Starting phenix.real_space_refine on Thu Mar 5 00:03:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzy_24783/03_2026/7rzy_24783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzy_24783/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rzy_24783/03_2026/7rzy_24783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzy_24783/03_2026/7rzy_24783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzy_24783/03_2026/7rzy_24783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzy_24783/03_2026/7rzy_24783.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.88, per 1000 atoms: 0.22 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: 1.37 Conformation dependent library (CDL) restraints added in 543.0 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: 0.48 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: 2.54 Time building geometry restraints manager: 1.73 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: 9817 17.95 - 35.90: 890 35.90 - 53.85: 282 53.85 - 71.79: 34 71.79 - 89.74: 16 Dihedral angle restraints: 11039 sinusoidal: 4697 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 11036 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.410 Find NCS groups from input model: 0.410 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3956 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 : 15.463 89.743 6937 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 covalent geometry : bond 0.01393 (17808) covalent geometry : angle 1.82720 (24129) hydrogen bonds : bond 0.15773 ( 697) hydrogen bonds : angle 6.48604 ( 2064) Misc. bond : bond 0.11440 ( 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 : 0.579 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: 0.1425 time to fit residues: 84.7046 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 : 0.538 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 65 GLN ** 2 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 GLN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 153 ASN 5 261 HIS 6 261 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159662 restraints weight = 27158.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.164083 restraints weight = 14817.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.166950 restraints weight = 9576.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.168957 restraints weight = 6961.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.170211 restraints weight = 5458.483| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4661 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17828 Z= 0.196 Angle : 0.772 13.811 24129 Z= 0.392 Chirality : 0.045 0.226 2695 Planarity : 0.005 0.049 3080 Dihedral : 10.356 88.210 2617 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.33 % Favored : 93.20 % Rotamer: Outliers : 2.18 % Allowed : 11.95 % Favored : 85.87 % 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: -1.33 (0.18), residues: 2163 helix: 0.33 (0.15), residues: 1148 sheet: -3.69 (0.31), residues: 168 loop : -1.94 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 7 187 TYR 0.018 0.002 TYR 4 173 PHE 0.020 0.003 PHE 3 288 TRP 0.022 0.002 TRP 4 284 HIS 0.010 0.002 HIS 5 185 Details of bonding type rmsd covalent geometry : bond 0.00424 (17808) covalent geometry : angle 0.77182 (24129) hydrogen bonds : bond 0.03864 ( 697) hydrogen bonds : angle 3.99637 ( 2064) Misc. bond : bond 0.00224 ( 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 422 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 381 time to evaluate : 0.751 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: 0.7287 (ttp-110) cc_final: 0.6641 (ptp90) REVERT: 1 24 LYS cc_start: 0.6658 (ttmm) cc_final: 0.6342 (tttp) REVERT: 1 132 ILE cc_start: 0.6335 (mt) cc_final: 0.5595 (mt) REVERT: 1 171 MET cc_start: 0.5314 (tpp) cc_final: 0.5108 (tpp) REVERT: 1 192 VAL cc_start: 0.5531 (OUTLIER) cc_final: 0.5259 (m) REVERT: 1 210 LEU cc_start: 0.6160 (tp) cc_final: 0.5700 (tp) REVERT: 2 13 LYS cc_start: 0.6982 (tppt) cc_final: 0.5469 (tppt) REVERT: 2 23 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6921 (ttp-110) REVERT: 2 43 THR cc_start: 0.7000 (p) cc_final: 0.6694 (m) REVERT: 2 192 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6166 (t) REVERT: 2 254 ILE cc_start: 0.6033 (mm) cc_final: 0.5831 (mm) REVERT: 2 266 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5714 (tp30) REVERT: 3 192 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7499 (m) REVERT: 4 101 MET cc_start: 0.5244 (tmm) cc_final: 0.5018 (ppp) REVERT: 4 169 PHE cc_start: 0.5531 (m-80) cc_final: 0.5009 (m-80) REVERT: 5 137 GLN cc_start: 0.3500 (mm-40) cc_final: 0.3202 (mm-40) REVERT: 5 168 ILE cc_start: 0.5122 (pt) cc_final: 0.4620 (pt) REVERT: 5 169 PHE cc_start: 0.5555 (m-80) cc_final: 0.4803 (m-80) REVERT: 6 79 VAL cc_start: 0.3666 (m) cc_final: 0.3276 (p) REVERT: 6 141 GLU cc_start: 0.4693 (mm-30) cc_final: 0.3448 (mp0) REVERT: 6 190 ILE cc_start: 0.5305 (mt) cc_final: 0.5016 (mt) REVERT: 6 246 ARG cc_start: 0.6658 (mmm-85) cc_final: 0.6278 (tpt90) REVERT: 7 41 GLU cc_start: 0.6304 (tt0) cc_final: 0.6045 (tt0) REVERT: 7 59 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6429 (mt) REVERT: 7 100 GLU cc_start: 0.6872 (tp30) cc_final: 0.6599 (mm-30) REVERT: 7 101 MET cc_start: 0.5592 (tpt) cc_final: 0.5295 (tpt) REVERT: 7 246 ARG cc_start: 0.5309 (mmm-85) cc_final: 0.4975 (tpp-160) outliers start: 41 outliers final: 14 residues processed: 403 average time/residue: 0.1501 time to fit residues: 87.0263 Evaluate side-chains 347 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 329 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 chunk 147 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 HIS ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 261 HIS 2 138 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 81 HIS ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 181 ASN ** 7 181 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 = 0.4261 r_free = 0.4261 target = 0.178628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.158519 restraints weight = 27442.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163214 restraints weight = 14627.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.166359 restraints weight = 9313.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168412 restraints weight = 6644.