Starting phenix.real_space_refine on Thu Aug 6 10:21:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d4n_46565/08_2026/9d4n_46565_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d4n_46565/08_2026/9d4n_46565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d4n_46565/08_2026/9d4n_46565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d4n_46565/08_2026/9d4n_46565.map" model { file = "/net/cci-nas-00/data/ceres_data/9d4n_46565/08_2026/9d4n_46565_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d4n_46565/08_2026/9d4n_46565_neut_trim.cif" } resolution = 2.9 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= 0.004 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 9192 2.51 5 N 2622 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14946 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.56, per 1000 atoms: 0.24 Number of scatterers: 14946 At special positions: 0 Unit cell: (114.54, 114.54, 157.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 36 15.00 Mg 6 11.99 O 3012 8.00 N 2622 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 689.9 milliseconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 18 sheets defined 52.5% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 4.008A pdb=" N LEU A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 190 through 207 removed outlier: 4.344A pdb=" N GLY A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.773A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 254 removed outlier: 4.169A pdb=" N GLU A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.679A pdb=" N LEU A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.630A pdb=" N GLN B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 25' Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.513A pdb=" N LYS B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.504A pdb=" N ILE B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.567A pdb=" N VAL B 136 " --> pdb=" O HIS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 190 through 206 removed outlier: 4.041A pdb=" N GLY B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.842A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 254 removed outlier: 4.349A pdb=" N SER B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.697A pdb=" N LEU B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 26 removed outlier: 4.238A pdb=" N ASN C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.566A pdb=" N LYS C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 50 through 57 removed outlier: 3.618A pdb=" N LYS C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 57 " --> pdb=" O HIS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 200 through 206 removed outlier: 4.136A pdb=" N GLU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 removed outlier: 3.821A pdb=" N VAL C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 254 removed outlier: 4.153A pdb=" N SER C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.673A pdb=" N LEU C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.060A pdb=" N ASN D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 38 Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 50 through 57 removed outlier: 3.564A pdb=" N ILE D 57 " --> pdb=" O HIS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.506A pdb=" N GLU D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.518A pdb=" N VAL D 136 " --> pdb=" O HIS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.544A pdb=" N ASN D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 200 through 207 removed outlier: 3.888A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 226 removed outlier: 4.680A pdb=" N PHE D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 254 Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.710A pdb=" N LEU D 287 " --> pdb=" O GLY D 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.721A pdb=" N GLN E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN E 24 " --> pdb=" O ASP E 20 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 25' Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.892A pdb=" N GLN E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 50 through 57 removed outlier: 3.793A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 57 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.505A pdb=" N ILE E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'E' and resid 100 through 108 Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.503A pdb=" N VAL E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 172 Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 200 through 206 removed outlier: 4.191A pdb=" N GLU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 removed outlier: 3.784A pdb=" N VAL E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 254 