Starting phenix.real_space_refine on Fri Jul 3 15:22:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d4n_46565/07_2026/9d4n_46565_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d4n_46565/07_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_46565/07_2026/9d4n_46565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d4n_46565/07_2026/9d4n_46565.map" model { file = "/net/cci-nas-00/data/ceres_data/9d4n_46565/07_2026/9d4n_46565_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d4n_46565/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.81, per 1000 atoms: 0.19 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: 1.02 Conformation dependent library (CDL) restraints added in 584.5 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: 0.45 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: 1.88 Time building geometry restraints manager: 1.42 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 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=" 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: 0.990 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.690 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- 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= 0.346 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 0.55545 / 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 : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.6155 time to fit residues: 72.3542 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 : 0.421 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.071211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.052902 restraints weight = 36112.245| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.83 r_work: 0.2608 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15161 Z= 0.159 Angle : 0.530 10.508 20510 Z= 0.290 Chirality : 0.042 0.188 2328 Planarity : 0.004 0.042 2586 Dihedral : 13.088 155.755 2409 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.51 % Allowed : 3.74 % Favored : 95.75 % 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: 1.26 (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 0.023 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 0.00343 / 0.16 (15161) covalent geometry : angle 0.53023 / 0.29 (20510) hydrogen bonds : bond 0.04483 / 2.93 ( 736) hydrogen bonds : angle 4.90283 / 3.63 ( 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 111 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.392 Fit side-chains REVERT: A 144 MET cc_start: 0.8975 (mtp) cc_final: 0.8693 (mtm) REVERT: B 21 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9172 (mp0) REVERT: B 112 MET cc_start: 0.8986 (mmm) cc_final: 0.8750 (tpp) REVERT: D 62 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8068 (tp30) REVERT: D 92 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8061 (ptt-90) REVERT: D 301 ARG cc_start: 0.8395 (mmp-170) cc_final: 0.8140 (mmm160) REVERT: E 28 ASN cc_start: 0.8546 (t0) cc_final: 0.8244 (t0) REVERT: E 199 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8532 (mt-10) outliers start: 8 outliers final: 0 residues processed: 108 average time/residue: 0.6052 time to fit residues: 71.5003 Evaluate side-chains 85 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 199 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN C 310 GLN F 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.050961 restraints weight = 36692.971| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.75 r_work: 0.2570 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15161 Z= 0.265 Angle : 0.540 7.980 20510 Z= 0.293 Chirality : 0.043 0.178 2328 Planarity : 0.003 0.029 2586 Dihedral : 12.756 149.307 2409 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.70 % Allowed : 5.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1842 helix: 1.31 (0.17), residues: 948 sheet: 1.05 (0.28), residues: 330 loop : -0.31 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 52 TYR 0.014 0.002 TYR F 153 PHE 0.010 0.001 PHE F 253 HIS 0.006 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 (15161) covalent geometry : angle 0.54046 / 0.29 (20510) hydrogen bonds : bond 0.03990 / 2.56 ( 736) hydrogen bonds : angle 4.63982 / 3.44 ( 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: 11 poor density : 93 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.9020 (mmm) cc_final: 0.8718 (tpp) REVERT: B 210 TYR cc_start: 0.9316 (m-80) cc_final: 0.9101 (m-80) REVERT: D 301 ARG cc_start: 0.8440 (mmp-170) cc_final: 0.8168 (mmm160) REVERT: E 28 ASN cc_start: 0.8532 (t0) cc_final: 0.8235 (t0) REVERT: E 199 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8595 (mt-10) outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 0.5913 time to fit residues: 66.7745 Evaluate side-chains 92 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 45 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.070235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.051719 restraints weight = 36338.610| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.78 r_work: 0.2604 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15161 Z= 0.164 Angle : 0.478 7.054 20510 Z= 0.263 Chirality : 0.041 0.161 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.404 145.945 2409 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.76 % Allowed : 6.