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.170063 restraints weight = 5144.921| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 17828 Z= 0.205 Angle : 0.781 15.823 24129 Z= 0.390 Chirality : 0.044 0.197 2695 Planarity : 0.006 0.159 3080 Dihedral : 10.535 87.271 2614 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.95 % Favored : 91.49 % Rotamer: Outliers : 3.29 % Allowed : 13.91 % Favored : 82.79 % 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: -1.25 (0.18), residues: 2163 helix: 0.44 (0.15), residues: 1141 sheet: -3.53 (0.32), residues: 210 loop : -1.84 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG 5 187 TYR 0.022 0.002 TYR 3 173 PHE 0.017 0.002 PHE 7 209 TRP 0.019 0.002 TRP 4 284 HIS 0.013 0.002 HIS 7 81 Details of bonding type rmsd covalent geometry : bond 0.00468 (17808) covalent geometry : angle 0.78105 (24129) hydrogen bonds : bond 0.03780 ( 697) hydrogen bonds : angle 4.07257 ( 2064) Misc. bond : bond 0.00617 ( 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 449 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 387 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 13 LYS cc_start: 0.8184 (tppt) cc_final: 0.7841 (tppt) REVERT: 1 14 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.6912 (ptp90) REVERT: 1 36 SER cc_start: 0.7562 (m) cc_final: 0.7234 (p) REVERT: 1 45 MET cc_start: 0.6949 (mtm) cc_final: 0.6731 (mtm) REVERT: 1 79 VAL cc_start: 0.6306 (m) cc_final: 0.6092 (t) REVERT: 1 89 LYS cc_start: 0.6536 (mtmm) cc_final: 0.6198 (mtmm) REVERT: 1 100 GLU cc_start: 0.5948 (mp0) cc_final: 0.5737 (mp0) REVERT: 1 132 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5709 (mt) REVERT: 1 207 LYS cc_start: 0.7581 (tppt) cc_final: 0.7065 (tptp) REVERT: 2 32 CYS cc_start: 0.5610 (m) cc_final: 0.5295 (m) REVERT: 2 169 PHE cc_start: 0.5280 (m-80) cc_final: 0.4484 (m-10) REVERT: 2 191 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.6516 (mp10) REVERT: 2 192 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.7135 (t) REVERT: 3 195 ARG cc_start: 0.7153 (mtp85) cc_final: 0.6646 (mtp85) REVERT: 4 43 THR cc_start: 0.6030 (OUTLIER) cc_final: 0.5535 (p) REVERT: 4 61 LYS cc_start: 0.8147 (tptp) cc_final: 0.7834 (tptp) REVERT: 4 137 GLN cc_start: 0.6074 (tp-100) cc_final: 0.5150 (tp-100) REVERT: 4 169 PHE cc_start: 0.6923 (m-80) cc_final: 0.6535 (m-10) REVERT: 6 16 PHE cc_start: 0.7482 (t80) cc_final: 0.7239 (t80) REVERT: 6 29 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6026 (mtm) REVERT: 6 45 MET cc_start: 0.7026 (ttp) cc_final: 0.6786 (ttt) REVERT: 6 62 TYR cc_start: 0.6144 (t80) cc_final: 0.5662 (t80) REVERT: 6 141 GLU cc_start: 0.4839 (mm-30) cc_final: 0.3526 (mp0) REVERT: 6 289 GLU cc_start: 0.6486 (tp30) cc_final: 0.6214 (tp30) REVERT: 7 41 GLU cc_start: 0.6632 (tt0) cc_final: 0.6026 (tt0) REVERT: 7 45 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5555 (ttm) REVERT: 7 59 ILE cc_start: 0.7637 (mt) cc_final: 0.7381 (mt) REVERT: 7 101 MET cc_start: 0.5937 (tpt) cc_final: 0.5620 (tpt) REVERT: 7 134 ASP cc_start: 0.5925 (m-30) cc_final: 0.5681 (m-30) REVERT: 7 153 ASN cc_start: 0.7138 (m110) cc_final: 0.6066 (m110) REVERT: 7 193 GLU cc_start: 0.5707 (mm-30) cc_final: 0.5315 (tm-30) REVERT: 7 246 ARG cc_start: 0.6271 (mmm-85) cc_final: 0.5811 (mmm160) outliers start: 62 outliers final: 25 residues processed: 421 average time/residue: 0.1532 time to fit residues: 93.9867 Evaluate side-chains 391 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 360 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 132 ILE 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 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 132 ILE 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 132 ILE 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 5 residue 19 THR Chi-restraints excluded: chain 5 residue 112 LEU 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 6 residue 147 VAL Chi-restraints excluded: chain 7 residue 45 MET Chi-restraints excluded: chain 7 residue 58 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 267 GLU 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: 0.0470 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 0.0170 chunk 163 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 HIS ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 153 ASN ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.179589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.159686 restraints weight = 27481.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164428 restraints weight = 14661.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.167406 restraints weight = 9314.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169790 restraints weight = 6641.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.171041 restraints weight = 5094.102| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17828 Z= 0.168 Angle : 0.703 10.596 24129 Z= 0.355 Chirality : 0.043 0.249 2695 Planarity : 0.006 0.161 3080 Dihedral : 10.246 81.752 2612 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.89 % Favored : 92.51 % Rotamer: Outliers : 3.93 % Allowed : 16.14 % Favored : 79.93 % 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: -1.03 (0.18), residues: 2163 helix: 0.66 (0.15), residues: 1141 sheet: -3.49 (0.35), residues: 168 loop : -1.93 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 243 TYR 0.027 0.002 TYR 4 173 PHE 0.025 0.002 PHE 6 288 TRP 0.033 0.002 TRP 4 154 HIS 0.006 0.001 HIS 2 185 Details of bonding type rmsd covalent geometry : bond 0.00362 (17808) covalent geometry : angle 0.70269 (24129) hydrogen bonds : bond 0.03184 ( 697) hydrogen bonds : angle 3.87565 ( 2064) Misc. bond : bond 0.00294 ( 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 474 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 400 time to evaluate : 0.721 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: 1 13 LYS cc_start: 0.8298 (tppt) cc_final: 0.7999 (tppt) REVERT: 1 14 ARG cc_start: 0.7637 (ttp-110) cc_final: 0.6976 (ptp90) REVERT: 1 23 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7739 (ttp-170) REVERT: 1 36 SER cc_start: 0.7460 (m) cc_final: 0.6915 (p) REVERT: 1 45 MET cc_start: 0.6893 (mtm) cc_final: 0.6639 (mtm) REVERT: 1 79 VAL cc_start: 0.6485 (m) cc_final: 0.6237 (t) REVERT: 1 89 LYS cc_start: 0.6561 (mtmm) cc_final: 0.6253 (mtmm) REVERT: 1 100 GLU cc_start: 0.6083 (mp0) cc_final: 0.5819 (mp0) REVERT: 1 132 ILE cc_start: 0.5792 (mt) cc_final: 0.5434 (mt) REVERT: 1 135 GLU cc_start: 0.4441 (tp30) cc_final: 0.4225 (tp30) REVERT: 1 239 GLN cc_start: 0.7192 (mp10) cc_final: 0.6687 (mp10) REVERT: 2 58 VAL cc_start: 0.4305 (t) cc_final: 0.4037 (t) REVERT: 2 60 LYS cc_start: 0.6535 (tppt) cc_final: 0.6281 (tppp) REVERT: 2 191 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: 2 298 MET cc_start: 0.2636 (ptm) cc_final: 0.2082 (ptp) REVERT: 3 43 THR cc_start: 0.6726 (p) cc_final: 0.6471 (p) REVERT: 3 45 MET cc_start: 0.6962 (ptm) cc_final: 0.6682 (ptp) REVERT: 3 61 LYS cc_start: 0.7948 (tptt) cc_final: 0.7587 (tptp) REVERT: 4 11 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6634 (ttp80) REVERT: 4 23 ARG cc_start: 0.6369 (mtm-85) cc_final: 0.6158 (mtt180) REVERT: 4 43 THR cc_start: 0.6087 (OUTLIER) cc_final: 