Starting phenix.real_space_refine on Fri Jun 13 07:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d4n_46565/06_2025/9d4n_46565_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d4n_46565/06_2025/9d4n_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_46565/06_2025/9d4n_46565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d4n_46565/06_2025/9d4n_46565.map" model { file = "/net/cci-nas-00/data/ceres_data/9d4n_46565/06_2025/9d4n_46565_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d4n_46565/06_2025/9d4n_46565_neut_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.39, per 1000 atoms: 0.63 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: 3.86 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.25 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: 4.80 Time building geometry restraints manager: 4.61 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=" 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=" P DT X 20 " pdb=" OP2 DT X 20 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" P DT X 19 " pdb=" OP1 DT X 19 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" P DT X 21 " pdb=" OP1 DT X 21 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 20076 1.45 - 2.90: 322 2.90 - 4.34: 76 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 120.20 113.41 6.79 1.50e+00 4.44e-01 2.05e+01 angle pdb=" C3' DT X 19 " pdb=" O3' DT X 19 " pdb=" P DT X 20 " ideal model delta sigma weight residual 120.20 113.86 6.34 1.50e+00 4.44e-01 1.79e+01 angle pdb=" C ARG A 142 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta sigma weight residual 121.54 127.85 -6.31 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C ARG B 142 " pdb=" N GLU B 143 " pdb=" CA GLU B 143 " ideal model delta sigma weight residual 121.54 127.85 -6.31 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C3' DT X 18 " pdb=" O3' DT X 18 " pdb=" P DT X 19 " ideal model delta sigma weight residual 120.20 116.00 4.20 1.50e+00 4.44e-01 7.82e+00 ... (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 - 0.105: 2251 0.105 - 0.211: 55 0.211 - 0.316: 18 0.316 - 0.421: 0 0.421 - 0.527: 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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.93e+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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.93e+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 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.53e+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: 1.360 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: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.640 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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= 0.182 Angle : 0.545 7.240 20510 Z= 0.305 Chirality : 0.050 0.527 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS C 242 PHE 0.007 0.001 PHE D 80 TYR 0.009 0.001 TYR F 210 ARG 0.005 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.21463 ( 736) hydrogen bonds : angle 7.33591 ( 2139) covalent geometry : bond 0.00386 (15161) covalent geometry : angle 0.54509 (20510) *********************** 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 : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.5063 time to fit residues: 177.8657 Evaluate side-chains 82 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 0.2980 chunk 48 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3165 r_free = 0.3165 target = 0.070908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052465 restraints weight = 35918.157| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.80 r_work: 0.2606 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15161 Z= 0.168 Angle : 0.530 11.144 20510 Z= 0.287 Chirality : 0.042 0.140 2328 Planarity : 0.003 0.028 2586 Dihedral : 12.783 153.690 2409 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.38 % Allowed : 3.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1842 helix: 1.38 (0.17), residues: 954 sheet: 1.26 (0.28), residues: 324 loop : -0.19 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 242 PHE 0.009 0.001 PHE F 253 TYR 0.025 0.001 TYR B 41 ARG 0.005 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 736) hydrogen bonds : angle 4.77527 ( 2139) covalent geometry : bond 0.00376 (15161) covalent geometry : angle 0.52992 (20510) *********************** 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 113 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.9001 (mmm) cc_final: 0.8715 (tpp) REVERT: D 62 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8094 (tp30) REVERT: D 301 ARG cc_start: 0.8422 (mmp-170) cc_final: 0.8181 (mmm160) REVERT: E 28 ASN cc_start: 0.8503 (t0) cc_final: 0.8183 (t0) REVERT: E 199 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: F 41 TYR cc_start: 0.8721 (m-80) cc_final: 0.8479 (m-80) outliers start: 6 outliers final: 1 residues processed: 110 average time/residue: 1.4953 time to fit residues: 180.6152 Evaluate side-chains 