT: 7 193 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6935 (mm-30) REVERT: 7 242 MET cc_start: 0.7605 (tpp) cc_final: 0.7196 (tpp) REVERT: 7 255 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6811 (tp30) outliers start: 82 outliers final: 54 residues processed: 493 average time/residue: 0.1537 time to fit residues: 107.6848 Evaluate side-chains 491 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 428 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LYS Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 254 ILE Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 130 LEU Chi-restraints excluded: chain 2 residue 173 TYR Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 265 THR Chi-restraints excluded: chain 3 residue 299 LEU Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 171 MET Chi-restraints excluded: chain 4 residue 174 SER Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 263 THR Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 118 ARG Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 225 LEU Chi-restraints excluded: chain 5 residue 227 ASN Chi-restraints excluded: chain 5 residue 267 GLU Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 288 PHE Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 27 SER Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 136 PHE Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 147 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 30 optimal weight: 2.9990 chunk 174 optimal weight: 0.0010 chunk 80 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 ASN 1 138 HIS 1 259 ASN ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 81 HIS ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS 4 179 GLN 4 227 ASN ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 81 HIS ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.176410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.155855 restraints weight = 26756.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.160348 restraints weight = 14609.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.163714 restraints weight = 9536.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165621 restraints weight = 6839.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166981 restraints weight = 5429.569| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 1.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17828 Z= 0.166 Angle : 0.761 14.417 24129 Z= 0.375 Chirality : 0.043 0.210 2695 Planarity : 0.008 0.296 3080 Dihedral : 7.927 179.635 2394 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.54 % Favored : 91.91 % Rotamer: Outliers : 3.45 % Allowed : 22.25 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2163 helix: 0.59 (0.16), residues: 1099 sheet: -3.10 (0.42), residues: 140 loop : -2.02 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG 6 187 TYR 0.024 0.002 TYR 3 173 PHE 0.029 0.002 PHE 6 288 TRP 0.011 0.002 TRP 5 154 HIS 0.006 0.001 HIS 3 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (17808) covalent geometry : angle 0.76127 / 0.38 (24129) hydrogen bonds : bond 0.03321 / 2.25 ( 697) hydrogen bonds : angle 3.99049 / 2.91 ( 2064) Misc. bond : bond 0.00324 / 0.19 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 436 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 60 LYS cc_start: 0.7929 (tptp) cc_final: 0.7705 (tppt) REVERT: 1 157 MET cc_start: 0.6448 (mtt) cc_final: 0.6219 (mtt) REVERT: 1 166 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7674 (mt) REVERT: 1 182 SER cc_start: 0.8444 (t) cc_final: 0.8190 (m) REVERT: 1 279 ASP cc_start: 0.6886 (p0) cc_final: 0.6635 (p0) REVERT: 2 136 PHE cc_start: 0.6466 (m-10) cc_final: 0.6223 (m-10) REVERT: 2 156 LYS cc_start: 0.7994 (tmmt) cc_final: 0.7506 (tttm) REVERT: 2 173 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7414 (p90) REVERT: 2 266 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7244 (mm-30) REVERT: 3 136 PHE cc_start: 0.7346 (m-80) cc_final: 0.6996 (m-80) REVERT: 3 181 ASN cc_start: 0.8350 (t0) cc_final: 0.8109 (t0) REVERT: 3 231 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7517 (mt0) REVERT: 3 255 GLU cc_start: 0.7385 (tp30) cc_final: 0.6966 (mm-30) REVERT: 3 299 LEU cc_start: 0.6553 (mt) cc_final: 0.6214 (mt) REVERT: 4 27 SER cc_start: 0.8255 (t) cc_final: 0.8003 (t) REVERT: 4 29 MET cc_start: 0.7624 (tpp) cc_final: 0.6848 (mtm) REVERT: 4 40 SER cc_start: 0.8315 (t) cc_final: 0.8072 (m) REVERT: 4 135 GLU cc_start: 0.6381 (mm-30) cc_final: 0.6030 (mm-30) REVERT: 4 195 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7705 (ttm-80) REVERT: 4 