0.5681 (p) REVERT: 4 61 LYS cc_start: 0.8343 (tptp) cc_final: 0.8011 (tptp) REVERT: 4 136 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: 4 169 PHE cc_start: 0.7234 (m-80) cc_final: 0.6638 (m-10) REVERT: 4 279 ASP cc_start: 0.5745 (t0) cc_final: 0.5351 (t0) REVERT: 4 280 LYS cc_start: 0.6249 (mmtt) cc_final: 0.5994 (mptt) REVERT: 5 101 MET cc_start: 0.6107 (tmm) cc_final: 0.5359 (tmm) REVERT: 5 136 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: 6 14 ARG cc_start: 0.7105 (mpp80) cc_final: 0.6822 (ptp-170) REVERT: 6 16 PHE cc_start: 0.7908 (t80) cc_final: 0.7559 (t80) REVERT: 6 29 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6373 (mtm) REVERT: 6 62 TYR cc_start: 0.6361 (t80) cc_final: 0.5667 (t80) REVERT: 6 81 HIS cc_start: 0.6983 (t-90) cc_final: 0.6412 (t-90) REVERT: 6 141 GLU cc_start: 0.5187 (mm-30) cc_final: 0.3678 (mp0) REVERT: 6 253 SER cc_start: 0.7209 (t) cc_final: 0.6961 (p) REVERT: 6 289 GLU cc_start: 0.6557 (tp30) cc_final: 0.6227 (tp30) REVERT: 7 29 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6495 (mtm) REVERT: 7 45 MET cc_start: 0.6525 (ttp) cc_final: 0.6153 (ttm) REVERT: 7 59 ILE cc_start: 0.7690 (mt) cc_final: 0.7404 (mt) REVERT: 7 101 MET cc_start: 0.5819 (tpt) cc_final: 0.5583 (tpt) REVERT: 7 153 ASN cc_start: 0.6986 (m-40) cc_final: 0.6600 (m-40) REVERT: 7 156 LYS cc_start: 0.6431 (ttpp) cc_final: 0.6214 (ttpp) REVERT: 7 193 GLU cc_start: 0.6010 (mm-30) cc_final: 0.5602 (tm-30) outliers start: 74 outliers final: 33 residues processed: 443 average time/residue: 0.1487 time to fit residues: 96.7652 Evaluate side-chains 402 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 363 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 200 ASN Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 148 LEU 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 45 MET 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 178 LEU Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 242 MET 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 45 MET Chi-restraints excluded: chain 5 residue 112 LEU 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 275 LEU Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 6 residue 29 MET Chi-restraints excluded: chain 7 residue 29 MET Chi-restraints excluded: chain 7 residue 58 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 267 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 171 optimal weight: 0.1980 chunk 187 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 231 GLN ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 185 HIS ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 247 ASN 6 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.180055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160271 restraints weight = 27258.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.164956 restraints weight = 14496.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168223 restraints weight = 9178.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169885 restraints weight = 6495.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.171722 restraints weight = 5168.129| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17828 Z= 0.189 Angle : 0.754 16.897 24129 Z= 0.377 Chirality : 0.045 0.425 2695 Planarity : 0.005 0.123 3080 Dihedral : 10.356 79.479 2611 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.63 % Favored : 91.77 % Rotamer: Outliers : 3.66 % Allowed : 18.06 % Favored : 78.28 % 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: -1.21 (0.18), residues: 2163 helix: 0.55 (0.15), residues: 1141 sheet: -3.57 (0.33), residues: 210 loop : -1.93 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 203 TYR 0.024 0.002 TYR 4 173 PHE 0.037 0.003 PHE 5 136 TRP 0.023 0.002 TRP 4 284 HIS 0.010 0.002 HIS 5 185 Details of bonding type rmsd covalent geometry : bond 0.00447 (17808) covalent geometry : angle 0.75373 (24129) hydrogen bonds : bond 0.03442 ( 697) hydrogen bonds : angle 4.00212 ( 2064) Misc. bond : bond 0.00220 ( 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 510 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 441 time to evaluate : 0.599 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: 1 13 LYS cc_start: 0.8342 (tppt) cc_final: 0.7737 (tppp) REVERT: 1 14 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7168 (ptp90) REVERT: 1 36 SER cc_start: 0.7583 (m) cc_final: 0.7136 (p) REVERT: 1 89 LYS cc_start: 0.6751 (mtmm) cc_final: 0.6426 (mtmm) REVERT: 1 100 GLU cc_start: 0.6213 (mp0) cc_final: 0.5928 (mp0) REVERT: 1 130 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7293 (mt) REVERT: 1 239 GLN cc_start: 0.7371 (mp10) cc_final: 0.6799 (mp10) REVERT: 2 45 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7630 (mtm) REVERT: 2 61 LYS cc_start: 0.7963 (tptt) cc_final: 0.7736 (tptt) REVERT: 2 132 ILE cc_start: 0.6202 (mp) cc_final: 0.5549 (mt) REVERT: 2 298 MET cc_start: 0.2888 (ptm) cc_final: 0.2332 (ptp) REVERT: 3 43 THR cc_start: 0.7087 (p) cc_final: 0.6835 (p) REVERT: 3 132 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7266 (mt) REVERT: 3 193 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6568 (mm-30) REVERT: 3 255 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6915 (mm-30) REVERT: 4 212 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.5905 (t80) REVERT: 4 214 ASP cc_start: 0.6803 (m-30) cc_final: 0.6517 (m-30) REVERT: 4 273 SER cc_start: 0.7845 (t) cc_final: 0.7379 (t) REVERT: 5 101 MET cc_start: 0.6275 (tmm) cc_final: 0.6028 (tmm) REVERT: 5 136 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: 5 288 PHE cc_start: 0.5650 (m-10) cc_final: 0.5184 (m-80) REVERT: 6 14 ARG cc_start: 0.7421 (mpp80) cc_final: 0.7099 (mtm180) REVERT: 6 16 PHE cc_start: 0.8032 (t80) cc_final: 0.7536 (t80) REVERT: 6 141 GLU cc_start: 0.5806 (mm-30) cc_final: 0.4262 (mp0) REVERT: 6 156 LYS cc_start: 0.7044 (ttpp) cc_final: 0.6523 (tttp) REVERT: 6 168 ILE cc_start: 0.7634 (pt) cc_final: 0.7431 (pt) REVERT: 6 171 MET cc_start: 0.4423 (OUTLIER) cc_final: 0.3435 (mtm) REVERT: 6 250 TYR cc_start: 0.7681 (t80) cc_final: 0.7440 (t80) REVERT: 6 253 SER cc_start: 0.7359 (t) cc_final: 0.7066 (p) REVERT: 7 60 LYS cc_start: 0.7685 (tptp) cc_final: 0.7076 (ttmm) REVERT: 7 153 ASN cc_start: 0.7111 (m-40) cc_final: 0.6842 (m-40) REVERT: 7 156 LYS cc_start: 0.6803 (ttpp) cc_final: 0.6580 (ttpp) REVERT: 7 181 ASN cc_start: 0.7217 (p0) cc_final: 0.7001 (p0) REVERT: 7 193 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6038 (tm-30) outliers start: 69 outliers final: 44 residues processed: 481 average time/residue: 0.1654 time to fit residues: 112.3519 Evaluate side-chains 459 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 409 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 130 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 160 ASN 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 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 200 ASN Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 238 SER Chi-restraints excluded: chain 3 residue 244 SER Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 153 ASN Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 242 MET 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 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 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 247 ASN Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 58 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 267 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 186 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 chunk 216 optimal weight: 0.0370 chunk 93 optimal weight: 1.