removed outlier: 4.253A pdb=" N SER E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 removed outlier: 3.673A pdb=" N LEU E 287 " --> pdb=" O GLY E 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 4.134A pdb=" N ASN F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 25' Processing helix chain 'F' and resid 28 through 38 Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 61 through 76 removed outlier: 3.620A pdb=" N ILE F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 91 Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 126 through 139 removed outlier: 4.013A pdb=" N GLN F 139 " --> pdb=" O CYS F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'F' and resid 175 through 182 Processing helix chain 'F' and resid 190 through 200 Processing helix chain 'F' and resid 200 through 206 removed outlier: 3.913A pdb=" N GLU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 226 removed outlier: 3.865A pdb=" N VAL F 224 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 254 removed outlier: 3.529A pdb=" N GLU F 252 " --> pdb=" O ARG F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 removed outlier: 3.665A pdb=" N LEU F 287 " --> pdb=" O GLY F 283 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.429A pdb=" N ARG A 294 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 117 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN A 261 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 119 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 211 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE A 258 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 213 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR A 260 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 215 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS A 150 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 212 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264 removed outlier: 3.730A pdb=" N LYS A 280 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.429A pdb=" N ARG B 294 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR B 117 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN B 261 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 119 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 211 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE B 258 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 213 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR B 260 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 215 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS B 150 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 212 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 264 removed outlier: 3.847A pdb=" N LYS B 280 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 331 removed outlier: 6.444A pdb=" N ARG C 294 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR C 117 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN C 261 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 119 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG C 211 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE C 258 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 213 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR C 260 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 215 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS C 150 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 212 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 263 through 264 removed outlier: 3.732A pdb=" N LYS C 280 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 331 removed outlier: 6.443A pdb=" N ARG D 294 " --> pdb=" O GLN D 310 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 117 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN D 261 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 119 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 211 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE D 258 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 213 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR D 260 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL D 215 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS D 150 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 212 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 264 removed outlier: 3.849A pdb=" N LYS D 280 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AB5, first strand: chain 'E' and resid 328 through 331 removed outlier: 6.455A pdb=" N ARG E 294 " --> pdb=" O GLN E 310 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR E 117 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN E 261 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 119 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS E 150 " --> pdb=" O TYR