212 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6132 (t80) REVERT: 4 242 MET cc_start: 0.6877 (ppp) cc_final: 0.6285 (ppp) REVERT: 4 284 TRP cc_start: 0.7666 (t60) cc_final: 0.7115 (t60) REVERT: 4 305 ASP cc_start: 0.7424 (p0) cc_final: 0.6958 (p0) REVERT: 5 31 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7405 (ttm-80) REVERT: 5 34 ASP cc_start: 0.7381 (m-30) cc_final: 0.6992 (t0) REVERT: 5 101 MET cc_start: 0.5801 (tmm) cc_final: 0.4919 (tmm) REVERT: 5 118 ARG cc_start: 0.4297 (OUTLIER) cc_final: 0.3196 (ptm160) REVERT: 5 220 GLU cc_start: 0.6007 (pm20) cc_final: 0.5424 (mt-10) REVERT: 5 284 TRP cc_start: 0.7981 (t60) cc_final: 0.7375 (t60) REVERT: 5 288 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: 5 309 GLU cc_start: 0.5781 (mm-30) cc_final: 0.5414 (mm-30) REVERT: 6 14 ARG cc_start: 0.7545 (mpp80) cc_final: 0.7316 (mtm180) REVERT: 6 39 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6864 (mt-10) REVERT: 6 62 TYR cc_start: 0.7657 (t80) cc_final: 0.7331 (t80) REVERT: 6 63 LEU cc_start: 0.8295 (tt) cc_final: 0.7935 (tp) REVERT: 6 136 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: 6 137 GLN cc_start: 0.6161 (mp10) cc_final: 0.5749 (mp10) REVERT: 6 153 ASN cc_start: 0.7641 (m-40) cc_final: 0.6921 (m110) REVERT: 6 156 LYS cc_start: 0.7461 (ttpp) cc_final: 0.7199 (ttpt) REVERT: 6 271 PHE cc_start: 0.6832 (t80) cc_final: 0.6558 (t80) REVERT: 7 33 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8148 (ttp80) REVERT: 7 116 THR cc_start: 0.6894 (m) cc_final: 0.6647 (p) REVERT: 7 242 MET cc_start: 0.7694 (tpp) cc_final: 0.7330 (tpp) outliers start: 65 outliers final: 48 residues processed: 468 average time/residue: 0.1623 time to fit residues: 107.0218 Evaluate side-chains 472 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 418 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 130 LEU Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 173 TYR Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 135 GLU Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 265 THR Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 118 ARG Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 227 ASN Chi-restraints excluded: chain 5 residue 288 PHE Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 136 PHE Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 7 residue 147 VAL Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 75 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 214 optimal weight: 0.3980 chunk 121 optimal weight: 0.0070 chunk 203 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 ASN ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.157731 restraints weight = 26352.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.162454 restraints weight = 14439.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.165058 restraints weight = 9334.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.167687 restraints weight = 6981.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168683 restraints weight = 5378.583| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 1.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17828 Z= 0.139 Angle : 0.768 12.824 24129 Z= 0.381 Chirality : 0.043 0.206 2695 Planarity : 0.010 0.399 3080 Dihedral : 8.052 178.947 2394 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.30 % Favored : 92.19 % Rotamer: Outliers : 2.39 % Allowed : 23.84 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2163 helix: 0.85 (0.16), residues: 1057 sheet: -2.54 (0.60), residues: 70 loop : -2.07 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG 6 187 TYR 0.020 0.001 TYR 4 173 PHE 0.035 0.002 PHE 2 136 TRP 0.012 0.001 TRP 5 154 HIS 0.006 0.001 HIS 3 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17808) covalent geometry : angle 0.76780 / 0.38 (24129) hydrogen bonds : bond 0.03210 / 2.12 ( 697) hydrogen bonds : angle 3.89574 / 2.85 ( 2064) Misc. bond : bond 0.00287 / 0.17 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8336 (tmm-80) cc_final: 0.7923 (ttp-170) REVERT: 1 41 GLU cc_start: 0.7378 (tt0) cc_final: 0.7166 (tt0) REVERT: 1 60 LYS cc_start: 0.7923 (tptp) cc_final: 0.7707 (tppt) REVERT: 1 157 MET cc_start: 0.6411 (mtt) cc_final: 0.6160 (mtt) REVERT: 1 166 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7718 (mt) REVERT: 1 279 ASP cc_start: 0.6829 (p0) cc_final: 0.6594 (p0) REVERT: 2 129 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8273 (mtmm) REVERT: 2 136 PHE cc_start: 0.6160 (m-10) cc_final: 0.5928 (m-10) REVERT: 2 255 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6304 (mt-10) REVERT: 3 136 