87 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 15 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.054166 restraints weight = 35714.336| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.80 r_work: 0.2643 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15161 Z= 0.106 Angle : 0.462 7.387 20510 Z= 0.252 Chirality : 0.040 0.134 2328 Planarity : 0.003 0.029 2586 Dihedral : 12.166 148.471 2409 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.57 % Allowed : 5.26 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1842 helix: 1.55 (0.17), residues: 954 sheet: 1.16 (0.28), residues: 330 loop : -0.11 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 242 PHE 0.008 0.001 PHE E 253 TYR 0.014 0.001 TYR E 41 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 736) hydrogen bonds : angle 4.19705 ( 2139) covalent geometry : bond 0.00221 (15161) covalent geometry : angle 0.46203 (20510) *********************** 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 115 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 135 CYS cc_start: 0.8367 (m) cc_final: 0.7993 (m) REVERT: B 21 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9225 (mp0) REVERT: B 229 ARG cc_start: 0.7697 (mpt-90) cc_final: 0.7404 (mpt-90) REVERT: C 23 GLN cc_start: 0.9151 (tp40) cc_final: 0.8903 (mm-40) REVERT: D 301 ARG cc_start: 0.8405 (mmp-170) cc_final: 0.8132 (mmm160) REVERT: E 28 ASN cc_start: 0.8552 (t0) cc_final: 0.8238 (t0) REVERT: E 33 GLN cc_start: 0.8857 (mp10) cc_final: 0.8631 (mp10) outliers start: 9 outliers final: 1 residues processed: 113 average time/residue: 1.3725 time to fit residues: 171.0829 Evaluate side-chains 91 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 31 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.050811 restraints weight = 36537.575| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.81 r_work: 0.2592 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1837 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= 0.241 Angle : 0.520 6.846 20510 Z= 0.281 Chirality : 0.042 0.168 2328 Planarity : 0.003 0.029 2586 Dihedral : 12.205 146.044 2409 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.82 % Allowed : 6.08 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1842 helix: 1.45 (0.17), residues: 954 sheet: 0.86 (0.28), residues: 330 loop : -0.17 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 242 PHE 0.009 0.001 PHE D 80 TYR 0.015 0.002 TYR A 41 ARG 0.003 0.000 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 736) hydrogen bonds : angle 4.34051 ( 2139) covalent geometry : bond 0.00560 (15161) covalent geometry : angle 0.51994 (20510) *********************** 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 109 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8615 (ptt90) REVERT: D 301 ARG cc_start: 0.8539 (mmp-170) cc_final: 0.8270 (mmm160) REVERT: E 28 ASN cc_start: 0.8670 (t0) cc_final: 0.8298 (t0) REVERT: E 33 GLN cc_start: 0.8892 (mp10) cc_final: 0.8667 (mp10) REVERT: E 199 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8720 (mt-10) outliers start: 13 outliers final: 5 residues processed: 107 average time/residue: 1.6224 time to fit residues: 189.7618 Evaluate side-chains 94 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 70 GLU 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 100 optimal weight: 8.9990 chunk 6 optimal weight: 0.0170 chunk 70 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 overall best weight: 1.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3193 r_free = 0.3193 target = 0.071345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.052652 restraints weight = 36388.116| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.76 r_work: 0.2642 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15161 Z= 0.125 Angle : 0.452 7.793 20510 Z= 0.248 Chirality : 0.040 0.156 2328 Planarity : 0.003 0.029 2586 Dihedral : 11.923 144.110 2409 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.95 % Allowed : 6.65 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1842 helix: 1.51 (0.17), residues: 960 sheet: 0.80 (0.28), residues: 324 loop : -0.17 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 242 PHE 0.006 0.001 PHE F 253 TYR 0.015 0.001 TYR A 41 ARG 0.003 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.02800 ( 736) hydrogen bonds : angle 4.06423 ( 2139) covalent geometry : bond 0.00272 (15161) covalent geometry : angle 0.45237 (20510) *********************** 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 110 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 CYS cc_start: 0.8543 (m) cc_final: 0.8259 (m) REVERT: B 143 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: B 210 TYR cc_start: 0.9200 (m-80) cc_final: 0.8987 (m-80) REVERT: D 92 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8654 (ptt90) REVERT: D 301 ARG cc_start: 0.8543 (mmp-170) cc_final: 0.8258 (mmm160) REVERT: E 28 ASN cc_start: 0.8671 (t0) cc_final: 0.8322 (t0) REVERT: E 33 GLN cc_start: 