E 210 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 212 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 263 through 264 removed outlier: 3.772A pdb=" N LYS E 280 " --> pdb=" O GLN E 264 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AB8, first strand: chain 'F' and resid 183 through 187 removed outlier: 5.276A pdb=" N LYS F 150 " --> pdb=" O TYR F 210 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU F 212 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG F 211 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE F 258 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 213 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR F 260 " --> pdb=" O ILE F 213 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL F 215 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR F 117 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASN F 261 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL F 119 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE F 116 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE F 295 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU F 118 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU F 297 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE F 120 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LYS F 299 " --> pdb=" O PHE F 120 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG F 294 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 263 through 264 removed outlier: 3.834A pdb=" N LYS F 280 " --> pdb=" O GLN F 264 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2139 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: 2.92 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4361 1.33 - 1.45: 2083 1.45 - 1.57: 8532 1.57 - 1.69: 65 1.69 - 1.81: 120 Bond restraints: 15161 Sorted by residual: bond pdb=" C3' DT X 6 " pdb=" C2' DT X 6 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.21e+00 bond pdb=" C3' DT X 10 " pdb=" C2' DT X 10 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.35e+00 bond pdb=" P DT X 18 " pdb=" OP2 DT X 18 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" P DT X 19 " pdb=" OP2 DT X 19 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C3' DT X 11 " pdb=" O3' DT X 11 " ideal model delta sigma weight residual 1.435 1.409 0.026 1.30e-02 5.92e+03 3.89e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 20037 1.45 - 2.90: 360 2.90 - 4.34: 77 4.34 - 5.79: 6 5.79 - 7.24: 30 Bond angle restraints: 20510 Sorted by residual: angle pdb=" C3' DT X 17 " pdb=" O3' DT X 17 " pdb=" P DT X 18 " ideal model delta sigma weight residual 119.70 113.41 6.29 1.20e+00 6.94e-01 2.75e+01 angle pdb=" C3' DT X 19 " pdb=" O3' DT X 19 " pdb=" P DT X 20 " ideal model delta sigma weight residual 119.70 113.86 5.84 1.20e+00 6.94e-01 2.37e+01 angle pdb=" N3 DT X 16 " pdb=" C4 DT X 16 " pdb=" O4 DT X 16 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT X 12 " pdb=" C4 DT X 12 " pdb=" O4 DT X 12 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 20505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 8941 32.80 - 65.61: 349 65.61 - 98.41: 30 98.41 - 131.21: 0 131.21 - 164.02: 1 Dihedral angle restraints: 9321 sinusoidal: 4041 harmonic: 5280 Sorted by residual: dihedral pdb=" C4' DT X 20 " pdb=" C3' DT X 20 " pdb=" O3' DT X 20 " pdb=" P DT X 21 " ideal model delta sinusoidal sigma weight residual 220.00 55.98 164.02 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CG ARG A 294 " pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " pdb=" CZ ARG A 294 " ideal model delta sinusoidal sigma weight residual -180.00 -135.06 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 294 " pdb=" CD ARG B 294 " pdb=" NE ARG B 294 " pdb=" CZ ARG B 294 " ideal model delta sinusoidal sigma weight residual -180.00 -135.22 -44.78 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 9318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2262 0.107 - 0.215: 44 0.215 - 0.322: 18 0.322 - 0.429: 0 0.429 - 0.537: 4 Chirality restraints: 2328 Sorted by residual: chirality pdb=" P DT X 19 " pdb=" OP1 DT X 19 " pdb=" OP2 DT X 19 " pdb=" O5' DT X 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" P DT X 21 " pdb=" OP1 DT X 21 " pdb=" OP2 DT X 21 " pdb=" O5' DT X 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" P DT X 18 " pdb=" OP1 DT X 18 " pdb=" OP2 DT X 18 " pdb=" O5' DT X 18 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.79e+00 ... (remaining 2325 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 312 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.63e+00 pdb=" N PRO B 313 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 312 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 313 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 313 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 