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 137 GLN ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159471 restraints weight = 27113.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.164074 restraints weight = 14801.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167312 restraints weight = 9552.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.169063 restraints weight = 6816.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170768 restraints weight = 5424.413| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.8400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17828 Z= 0.140 Angle : 0.703 10.900 24129 Z= 0.348 Chirality : 0.042 0.326 2695 Planarity : 0.006 0.191 3080 Dihedral : 10.264 83.702 2611 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.61 % Favored : 92.79 % Rotamer: Outliers : 3.66 % Allowed : 19.49 % Favored : 76.85 % 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: -1.01 (0.18), residues: 2163 helix: 0.75 (0.16), residues: 1099 sheet: -3.19 (0.36), residues: 196 loop : -1.91 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG 6 187 TYR 0.024 0.001 TYR 3 173 PHE 0.026 0.002 PHE 3 271 TRP 0.016 0.001 TRP 4 154 HIS 0.004 0.001 HIS 7 138 Details of bonding type rmsd covalent geometry : bond 0.00321 (17808) covalent geometry : angle 0.70264 (24129) hydrogen bonds : bond 0.02954 ( 697) hydrogen bonds : angle 3.79532 ( 2064) Misc. bond : bond 0.00315 ( 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 501 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 432 time to evaluate : 0.649 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: 1 100 GLU cc_start: 0.6280 (mp0) cc_final: 0.5931 (mp0) REVERT: 1 130 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7324 (mt) REVERT: 1 132 ILE cc_start: 0.5972 (mp) cc_final: 0.5502 (mt) REVERT: 1 211 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6862 (mm-30) REVERT: 1 239 GLN cc_start: 0.7542 (mp10) cc_final: 0.6918 (mp10) REVERT: 2 23 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7634 (ttp-170) REVERT: 2 61 LYS cc_start: 0.7761 (tptt) cc_final: 0.7559 (tptt) REVERT: 2 132 ILE cc_start: 0.6188 (mp) cc_final: 0.5851 (mt) REVERT: 2 182 SER cc_start: 0.7664 (t) cc_final: 0.7076 (m) REVERT: 2 191 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: 2 212 TYR cc_start: 0.5809 (OUTLIER) cc_final: 0.5270 (t80) REVERT: 2 298 MET cc_start: 0.2921 (ptm) cc_final: 0.2606 (ptp) REVERT: 3 43 THR cc_start: 0.6950 (p) cc_final: 0.6663 (p) REVERT: 3 195 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7488 (ttm-80) REVERT: 3 255 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6800 (mm-30) REVERT: 4 41 GLU cc_start: 0.5952 (tp30) cc_final: 0.5634 (tp30) REVERT: 4 79 VAL cc_start: 0.7856 (m) cc_final: 0.7640 (t) REVERT: 4 135 GLU cc_start: 0.4823 (mm-30) cc_final: 0.4542 (mm-30) REVERT: 4 212 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6077 (t80) REVERT: 4 214 ASP cc_start: 0.6947 (m-30) cc_final: 0.6650 (m-30) REVERT: 4 255 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7216 (mm-30) REVERT: 4 273 SER cc_start: 0.7895 (t) cc_final: 0.7430 (t) REVERT: 5 41 GLU cc_start: 0.7504 (tp30) cc_final: 0.7123 (tp30) REVERT: 5 101 MET cc_start: 0.6278 (tmm) cc_final: 0.5897 (tmm) REVERT: 5 227 ASN cc_start: 0.6158 (p0) cc_final: 0.5225 (m-40) REVERT: 5 271 PHE cc_start: 0.7641 (t80) cc_final: 0.7220 (t80) REVERT: 5 288 PHE cc_start: 0.5493 (m-10) cc_final: 0.5131 (m-80) REVERT: 6 14 ARG cc_start: 0.7473 (mpp80) cc_final: 0.7137 (mtm180) REVERT: 6 156 LYS cc_start: 0.7133 (ttpp) cc_final: 0.6712 (ttmm) REVERT: 6 192 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7363 (t) REVERT: 6 195 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7143 (tpp-160) REVERT: 6 211 GLU cc_start: 0.6408 (tt0) cc_final: 0.5959 (tt0) REVERT: 6 253 SER cc_start: 0.7343 (t) cc_final: 0.6973 (p) REVERT: 7 31 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7390 (ttm170) REVERT: 7 38 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6889 (mm) REVERT: 7 41 GLU cc_start: 0.7653 (tt0) cc_final: 0.7292 (tm-30) REVERT: 7 60 LYS cc_start: 0.7698 (tptp) cc_final: 0.7074 (ttmm) REVERT: 7 101 MET cc_start: 0.6039 (tpt) cc_final: 0.5704 (tpt) REVERT: 7 153 ASN cc_start: 0.7097 (m-40) cc_final: 0.6854 (m-40) REVERT: 7 156 LYS cc_start: 0.6987 (ttpp) cc_final: 0.6711 (ttpp) REVERT: 7 181 ASN cc_start: 0.7233 (p0) cc_final: 0.7027 (p0) REVERT: 7 193 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6181 (tm-30) outliers start: 69 outliers final: 45 residues processed: 467 average time/residue: 0.1649 time to fit residues: 108.9796 Evaluate side-chains 460 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain 1 residue 130 LEU 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 29 MET Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 212 TYR Chi-restraints excluded: chain 2 residue 248 LEU Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 261 HIS 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 153 ASN Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS 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 267 GLU Chi-restraints excluded: chain 5 residue 275 LEU Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 195 ARG Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 58 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 97 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 104 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 123 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 ASN 1 183 GLN 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** 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 ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 282 ASN 5 81 HIS ** 6 200 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 = 0.4236 r_free = 0.4236 target = 0.177289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.156776 restraints weight = 27046.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.161539 restraints weight = 14487.