PHE cc_start: 0.7317 (m-80) cc_final: 0.7031 (m-80) REVERT: 3 146 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.5979 (mtm110) REVERT: 3 231 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7562 (mt0) REVERT: 3 299 LEU cc_start: 0.6551 (mt) cc_final: 0.6241 (mt) REVERT: 4 24 LYS cc_start: 0.8044 (tttm) cc_final: 0.7823 (tttm) REVERT: 4 27 SER cc_start: 0.8282 (t) cc_final: 0.7988 (t) REVERT: 4 29 MET cc_start: 0.7587 (tpp) cc_final: 0.6844 (mtm) REVERT: 4 40 SER cc_start: 0.8352 (t) cc_final: 0.8083 (m) REVERT: 4 132 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7471 (mp) REVERT: 4 135 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5966 (mm-30) REVERT: 4 195 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7581 (ttm-80) REVERT: 4 212 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6053 (t80) REVERT: 4 242 MET cc_start: 0.6709 (ppp) cc_final: 0.6234 (ppp) REVERT: 4 255 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7672 (mm-30) REVERT: 4 305 ASP cc_start: 0.7434 (p0) cc_final: 0.6904 (p0) REVERT: 5 31 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7311 (ttm-80) REVERT: 5 33 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7711 (ttp80) REVERT: 5 34 ASP cc_start: 0.7430 (m-30) cc_final: 0.7065 (t0) REVERT: 5 101 MET cc_start: 0.5678 (tmm) cc_final: 0.4890 (tmm) REVERT: 5 118 ARG cc_start: 0.4225 (OUTLIER) cc_final: 0.3861 (ttt90) REVERT: 5 220 GLU cc_start: 0.5925 (pm20) cc_final: 0.5316 (mt-10) REVERT: 5 227 ASN cc_start: 0.6069 (m-40) cc_final: 0.5862 (p0) REVERT: 5 284 TRP cc_start: 0.7932 (t60) cc_final: 0.7316 (t60) REVERT: 5 288 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: 5 309 GLU cc_start: 0.5714 (mm-30) cc_final: 0.5346 (mm-30) REVERT: 6 14 ARG cc_start: 0.7558 (mpp80) cc_final: 0.7336 (mtm180) REVERT: 6 63 LEU cc_start: 0.8173 (tt) cc_final: 0.7895 (tp) REVERT: 6 137 GLN cc_start: 0.6098 (mp10) cc_final: 0.5700 (mp10) REVERT: 6 153 ASN cc_start: 0.7642 (m-40) cc_final: 0.6907 (m-40) REVERT: 6 156 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7331 (ttpt) REVERT: 6 214 ASP cc_start: 0.7817 (t0) cc_final: 0.7592 (t0) REVERT: 7 116 THR cc_start: 0.7360 (m) cc_final: 0.7066 (p) REVERT: 7 135 GLU cc_start: 0.7865 (mp0) cc_final: 0.7325 (mp0) REVERT: 7 284 TRP cc_start: 0.7727 (t60) cc_final: 0.7339 (t60) outliers start: 45 outliers final: 28 residues processed: 441 average time/residue: 0.1648 time to fit residues: 102.7079 Evaluate side-chains 442 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 408 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 130 LEU Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 118 ARG Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 242 MET Chi-restraints excluded: chain 5 residue 288 PHE Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 212 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 176 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 ASN ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS 3 81 HIS ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS ** 6 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN 7 65 GLN ** 7 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154847 restraints weight = 26754.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159479 restraints weight = 14817.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.162259 restraints weight = 9669.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164654 restraints weight = 7215.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.166037 restraints weight = 5645.985| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 1.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17828 Z= 0.163 Angle : 0.775 13.119 24129 Z= 0.386 Chirality : 0.044 0.198 2695 Planarity : 0.010 0.394 3080 Dihedral : 8.226 179.426 2394 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.72 % Favored : 91.82 % Rotamer: Outliers : 2.50 % Allowed : 23.95 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2163 helix: 0.80 (0.16), residues: 1064 sheet: -2.93 (0.50), residues: 112 loop : -2.08 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG 6 187 TYR 0.029 0.002 TYR 1 48 PHE 0.025 0.002 PHE 2 136 TRP 0.012 0.001 TRP 5 154 HIS 0.008 0.001 HIS 7 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (17808) covalent geometry : angle 0.77516 / 0.39 (24129) hydrogen bonds : bond 0.03345 / 2.26 ( 697) hydrogen bonds : angle 3.94391 / 2.89 ( 2064) Misc. bond : bond 0.00367 / 0.25 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.83 seconds wall clock time: 51 minutes 41.28 seconds (3101.28 seconds total)