0.8914 (mp10) cc_final: 0.8682 (mp10) REVERT: E 199 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8652 (mt-10) REVERT: E 200 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8190 (pp30) outliers start: 15 outliers final: 5 residues processed: 106 average time/residue: 1.5962 time to fit residues: 185.3065 Evaluate side-chains 97 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 E residue 189 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 315 MET 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 21 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 29 optimal weight: 0.0270 chunk 132 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051451 restraints weight = 36509.604| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.83 r_work: 0.2612 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15161 Z= 0.177 Angle : 0.482 8.247 20510 Z= 0.262 Chirality : 0.041 0.165 2328 Planarity : 0.003 0.029 2586 Dihedral : 11.945 144.787 2409 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.82 % Allowed : 7.79 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1842 helix: 1.51 (0.17), residues: 960 sheet: 0.70 (0.28), residues: 324 loop : -0.20 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 242 PHE 0.007 0.001 PHE B 123 TYR 0.017 0.001 TYR A 41 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 736) hydrogen bonds : angle 4.11570 ( 2139) covalent geometry : bond 0.00403 (15161) covalent geometry : angle 0.48157 (20510) *********************** 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 104 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 92 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8657 (ptt90) REVERT: D 301 ARG cc_start: 0.8568 (mmp-170) cc_final: 0.8272 (mmm160) REVERT: E 28 ASN cc_start: 0.8681 (t0) cc_final: 0.8334 (t0) REVERT: E 199 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: E 200 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8211 (pp30) outliers start: 13 outliers final: 5 residues processed: 100 average time/residue: 1.4412 time to fit residues: 158.5402 Evaluate side-chains 95 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 144 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU 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 158 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN C 310 GLN E 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050313 restraints weight = 36908.540| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.81 r_work: 0.2573 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15161 Z= 0.269 Angle : 0.535 7.802 20510 Z= 0.289 Chirality : 0.043 0.154 2328 Planarity : 0.003 0.035 2586 Dihedral : 12.035 145.811 2409 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.95 % Allowed : 8.11 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1842 helix: 1.41 (0.17), residues: 954 sheet: 0.51 (0.28), residues: 324 loop : -0.29 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 242 PHE 0.009 0.001 PHE D 80 TYR 0.018 0.002 TYR A 185 ARG 0.004 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 736) hydrogen bonds : angle 4.31338 ( 2139) covalent geometry : bond 0.00621 (15161) covalent geometry : angle 0.53497 (20510) *********************** 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 105 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 143 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: B 229 ARG cc_start: 0.8199 (mpt-90) cc_final: 0.7673 (mpt-90) REVERT: D 92 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8678 (ptt90) REVERT: E 28 ASN cc_start: 0.8719 (t0) cc_final: 0.8405 (t0) REVERT: E 199 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: E 200 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8139 (pp30) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 1.8368 time to fit residues: 204.9886 Evaluate side-chains 95 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU 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 67 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 140 optimal weight: 0.0870 chunk 146 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3179 r_free = 0.3179 target = 0.070755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.051838 restraints weight = 36423.093| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.82 r_work: 0.2618 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15161 Z= 0.137 Angle : 0.473 10.306 20510 Z= 0.258 Chirality : 0.040 0.149 2328 Planarity : 0.003 0.031 2586 Dihedral : 11.809 143.239 2409 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.82 % Allowed : 9.