313 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 142 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" C ARG B 142 " 0.018 2.00e-02 2.50e+03 pdb=" O ARG B 142 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU B 143 " -0.006 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 119 2.48 - 3.09: 11632 3.09 - 3.69: 22682 3.69 - 4.30: 36636 4.30 - 4.90: 59450 Nonbonded interactions: 130519 Sorted by model distance: nonbonded pdb=" O2B ATP D 401 " pdb="MG MG D 402 " model vdw 1.880 2.170 nonbonded pdb=" O2B ATP E 401 " pdb="MG MG E 402 " model vdw 1.887 2.170 nonbonded pdb=" OE1 GLU D 157 " pdb="MG MG D 402 " model vdw 1.893 2.170 nonbonded pdb=" O2B ATP C 401 " pdb="MG MG C 402 " model vdw 1.901 2.170 nonbonded pdb=" O2B ATP F 401 " pdb="MG MG F 402 " model vdw 1.906 2.170 ... (remaining 130514 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.640 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 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 : 0.004 0.041 15161 Z= 0.213 Angle : 0.555 7.240 20510 Z= 0.347 Chirality : 0.051 0.537 2328 Planarity : 0.003 0.032 2586 Dihedral : 15.813 164.017 5949 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.35 (0.20), residues: 1842 helix: 1.39 (0.18), residues: 900 sheet: 1.43 (0.28), residues: 330 loop : -0.04 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 124 TYR 0.009 0.001 TYR F 210 PHE 0.007 0.001 PHE D 80 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (15161) covalent geometry : angle 0.55493 / 0.35 (20510) hydrogen bonds : bond 0.21463 / 14.13 ( 736) hydrogen bonds : angle 7.33591 / 5.36 ( 2139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.7651 time to fit residues: 89.6066 Evaluate side-chains 81 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN D 23 GLN D 262 GLN E 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052791 restraints weight = 36113.229| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.83 r_work: 0.2607 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15161 Z= 0.161 Angle : 0.532 10.599 20510 Z= 0.290 Chirality : 0.042 0.205 2328 Planarity : 0.004 0.044 2586 Dihedral : 13.143 155.134 2409 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.51 % Allowed : 3.68 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.26 (0.20), residues: 1842 helix: 1.35 (0.17), residues: 954 sheet: 1.23 (0.28), residues: 324 loop : -0.17 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 124 TYR 0.022 0.001 TYR B 41 PHE 0.008 0.001 PHE F 253 HIS 0.003 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (15161) covalent geometry : angle 0.53211 / 0.29 (20510) hydrogen bonds : bond 0.04559 / 2.97 ( 736) hydrogen bonds : angle 4.92860 / 3.65 ( 2139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8974 (mtp) cc_final: 0.8691 (mtm) REVERT: B 21 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9172 (mp0) REVERT: B 112 MET cc_start: 0.8990 (mmm) cc_final: 0.8753 (tpp) REVERT: D 92 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8041 (ptt-90) REVERT: D 301 ARG cc_start: 0.8393 (mmp-170) cc_final: 0.8138 (mmm160) REVERT: E 28 ASN cc_start: 0.8547 (t0) cc_final: 0.8247 (t0) REVERT: E 199 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8541 (mt-10) outliers start: 8 outliers final: 1 residues processed: 107 average time/residue: 0.5769 time to fit residues: 67.7080 Evaluate side-chains 86 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 70 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 116 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN C 262 GLN C 310 GLN F 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.050991 restraints weight = 36627.935| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.80 r_work: 0.2568 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15161 Z= 0.248 Angle : 0.533 7.626 20510 Z= 0.289 Chirality : 0.043 0.190 2328 Planarity : 0.003 0.029 2586 Dihedral : 12.738 148.390 2409 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.57 % Allowed : 5.20 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.09 (0.20), residues: 1842 helix: 1.34 (0.17), residues: 948 sheet: 0.93 (0.28), residues: 324 loop : -0.32 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 92 TYR 0.014 0.002 TYR F 153 PHE 0.011 0.001 PHE F 253 HIS 0.006 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (15161) covalent geometry : angle 0.53287 / 0.29 (20510) hydrogen bonds : bond 0.03885 / 2.49 ( 736) hydrogen bonds : angle 4.60551 / 3.41 ( 2139) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8994 (mmm) cc_final: 0.8688 (tpp) REVERT: B 200 GLN cc_start: 0.9023 (pt0) cc_final: 0.8468 (tm-30) REVERT: B 210 TYR cc_start: 0.9313 (m-80) cc_final: 0.9083 (m-80) REVERT: D 301 ARG cc_start: 0.8433 (mmp-170) cc_final: 0.8161 (mmm160) REVERT: E 28 ASN