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.164794 restraints weight = 9232.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166827 restraints weight = 6593.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.168500 restraints weight = 5153.182| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.9272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17828 Z= 0.157 Angle : 0.727 16.408 24129 Z= 0.360 Chirality : 0.043 0.242 2695 Planarity : 0.006 0.161 3080 Dihedral : 10.401 88.616 2611 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.40 % Favored : 92.00 % Rotamer: Outliers : 3.77 % Allowed : 20.61 % Favored : 75.62 % 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: -1.01 (0.19), residues: 2163 helix: 0.77 (0.16), residues: 1099 sheet: -3.14 (0.37), residues: 196 loop : -1.94 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 6 187 TYR 0.031 0.002 TYR 4 173 PHE 0.024 0.002 PHE 5 269 TRP 0.015 0.002 TRP 4 154 HIS 0.006 0.001 HIS 7 81 Details of bonding type rmsd covalent geometry : bond 0.00363 (17808) covalent geometry : angle 0.72683 (24129) hydrogen bonds : bond 0.03109 ( 697) hydrogen bonds : angle 3.85994 ( 2064) Misc. bond : bond 0.00358 ( 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 533 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 462 time to evaluate : 0.592 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: 1 60 LYS cc_start: 0.7370 (tptt) cc_final: 0.7098 (tppp) REVERT: 1 100 GLU cc_start: 0.6245 (mp0) cc_final: 0.5992 (mp0) REVERT: 1 101 MET cc_start: 0.6837 (tpp) cc_final: 0.6585 (tpp) REVERT: 1 130 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7449 (mt) REVERT: 1 239 GLN cc_start: 0.7771 (mp10) cc_final: 0.7174 (mp10) REVERT: 1 279 ASP cc_start: 0.6746 (p0) cc_final: 0.6401 (p0) REVERT: 2 132 ILE cc_start: 0.6301 (mp) cc_final: 0.5992 (mt) REVERT: 2 156 LYS cc_start: 0.6715 (tptp) cc_final: 0.6468 (tptp) REVERT: 2 171 MET cc_start: 0.7473 (mtp) cc_final: 0.7181 (mtp) REVERT: 2 182 SER cc_start: 0.7762 (t) cc_final: 0.7236 (m) REVERT: 2 191 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: 2 239 GLN cc_start: 0.7286 (mt0) cc_final: 0.7019 (mt0) REVERT: 2 298 MET cc_start: 0.2818 (ptm) cc_final: 0.2300 (ptp) REVERT: 3 167 VAL cc_start: 0.5625 (t) cc_final: 0.4607 (p) REVERT: 3 195 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7228 (mtp85) REVERT: 4 41 GLU cc_start: 0.6327 (tp30) cc_final: 0.5793 (tp30) REVERT: 4 161 LYS cc_start: 0.7486 (mttt) cc_final: 0.7020 (mmtp) REVERT: 4 212 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6042 (t80) REVERT: 4 214 ASP cc_start: 0.7190 (m-30) cc_final: 0.6979 (m-30) REVERT: 4 255 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7354 (mm-30) REVERT: 4 273 SER cc_start: 0.8004 (t) cc_final: 0.7514 (t) REVERT: 4 274 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7661 (ttmm) REVERT: 5 23 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7133 (mtt180) REVERT: 5 31 ARG cc_start: 0.6768 (ttm-80) cc_final: 0.6266 (ttm-80) REVERT: 5 81 HIS cc_start: 0.6681 (t-170) cc_final: 0.5821 (t-90) REVERT: 5 101 MET cc_start: 0.6232 (tmm) cc_final: 0.5771 (tmm) REVERT: 5 134 ASP cc_start: 0.6254 (t0) cc_final: 0.6043 (t0) REVERT: 5 150 GLN cc_start: 0.7524 (mp10) cc_final: 0.7200 (mp10) REVERT: 5 227 ASN cc_start: 0.6223 (p0) cc_final: 0.5661 (m-40) REVERT: 5 271 PHE cc_start: 0.7743 (t80) cc_final: 0.7174 (t80) REVERT: 5 288 PHE cc_start: 0.5938 (m-10) cc_final: 0.5646 (m-80) REVERT: 6 14 ARG cc_start: 0.7545 (mpp80) cc_final: 0.7288 (mtm180) REVERT: 6 134 ASP cc_start: 0.6472 (m-30) cc_final: 0.6039 (m-30) REVERT: 6 136 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: 6 171 MET cc_start: 0.4234 (OUTLIER) cc_final: 0.3749 (mtm) REVERT: 6 253 SER cc_start: 0.7410 (t) cc_final: 0.6970 (p) REVERT: 7 31 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7378 (ttm170) REVERT: 7 33 ARG cc_start: 0.8619 (ttp80) cc_final: 0.8142 (ptm-80) REVERT: 7 38 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6982 (mm) REVERT: 7 60 LYS cc_start: 0.7686 (tptp) cc_final: 0.7187 (ttmm) REVERT: 7 83 GLU cc_start: 0.6133 (mp0) cc_final: 0.5908 (mp0) REVERT: 7 101 MET cc_start: 0.6200 (tpt) cc_final: 0.5851 (tpt) REVERT: 7 129 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7454 (mtmm) REVERT: 7 135 GLU cc_start: 0.7811 (mp0) cc_final: 0.7430 (mp0) REVERT: 7 153 ASN cc_start: 0.7165 (m-40) cc_final: 0.6925 (m-40) REVERT: 7 156 LYS cc_start: 0.7055 (ttpp) cc_final: 0.6727 (ttpp) REVERT: 7 181 ASN cc_start: 0.7400 (p0) cc_final: 0.7063 (p0) REVERT: 7 193 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6353 (tm-30) REVERT: 7 239 GLN cc_start: 0.7429 (mp10) cc_final: 0.7204 (mp10) REVERT: 7 242 MET cc_start: 0.7663 (tpp) cc_final: 0.7381 (tpp) REVERT: 7 255 GLU cc_start: 0.6799 (tp30) cc_final: 0.6472 (tp30) outliers start: 71 outliers final: 42 residues processed: 495 average time/residue: 0.1642 time to fit residues: 113.8077 Evaluate side-chains 492 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 444 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain 1 residue 130 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 210 LEU 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 110 THR Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 261 HIS 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 153 ASN Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 242 MET Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 19 THR 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 194 LEU Chi-restraints excluded: chain 6 residue 79 VAL 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 171 MET Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 58 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU 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: 0.4980 chunk 130 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.0270 chunk 191 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 144 optimal weight: 0.1980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS 4 153 ASN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 200 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.157301 restraints weight = 26872.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.162116 restraints weight = 14359.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165191 restraints weight = 9136.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167591 restraints weight = 6574.