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1842 helix: 1.55 (0.17), residues: 960 sheet: 0.60 (0.28), residues: 324 loop : -0.21 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 242 PHE 0.006 0.001 PHE F 253 TYR 0.020 0.001 TYR A 185 ARG 0.003 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.02854 ( 736) hydrogen bonds : angle 4.07635 ( 2139) covalent geometry : bond 0.00304 (15161) covalent geometry : angle 0.47311 (20510) *********************** 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 102 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8610 (ptt90) REVERT: E 28 ASN cc_start: 0.8748 (t0) cc_final: 0.8464 (t0) REVERT: E 199 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: E 200 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8151 (pp30) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 1.7239 time to fit residues: 187.4018 Evaluate side-chains 93 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 GLU 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 49 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 161 optimal weight: 0.0040 chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3219 r_free = 0.3219 target = 0.072741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054119 restraints weight = 35840.434| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.74 r_work: 0.2692 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15161 Z= 0.098 Angle : 0.449 7.357 20510 Z= 0.248 Chirality : 0.039 0.143 2328 Planarity : 0.003 0.031 2586 Dihedral : 11.598 139.485 2409 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.38 % Allowed : 9.57 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1842 helix: 1.63 (0.17), residues: 966 sheet: 0.82 (0.29), residues: 324 loop : -0.18 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 289 PHE 0.005 0.001 PHE A 253 TYR 0.017 0.001 TYR A 41 ARG 0.003 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.02441 ( 736) hydrogen bonds : angle 3.85895 ( 2139) covalent geometry : bond 0.00206 (15161) covalent geometry : angle 0.44893 (20510) *********************** 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 103 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 CYS cc_start: 0.8375 (m) cc_final: 0.8170 (m) REVERT: C 23 GLN cc_start: 0.9117 (tp40) cc_final: 0.8772 (tp40) REVERT: E 28 ASN cc_start: 0.8746 (t0) cc_final: 0.8477 (t0) REVERT: E 77 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8191 (mm-40) REVERT: E 200 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8213 (pp30) outliers start: 6 outliers final: 5 residues processed: 102 average time/residue: 1.4789 time to fit residues: 168.0524 Evaluate side-chains 93 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3180 r_free = 0.3180 target = 0.070783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.051904 restraints weight = 36656.726| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.82 r_work: 0.2615 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15161 Z= 0.174 Angle : 0.498 10.218 20510 Z= 0.269 Chirality : 0.040 0.147 2328 Planarity : 0.003 0.032 2586 Dihedral : 11.734 141.995 2409 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.25 % Allowed : 10.33 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1842 helix: 1.59 (0.17), residues: 966 sheet: 0.77 (0.28), residues: 324 loop : -0.19 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 242 PHE 0.007 0.001 PHE B 123 TYR 0.018 0.002 TYR A 41 ARG 0.002 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 736) hydrogen bonds : angle 4.02255 ( 2139) covalent geometry : bond 0.00399 (15161) covalent geometry : angle 0.49769 (20510) ********************** 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 94 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 ASN cc_start: 0.8751 (t0) cc_final: 0.8484 (t0) REVERT: E 77 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8210 (mm-40) REVERT: E 200 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8207 (pp30) outliers start: 4 outliers final: 4 residues processed: 93 average time/residue: 1.5413 time to fit residues: 157.6415 Evaluate side-chains 92 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 198 VAL 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 75 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 163 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 157 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053684 restraints weight = 36094.328| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.76 r_work: 0.2672 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15161 Z= 0.105 Angle : 0.463 9.786 20510 Z= 0.252 Chirality : 0.039 0.150 2328 Planarity : 0.003 0.031 2586 Dihedral : 11.603 139.976 2409 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.57 % Allowed : 10.14 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1842 helix: 1.68 (0.17), residues: 960 sheet: 0.86 (0.29), residues: 324 loop : -0.21 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 289 PHE 0.005 0.001 PHE F 253 TYR 0.019 0.001 TYR A 41 ARG 0.002 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.02506 ( 736) hydrogen bonds : angle 3.88028 ( 2139) covalent geometry : bond 0.00226 (15161) covalent geometry : angle 0.46303 (20510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8358.52 seconds wall clock time: 151 minutes 31.02 seconds (9091.02 seconds total)