cc_start: 0.8547 (t0) cc_final: 0.8234 (t0) REVERT: E 33 GLN cc_start: 0.8877 (mp10) cc_final: 0.8636 (mp10) REVERT: E 199 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: E 327 LYS cc_start: 0.9188 (mttt) cc_final: 0.8985 (mtmt) outliers start: 9 outliers final: 4 residues processed: 102 average time/residue: 0.5923 time to fit residues: 66.3248 Evaluate side-chains 95 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 45 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051113 restraints weight = 36503.191| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.77 r_work: 0.2585 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15161 Z= 0.210 Angle : 0.502 7.019 20510 Z= 0.274 Chirality : 0.042 0.183 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.446 144.829 2409 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.82 % Allowed : 6.21 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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 (0.20), residues: 1842 helix: 1.36 (0.17), residues: 948 sheet: 0.78 (0.28), residues: 324 loop : -0.35 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 52 TYR 0.014 0.002 TYR E 41 PHE 0.008 0.001 PHE E 253 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (15161) covalent geometry : angle 0.50199 / 0.27 (20510) hydrogen bonds : bond 0.03392 / 2.17 ( 736) hydrogen bonds : angle 4.37197 / 3.24 ( 2139) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9194 (mp0) REVERT: B 112 MET cc_start: 0.8979 (mmm) cc_final: 0.8685 (tpp) REVERT: B 200 GLN cc_start: 0.8994 (pt0) cc_final: 0.8405 (tm-30) REVERT: B 210 TYR cc_start: 0.9341 (m-80) cc_final: 0.9130 (m-80) REVERT: B 229 ARG cc_start: 0.8081 (mpt-90) cc_final: 0.7719 (mpt-90) REVERT: C 23 GLN cc_start: 0.9123 (tp40) cc_final: 0.8772 (tp40) REVERT: D 92 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8013 (ptt-90) REVERT: D 301 ARG cc_start: 0.8462 (mmp-170) cc_final: 0.8203 (mmm160) REVERT: E 28 ASN cc_start: 0.8622 (t0) cc_final: 0.8244 (t0) REVERT: E 199 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: E 327 LYS cc_start: 0.9202 (mttt) cc_final: 0.8995 (mtmt) outliers start: 13 outliers final: 5 residues processed: 109 average time/residue: 0.6484 time to fit residues: 77.6486 Evaluate side-chains 100 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 227 CYS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN B 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051134 restraints weight = 36753.519| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.78 r_work: 0.2586 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15161 Z= 0.200 Angle : 0.500 8.464 20510 Z= 0.273 Chirality : 0.041 0.177 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.334 143.808 2409 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.82 % Allowed : 7.03 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.05 (0.20), residues: 1842 helix: 1.39 (0.17), residues: 948 sheet: 0.69 (0.28), residues: 324 loop : -0.35 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 52 TYR 0.015 0.002 TYR A 41 PHE 0.008 0.001 PHE D 80 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (15161) covalent geometry : angle 0.49973 / 0.27 (20510) hydrogen bonds : bond 0.03284 / 2.10 ( 736) hydrogen bonds : angle 4.30179 / 3.19 ( 2139) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9194 (mp0) REVERT: B 112 MET cc_start: 0.8985 (mmm) cc_final: 0.8736 (tpp) REVERT: B 200 GLN cc_start: 0.8981 (pt0) cc_final: 0.8400 (tm-30) REVERT: B 210 TYR cc_start: 0.9339 (m-80) cc_final: 0.9095 (m-80) REVERT: C 23 GLN cc_start: 0.9109 (tp40) cc_final: 0.8742 (tp-100) REVERT: D 301 ARG cc_start: 0.8469 (mmp-170) cc_final: 0.8202 (mmm160) REVERT: E 28 ASN cc_start: 0.8718 (t0) cc_final: 0.8418 (t0) REVERT: E 199 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: E 327 LYS cc_start: 0.9208 (mttt) cc_final: 0.9008 (mtmt) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 0.6946 time to fit residues: 77.3206 Evaluate side-chains 94 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.051597 restraints weight = 36083.888| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.76 r_work: 0.2599 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15161 Z= 0.166 Angle : 0.486 8.559 20510 Z= 0.268 Chirality : 0.041 0.171 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.246 142.943 2409 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.76 % Allowed : 7.92 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.10 (0.20), residues: 1842 helix: 1.43 (0.17), residues: 948 sheet: 0.70 (0.28), residues: 324 loop : -0.32 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 142 TYR 0.016 0.001 TYR A 41 PHE 0.006 0.001 PHE E 253 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (15161) covalent geometry : angle 0.48620 / 0.27 (20510) hydrogen bonds : bond 0.03102 / 2.00 ( 736) hydrogen bonds : angle 4.22418 / 3.13 ( 2139) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8845 (pm20) REVERT: B 21 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9189 (mp0) REVERT: B 112 MET cc_start: 0.8972 (mmm) cc_final: 0.8720 (tpp) REVERT: B 200 GLN cc_start: 0.8964 (pt0) cc_final: 0.8383 (tm-30) REVERT: B 210 TYR cc_start: 0.9308 (m-80) cc_final: 0.9066 (m-80) REVERT: C 23 GLN cc_start: 0.9101 (tp40) cc_final: 0.8711 (tp40) REVERT: D 301 ARG cc_start: 0.8475 (mmp-170) cc_final: 0.8197 (mmm160) REVERT: E 28 ASN cc_start: 0.8737 (t0) cc_final: 0.8435 (t0) REVERT: E 199 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: E 327 LYS cc_start: 0.9211 (mttt) cc_final: 0.9000 (mtmt) outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 0.6812 time to fit residues: 76.7332 Evaluate side-chains 99 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 227 CYS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 153 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.050841 restraints weight = 36407.806| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.76 r_work: 0.2576 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15161 Z= 0.228 Angle : 0.507 8.404 20510 Z= 0.277 Chirality : 0.042 0.184 2328 Planarity : 0.003 0.031 2586 Dihedral : 12.234 142.774 2409 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.89 % Allowed : 8.37 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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 (0.20), residues: 1842 helix: 1.44 (0.17), residues: 948 sheet: 0.60 (0.28), residues: 324 loop : -0.36 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 52 TYR 0.019 0.002 TYR A 185 PHE 0.008 0.001 PHE D 80 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (15161) covalent geometry : angle 0.50670 / 0.28 (20510) hydrogen bonds : bond 0.03298 / 2.11 ( 736) hydrogen bonds : angle 4.28778 / 3.18 ( 2139) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9170 (mp0) REVERT: B 23 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8525 (mm-40) REVERT: B 112 MET cc_start: 0.8975 (mmm) cc_final: 0.8689 (tpp) REVERT: B 200 GLN cc_start: 0.8971 (pt0) cc_final: 0.8392 (tm-30) REVERT: B 210 TYR cc_start: 0.9340 (m-80) cc_final: 0.9132 (m-80) REVERT: B 229 ARG cc_start: 0.7997 (mpt-90) cc_final: 0.7531 (mpt-90) REVERT: D 92 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8210 (ptt-90) REVERT: D 301 ARG cc_start: 0.8480 (mmp-170) cc_final: 0.8182 (mmm160) REVERT: E 28 ASN cc_start: 0.8757 (t0) cc_final: 0.8426 (t0) REVERT: E 199 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8596 (mt-10) outliers start: 14 outliers final: 6 residues processed: 104 average time/residue: 0.6525 time to fit residues: 74.0385 Evaluate side-chains 96 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 227 CYS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.053291 restraints weight = 36132.434| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.79 r_work: 0.2637 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15161 Z= 0.100 Angle : 0.468 9.529 20510 Z= 0.258 Chirality : 0.040 0.189 2328 Planarity : 0.003 0.030 2586 Dihedral : 11.971 141.077 2409 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.70 % Allowed : 9.13 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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 (0.20), residues: 1842 helix: 1.50 (0.17), residues: 960 sheet: 0.64 (0.29), residues: 324 loop : -0.20 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 92 TYR 0.018 0.001 TYR A 185 PHE 0.006 0.001 PHE A 120 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (15161) covalent geometry : angle 0.46820 / 0.26 (20510) hydrogen bonds : bond 0.02665 / 1.73 ( 736) hydrogen bonds : angle 3.99410 / 2.96 ( 2139) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 CYS cc_start: 0.8440 (m) cc_final: 0.8144 (m) REVERT: A 144 MET cc_start: 0.9102 (mtp) cc_final: 0.8776 (mtm) REVERT: B 21 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9155 (mp0) REVERT: B 112 MET cc_start: 0.8936 (mmm) cc_final: 0.8708 (tpp) REVERT: B 143 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8716 (pp20) REVERT: B 144 MET cc_start: 0.9187 (mtp) cc_final: 0.8872 (ttm) REVERT: B 200 GLN cc_start: 0.8936 (pt0) cc_final: 0.8291 (tm-30) REVERT: B 210 TYR cc_start: 0.9131 (m-80) cc_final: 0.8930 (m-80) REVERT: B 229 ARG cc_start: 0.7908 (mpt-90) cc_final: 0.7543 (mpt-90) REVERT: C 23 GLN cc_start: 0.9116 (tp40) cc_final: 0.8734 (tp40) REVERT: D 92 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8585 (ptt90) REVERT: D 301 ARG cc_start: 0.8457 (mmp-170) cc_final: 0.8165 (mmm160) REVERT: E 28 ASN cc_start: 0.8751 (t0) cc_final: 0.8434 (t0) REVERT: E 200 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8125 (pp30) outliers start: 11 outliers final: 4 residues processed: 107 average time/residue: 0.5899 time to fit residues: 69.4924 Evaluate side-chains 96 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 34 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.051581 restraints weight = 36659.577| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.78 r_work: 0.2593 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15161 Z= 0.193 Angle : 0.491 8.381 20510 Z= 0.268 Chirality : 0.041 0.181 2328 Planarity : 0.003 0.031 2586 Dihedral : 11.989 142.021 2409 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.44 % Allowed : 9.32 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.19 (0.20), residues: 1842 helix: 1.53 (0.17), residues: 960 sheet: 0.57 (0.28), residues: 324 loop : -0.25 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 211 TYR 0.021 0.002 TYR F 41 PHE 0.007 0.001 PHE B 123 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (15161) covalent geometry : angle 0.49062 / 0.27 (20510) hydrogen bonds : bond 0.03026 / 1.94 ( 736) hydrogen bonds : angle 4.12653 / 3.06 ( 2139) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9165 (mp0) REVERT: B 23 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8544 (mm-40) REVERT: B 112 MET cc_start: 0.8973 (mmm) cc_final: 0.8699 (tpp) REVERT: B 200 GLN cc_start: 0.8928 (pt0) cc_final: 0.8331 (tm-30) REVERT: B 210 TYR cc_start: 0.9277 (m-80) cc_final: 0.9053 (m-80) REVERT: C 23 GLN cc_start: 0.9094 (tp40) cc_final: 0.8696 (tp40) REVERT: D 92 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8217 (ptt-90) REVERT: D 301 ARG cc_start: 0.8486 (mmp-170) cc_final: 0.8179 (mmm160) REVERT: E 28 ASN cc_start: 0.8745 (t0) cc_final: 0.8415 (t0) REVERT: E 200 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8095 (pp30) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 0.6236 time to fit residues: 66.1877 Evaluate side-chains 94 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 23 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.051451 restraints weight = 36456.970| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.77 r_work: 0.2590 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15161 Z= 0.190 Angle : 0.503 10.265 20510 Z= 0.274 Chirality : 0.041 0.175 2328 Planarity : 0.003 0.032 2586 Dihedral : 12.006 141.930 2409 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.44 % Allowed : 9.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.17 (0.20), residues: 1842 helix: 1.52 (0.17), residues: 960 sheet: 0.53 (0.28), residues: 324 loop : -0.25 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.021 0.002 TYR A 185 PHE 0.007 0.001 PHE D 80 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (15161) covalent geometry : angle 0.50277 / 0.27 (20510) hydrogen bonds : bond 0.03065 / 1.97 ( 736) hydrogen bonds : angle 4.14819 / 3.08 ( 2139) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9146 (mp0) REVERT: B 23 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8558 (mm-40) REVERT: B 112 MET cc_start: 0.8998 (mmm) cc_final: 0.8700 (tpp) REVERT: B 143 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8721 (pm20) REVERT: B 200 GLN cc_start: 0.8952 (pt0) cc_final: 0.8326 (tm-30) REVERT: B 210 TYR cc_start: 0.9274 (m-80) cc_final: 0.9047 (m-80) REVERT: D 92 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8218 (ptt-90) REVERT: E 28 ASN cc_start: 0.8733 (t0) cc_final: 0.8429 (t0) REVERT: E 200 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8094 (pp30) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 0.6611 time to fit residues: 70.3621 Evaluate side-chains 95 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 56 optimal weight: 0.0980 chunk 156 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 0.0040 chunk 170 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.053432 restraints weight = 35936.919| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.81 r_work: 0.2632 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15161 Z= 0.100 Angle : 0.466 8.572 20510 Z= 0.257 Chirality : 0.040 0.149 2328 Planarity : 0.003 0.031 2586 Dihedral : 11.892 140.204 2409 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.51 % Allowed : 9.82 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 1.27 (0.20), residues: 1842 helix: 1.55 (0.17), residues: 960 sheet: 0.74 (0.29), residues: 324 loop : -0.24 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.022 0.001 TYR F 41 PHE 0.006 0.001 PHE A 120 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (15161) covalent geometry : angle 0.46646 / 0.26 (20510) hydrogen bonds : bond 0.02608 / 1.69 ( 736) hydrogen bonds : angle 3.93203 / 2.92 ( 2139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3301.58 seconds wall clock time: 57 minutes 27.44 seconds (3447.44 seconds total)