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168796 restraints weight = 5039.460| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.9852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17828 Z= 0.141 Angle : 0.751 16.640 24129 Z= 0.370 Chirality : 0.043 0.266 2695 Planarity : 0.009 0.416 3080 Dihedral : 10.361 97.971 2611 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.70 % Favored : 92.70 % Rotamer: Outliers : 3.35 % Allowed : 21.72 % Favored : 74.93 % 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: -0.88 (0.19), residues: 2163 helix: 0.81 (0.16), residues: 1099 sheet: -2.95 (0.41), residues: 154 loop : -1.91 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.001 ARG 6 187 TYR 0.028 0.002 TYR 3 173 PHE 0.022 0.002 PHE 1 206 TRP 0.022 0.001 TRP 4 154 HIS 0.004 0.001 HIS 3 81 Details of bonding type rmsd covalent geometry : bond 0.00323 (17808) covalent geometry : angle 0.75149 (24129) hydrogen bonds : bond 0.03089 ( 697) hydrogen bonds : angle 3.77343 ( 2064) Misc. bond : bond 0.00166 ( 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 506 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 443 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: 1 14 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7239 (ptp90) REVERT: 1 60 LYS cc_start: 0.7364 (tptt) cc_final: 0.7080 (tppt) REVERT: 1 100 GLU cc_start: 0.6200 (mp0) cc_final: 0.5782 (mp0) REVERT: 1 101 MET cc_start: 0.6744 (tpp) cc_final: 0.6444 (tpp) REVERT: 1 130 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7406 (mt) REVERT: 1 132 ILE cc_start: 0.6039 (mp) cc_final: 0.5481 (mt) REVERT: 1 135 GLU cc_start: 0.4103 (tp30) cc_final: 0.3847 (tp30) REVERT: 1 211 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6341 (tp30) REVERT: 1 239 GLN cc_start: 0.7446 (mp10) cc_final: 0.6925 (mp10) REVERT: 1 279 ASP cc_start: 0.6869 (p0) cc_final: 0.6606 (p0) REVERT: 2 62 TYR cc_start: 0.7040 (t80) cc_final: 0.6818 (t80) REVERT: 2 156 LYS cc_start: 0.6631 (tptp) cc_final: 0.6410 (tptp) REVERT: 2 171 MET cc_start: 0.7638 (mtp) cc_final: 0.7308 (mtp) REVERT: 2 182 SER cc_start: 0.7823 (t) cc_final: 0.7329 (m) REVERT: 2 191 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: 2 239 GLN cc_start: 0.7394 (mt0) cc_final: 0.7115 (mt0) REVERT: 2 298 MET cc_start: 0.2379 (ptm) cc_final: 0.1890 (ptp) REVERT: 3 25 ILE cc_start: 0.7904 (tp) cc_final: 0.7703 (tt) REVERT: 3 136 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: 3 167 VAL cc_start: 0.5716 (t) cc_final: 0.4727 (p) REVERT: 3 181 ASN cc_start: 0.7969 (t0) cc_final: 0.7727 (t0) REVERT: 3 195 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7596 (ttm-80) REVERT: 4 41 GLU cc_start: 0.6482 (tp30) cc_final: 0.5868 (tp30) REVERT: 4 132 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7080 (mp) REVERT: 4 157 MET cc_start: 0.7626 (tmm) cc_final: 0.7239 (tmm) REVERT: 4 212 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.5980 (t80) REVERT: 4 255 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7345 (mm-30) REVERT: 4 273 SER cc_start: 0.8265 (t) cc_final: 0.7851 (t) REVERT: 4 274 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7406 (ttmm) REVERT: 4 280 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7255 (mmtt) REVERT: 4 284 TRP cc_start: 0.7464 (t60) cc_final: 0.7089 (t60) REVERT: 5 31 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6677 (ttm-80) REVERT: 5 34 ASP cc_start: 0.7261 (m-30) cc_final: 0.6810 (t0) REVERT: 5 81 HIS cc_start: 0.6645 (t-170) cc_final: 0.5873 (t-90) REVERT: 5 83 GLU cc_start: 0.6417 (mp0) cc_final: 0.5846 (mp0) REVERT: 5 101 MET cc_start: 0.5585 (tmm) cc_final: 0.5004 (tmm) REVERT: 5 134 ASP cc_start: 0.6311 (t0) cc_final: 0.6066 (t0) REVERT: 5 137 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5906 (mp10) REVERT: 5 227 ASN cc_start: 0.6049 (p0) cc_final: 0.5697 (m-40) REVERT: 5 271 PHE cc_start: 0.7820 (t80) cc_final: 0.7303 (t80) REVERT: 5 277 SER cc_start: 0.7399 (p) cc_final: 0.7119 (m) REVERT: 5 288 PHE cc_start: 0.6011 (m-10) cc_final: 0.5718 (m-80) REVERT: 6 14 ARG cc_start: 0.7602 (mpp80) cc_final: 0.7241 (mtm180) REVERT: 6 101 MET cc_start: 0.6156 (tpt) cc_final: 0.5592 (tmm) REVERT: 6 134 ASP cc_start: 0.6428 (m-30) cc_final: 0.6042 (m-30) REVERT: 6 136 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: 6 171 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3799 (mtm) REVERT: 6 195 ARG cc_start: 0.7526 (mmp80) cc_final: 0.7207 (tpp-160) REVERT: 6 253 SER cc_start: 0.7458 (t) cc_final: 0.7018 (p) REVERT: 7 60 LYS cc_start: 0.7653 (tptp) cc_final: 0.7249 (tppt) REVERT: 7 83 GLU cc_start: 0.6231 (mp0) cc_final: 0.5810 (mp0) REVERT: 7 101 MET cc_start: 0.6279 (tpt) cc_final: 0.5943 (tpt) REVERT: 7 129 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7875 (mtmt) REVERT: 7 153 ASN cc_start: 0.7344 (m-40) cc_final: 0.7112 (m-40) REVERT: 7 156 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6849 (ttpp) REVERT: 7 181 ASN cc_start: 0.7378 (p0) cc_final: 0.7097 (p0) REVERT: 7 193 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6433 (tm-30) REVERT: 7 211 GLU cc_start: 0.7320 (tp30) cc_final: 0.7093 (mm-30) REVERT: 7 242 MET cc_start: 0.7699 (tpp) cc_final: 0.7483 (tpp) REVERT: 7 255 GLU cc_start: 0.6827 (tp30) cc_final: 0.6586 (tp30) outliers start: 63 outliers final: 42 residues processed: 470 average time/residue: 0.1659 time to fit residues: 110.4865 Evaluate side-chains 488 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 438 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain 1 residue 130 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 200 ASN Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN 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 59 ILE Chi-restraints excluded: chain 3 residue 136 PHE Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 261 HIS 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 153 ASN Chi-restraints excluded: chain 4 residue 178 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 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 305 ASP 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 171 MET Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU 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: 0.8980 chunk 174 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 28 optimal weight: 0.0170 chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 ASN ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 179 GLN ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** 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** ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 81 HIS ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 314 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.156083 restraints weight = 27035.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160917 restraints weight = 14376.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.164241 restraints weight = 9146.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166129 restraints weight = 6514.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167875 restraints weight = 5162.891| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 1.0374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17828 Z= 0.160 Angle : 0.764 16.856 24129 Z= 0.377 Chirality : 0.043 0.263 2695 Planarity : 0.006 0.136 3080 Dihedral : 10.884 176.639 2611 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.30 % Favored : 92.09 % Rotamer: Outliers : 3.24 % Allowed : 22.41 % Favored : 74.35 % 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: -0.95 (0.19), residues: 2163 helix: 0.74 (0.16), residues: 1099 sheet: -2.93 (0.39), residues: 182 loop : -1.88 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 7 14 TYR 0.027 0.002 TYR 4 173 PHE 0.021 0.002 PHE 3 271 TRP 0.014 0.002 TRP 4 154 HIS 0.006 0.001 HIS 3 138 Details of bonding type rmsd covalent geometry : bond 0.00376 (17808) covalent geometry : angle 0.76403 (24129) hydrogen bonds : bond 0.03172 ( 697) hydrogen bonds : angle 3.85022 ( 2064) Misc. bond : bond 0.00202 ( 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 503 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 442 time to evaluate : 0.600 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: 1 60 LYS cc_start: 0.7475 (tptt) cc_final: 0.7178 (tppt) REVERT: 1 96 GLU cc_start: 0.5770 (mt-10) cc_final: 0.5495 (tt0) REVERT: 1 100 GLU cc_start: 0.6230 (mp0) cc_final: 0.5683 (mp0) REVERT: 1 101 MET cc_start: 0.6895 (tpp) cc_final: 0.6598 (tpp) REVERT: 1 279 ASP cc_start: 0.7055 (p0) cc_final: 0.6830 (p0) REVERT: 2 130 LEU cc_start: 0.7932 (tt) cc_final: 0.7713 (tt) REVERT: 2 157 MET cc_start: 0.6541 (tpp) cc_final: 0.6323 (tpp) REVERT: 2 171 MET cc_start: 0.7687 (mtp) cc_final: 0.7468 (mtp) REVERT: 2 182 SER cc_start: 0.7905 (t) cc_final: 0.7446 (m) REVERT: 2 191 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: 2 239 GLN cc_start: 0.7618 (mt0) cc_final: 0.7333 (mt0) REVERT: 2 298 MET cc_start: 0.2926 (ptm) cc_final: 0.2329 (ptt) REVERT: 3 5 ARG cc_start: 0.6643 (ttm170) cc_final: 0.6243 (ttm170) REVERT: 3 136 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: 3 181 ASN cc_start: 0.8090 (t0) cc_final: 0.7843 (t0) REVERT: 3 195 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7644 (ttm-80) REVERT: 4 27 SER cc_start: 0.8076 (t) cc_final: 0.7759 (t) REVERT: 4 30 ASP cc_start: 0.6419 (m-30) cc_final: 0.6198 (t70) REVERT: 4 33 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6823 (ttp-170) REVERT: 4 41 GLU cc_start: 0.6812 (tp30) cc_final: 0.6042 (tp30) REVERT: 4 135 GLU cc_start: 0.6022 (mt-10) cc_final: 0.5797 (mt-10) REVERT: 4 212 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.5941 (t80) REVERT: 4 255 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7283 (mm-30) REVERT: 4 274 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7532 (ttmm) REVERT: 4 284 TRP cc_start: 0.7589 (t60) cc_final: 0.7157 (t60) REVERT: 5 34 ASP cc_start: 0.7299 (m-30) cc_final: 0.6944 (t0) REVERT: 5 81 HIS cc_start: 0.6606 (t-170) cc_final: 0.5962 (t-170) REVERT: 5 83 GLU cc_start: 0.6250 (mp0) cc_final: 0.6020 (mp0) REVERT: 5 101 MET cc_start: 0.5874 (tmm) cc_final: 0.5171 (tmm) REVERT: 5 134 ASP cc_start: 0.6403 (t0) cc_final: 0.6127 (t0) REVERT: 5 137 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: 5 271 PHE cc_start: 0.7968 (t80) cc_final: 0.7756 (t80) REVERT: 5 288 PHE cc_start: 0.6221 (m-10) cc_final: 0.5898 (m-80) REVERT: 6 14 ARG cc_start: 0.7594 (mpp80) cc_final: 0.7267 (mtm180) REVERT: 6 101 MET cc_start: 0.6109 (tpt) cc_final: 0.5748 (tmm) REVERT: 6 136 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: 6 171 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.4717 (mtm) REVERT: 6 253 SER cc_start: 0.7650 (t) cc_final: 0.7212 (p) REVERT: 6 288 PHE cc_start: 0.5180 (t80) cc_final: 0.4598 (t80) REVERT: 7 14 ARG cc_start: 0.7956 (ptp90) cc_final: 0.7689 (ptp90) REVERT: 7 31 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7358 (ttm170) REVERT: 7 33 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8315 (ttp80) REVERT: 7 60 LYS cc_start: 0.7716 (tptp) cc_final: 0.7297 (tppt) REVERT: 7 101 MET cc_start: 0.6310 (tpt) cc_final: 0.5992 (tpt) REVERT: 7 116 THR cc_start: 0.6491 (m) cc_final: 0.6238 (p) REVERT: 7 129 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7865 (mtmt) REVERT: 7 156 LYS cc_start: 0.7411 (ttpp) cc_final: 0.7113 (ttpp) REVERT: 7 193 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6535 (tm-30) REVERT: 7 255 GLU cc_start: 0.6895 (tp30) cc_final: 0.5977 (tp30) outliers start: 61 outliers final: 40 residues processed: 474 average time/residue: 0.1780 time to fit residues: 117.6098 Evaluate side-chains 475 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 429 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 265 THR 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 129 LYS Chi-restraints excluded: chain 3 residue 136 PHE Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 261 HIS 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 176 VAL Chi-restraints excluded: chain 4 residue 178 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 19 THR Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 194 LEU 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 171 MET Chi-restraints excluded: chain 7 residue 115 LEU 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: 0.4980 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 214 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 ASN ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 200 ASN ** 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 4 179 GLN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 179 GLN ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 81 HIS ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 314 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151962 restraints weight = 26935.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156966 restraints weight = 14072.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.160518 restraints weight = 8892.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.162432 restraints weight = 6344.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164326 restraints weight = 5030.683| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 1.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17828 Z= 0.175 Angle : 0.798 16.761 24129 Z= 0.397 Chirality : 0.044 0.235 2695 Planarity : 0.006 0.128 3080 Dihedral : 10.982 177.446 2611 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.21 % Favored : 92.19 % Rotamer: Outliers : 2.87 % Allowed : 23.58 % 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: -1.06 (0.19), residues: 2163 helix: 0.63 (0.16), residues: 1099 sheet: -2.96 (0.40), residues: 182 loop : -1.91 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 203 TYR 0.029 0.002 TYR 4 173 PHE 0.029 0.002 PHE 3 237 TRP 0.033 0.002 TRP 4 154 HIS 0.006 0.001 HIS 1 261 Details of bonding type rmsd covalent geometry : bond 0.00409 (17808) covalent geometry : angle 0.79820 (24129) hydrogen bonds : bond 0.03363 ( 697) hydrogen bonds : angle 3.97174 ( 2064) Misc. bond : bond 0.00207 ( 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 495 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 441 time to evaluate : 0.642 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: 1 45 MET cc_start: 0.7865 (ttm) cc_final: 0.7492 (ttm) REVERT: 1 60 LYS cc_start: 0.7510 (tptt) cc_final: 0.7220 (tppt) REVERT: 1 96 GLU cc_start: 0.5717 (mt-10) cc_final: 0.5438 (tt0) REVERT: 1 101 MET cc_start: 0.6885 (tpp) cc_final: 0.6542 (tpp) REVERT: 1 182 SER cc_start: 0.8347 (t) cc_final: 0.8052 (m) REVERT: 2 5 ARG cc_start: 0.6244 (ttm170) cc_final: 0.5980 (ttm170) REVERT: 2 171 MET cc_start: 0.7559 (mtp) cc_final: 0.7328 (mtp) REVERT: 2 182 SER cc_start: 0.8157 (t) cc_final: 0.7710 (m) REVERT: 2 191 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: 2 266 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7158 (mm-30) REVERT: 2 298 MET cc_start: 0.3233 (ptm) cc_final: 0.3001 (ptp) REVERT: 3 29 MET cc_start: 0.7822 (tpp) cc_final: 0.7196 (mtm) REVERT: 3 129 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8042 (mttm) REVERT: 3 136 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: 3 181 ASN cc_start: 0.8197 (t0) cc_final: 0.7924 (t0) REVERT: 3 195 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7574 (ttm-80) REVERT: 4 27 SER cc_start: 0.8153 (t) cc_final: 0.7869 (t) REVERT: 4 30 ASP cc_start: 0.6715 (m-30) cc_final: 0.6482 (t70) REVERT: 4 33 ARG cc_start: 0.7349 (ttt-90) cc_final: 0.6984 (ttp-170) REVERT: 4 40 SER cc_start: 0.7965 (t) cc_final: 0.7640 (m) REVERT: 4 41 GLU cc_start: 0.7126 (tp30) cc_final: 0.6488 (tp30) REVERT: 4 135 GLU cc_start: 0.6317 (mt-10) cc_final: 0.6007 (mt-10) REVERT: 4 157 MET cc_start: 0.7709 (tmm) cc_final: 0.7211 (tmm) REVERT: 4 185 HIS cc_start: 0.7523 (t70) cc_final: 0.7068 (t-90) REVERT: 4 195 ARG cc_start: 0.7935 (mmm160) cc_final: 0.7472 (ttm-80) REVERT: 4 212 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.5983 (t80) REVERT: 4 230 LEU cc_start: 0.7151 (tt) cc_final: 0.6783 (tt) REVERT: 4 255 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7463 (mm-30) REVERT: 4 274 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7789 (ttmt) REVERT: 5 81 HIS cc_start: 0.6566 (t-170) cc_final: 0.5912 (t-170) REVERT: 5 83 GLU cc_start: 0.6299 (mp0) cc_final: 0.6086 (mp0) REVERT: 5 134 ASP cc_start: 0.6482 (t0) cc_final: 0.6233 (t0) REVERT: 5 273 SER cc_start: 0.8321 (t) cc_final: 0.7666 (t) REVERT: 5 277 SER cc_start: 0.7683 (p) cc_final: 0.7437 (m) REVERT: 5 284 TRP cc_start: 0.7733 (t60) cc_final: 0.6872 (t60) REVERT: 5 305 ASP cc_start: 0.7297 (m-30) cc_final: 0.6748 (p0) REVERT: 5 309 GLU cc_start: 0.5467 (mm-30) cc_final: 0.4936 (mm-30) REVERT: 6 14 ARG cc_start: 0.7602 (mpp80) cc_final: 0.7299 (mtm180) REVERT: 6 41 GLU cc_start: 0.7332 (tt0) cc_final: 0.7122 (tt0) REVERT: 6 101 MET cc_start: 0.6235 (tpt) cc_final: 0.5955 (tmm) REVERT: 6 136 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: 6 156 LYS cc_start: 0.7331 (ttpt) cc_final: 0.6996 (tttt) REVERT: 6 253 SER cc_start: 0.7731 (t) cc_final: 0.7254 (p) REVERT: 7 53 VAL cc_start: 0.8279 (t) cc_final: 0.8002 (m) REVERT: 7 60 LYS cc_start: 0.7725 (tptp) cc_final: 0.7378 (tppt) REVERT: 7 83 GLU cc_start: 0.6217 (mp0) cc_final: 0.5964 (mp0) REVERT: 7 101 MET cc_start: 0.6471 (tpt) cc_final: 0.6200 (tpt) REVERT: 7 116 THR cc_start: 0.6591 (m) cc_final: 0.6357 (p) REVERT: 7 156 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7132 (ttpp) REVERT: 7 157 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6307 (mtt) REVERT: 7 181 ASN cc_start: 0.7731 (p0) cc_final: 0.7461 (p0) REVERT: 7 193 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6722 (tm-30) REVERT: 7 255 GLU cc_start: 0.7098 (tp30) cc_final: 0.6282 (tp30) outliers start: 54 outliers final: 39 residues processed: 472 average time/residue: 0.1782 time to fit residues: 117.0925 Evaluate side-chains 473 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 428 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 39 GLU Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 129 LYS Chi-restraints excluded: chain 3 residue 136 PHE Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 265 THR Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 45 MET 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 176 VAL Chi-restraints excluded: chain 4 residue 178 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 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 194 LEU 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 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 157 MET 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: 1.9990 chunk 205 optimal weight: 0.0000 chunk 66 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 0.0040 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 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** 2 179 GLN ** 2 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 138 HIS ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS 4 179 GLN 4 227 ASN ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 137 GLN ** 6 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 314 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156701 restraints weight = 27012.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.161356 restraints weight = 14585.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164579 restraints weight = 9400.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166230 restraints weight = 6753.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.168122 restraints weight = 5422.171| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 1.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17828 Z= 0.140 Angle : 0.776 16.287 24129 Z= 0.380 Chirality : 0.043 0.206 2695 Planarity : 0.005 0.111 3080 Dihedral : 10.782 177.640 2611 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.30 % Favored : 92.09 % Rotamer: Outliers : 2.18 % Allowed : 24.75 % Favored : 73.07 % 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: -0.94 (0.19), residues: 2163 helix: 0.76 (0.16), residues: 1099 sheet: -2.85 (0.40), residues: 182 loop : -1.90 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 14 TYR 0.027 0.002 TYR 4 173 PHE 0.025 0.002 PHE 5 271 TRP 0.024 0.001 TRP 4 154 HIS 0.007 0.001 HIS 3 138 Details of bonding type rmsd covalent geometry : bond 0.00321 (17808) covalent geometry : angle 0.77606 (24129) hydrogen bonds : bond 0.03043 ( 697) hydrogen bonds : angle 3.80159 ( 2064) Misc. bond : bond 0.00155 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.27 seconds wall clock time: 53 minutes 11.08 seconds (3191.08 seconds total)