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1842 helix: 1.39 (0.17), residues: 948 sheet: 0.87 (0.28), residues: 324 loop : -0.32 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 92 TYR 0.014 0.001 TYR D 41 PHE 0.008 0.001 PHE E 253 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15161) covalent geometry : angle 0.47849 / 0.26 (20510) hydrogen bonds : bond 0.03221 / 2.07 ( 736) hydrogen bonds : angle 4.30318 / 3.19 ( 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 109 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8963 (mmm) cc_final: 0.8699 (tpp) REVERT: B 229 ARG cc_start: 0.8048 (mpt-90) cc_final: 0.7682 (mpt-90) REVERT: C 23 GLN cc_start: 0.9122 (tp40) cc_final: 0.8767 (tp40) REVERT: D 92 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7982 (ptt-90) REVERT: D 301 ARG cc_start: 0.8456 (mmp-170) cc_final: 0.8194 (mmm160) REVERT: E 28 ASN cc_start: 0.8610 (t0) cc_final: 0.8249 (t0) REVERT: E 199 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8582 (mt-10) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.6413 time to fit residues: 75.1189 Evaluate side-chains 99 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 70 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: 3.9990 chunk 79 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 chunk 68 optimal weight: 0.0060 chunk 19 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.0600 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.070755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052316 restraints weight = 36481.513| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.79 r_work: 0.2614 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15161 Z= 0.137 Angle : 0.469 8.518 20510 Z= 0.258 Chirality : 0.040 0.164 2328 Planarity : 0.003 0.029 2586 Dihedral : 12.210 144.161 2409 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.76 % Allowed : 6.59 % Favored : 92.65 % 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: 1.14 (0.20), residues: 1842 helix: 1.43 (0.17), residues: 960 sheet: 0.76 (0.28), residues: 318 loop : -0.31 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.016 0.001 TYR A 41 PHE 0.007 0.001 PHE E 253 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15161) covalent geometry : angle 0.46895 / 0.26 (20510) hydrogen bonds : bond 0.02970 / 1.90 ( 736) hydrogen bonds : angle 4.15442 / 3.08 ( 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 105 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 CYS cc_start: 0.8540 (m) cc_final: 0.8211 (m) REVERT: A 144 MET cc_start: 0.9086 (mtp) cc_final: 0.8804 (mtm) REVERT: B 21 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9209 (mp0) REVERT: B 112 MET cc_start: 0.8961 (mmm) cc_final: 0.8693 (tpp) REVERT: B 210 TYR cc_start: 0.9277 (m-80) cc_final: 0.9045 (m-80) REVERT: C 23 GLN cc_start: 0.9105 (tp40) cc_final: 0.8726 (tp40) REVERT: D 301 ARG cc_start: 0.8483 (mmp-170) cc_final: 0.8210 (mmm160) REVERT: E 28 ASN cc_start: 0.8737 (t0) cc_final: 0.8418 (t0) REVERT: E 199 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8580 (mt-10) outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.6049 time to fit residues: 67.5642 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 70 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: 8.9990 chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 19 optimal weight: 0.0670 chunk 120 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.069630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.051189 restraints weight = 36229.068| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.76 r_work: 0.2586 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.005 0.034 15161 Z= 0.219 Angle : 0.507 7.549 20510 Z= 0.275 Chirality : 0.042 0.163 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.239 143.713 2409 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.70 % Allowed : 7.86 % Favored : 91.44 % 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: 1.08 (0.20), residues: 1842 helix: 1.44 (0.17), residues: 960 sheet: 0.60 (0.28), residues: 318 loop : -0.37 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 52 TYR 0.017 0.002 TYR A 41 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 0.00499 / 0.22 (15161) covalent geometry : angle 0.50666 / 0.28 (20510) hydrogen bonds : bond 0.03238 / 2.07 ( 736) hydrogen bonds : angle 4.23952 / 3.14 ( 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 99 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8849 (pm20) REVERT: B 21 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9169 (mp0) REVERT: B 112 MET cc_start: 0.8974 (mmm) cc_final: 0.8717 (tpp) REVERT: D 92 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8204 (ptt-90) REVERT: D 301 ARG cc_start: 0.8486 (mmp-170) cc_final: 0.8199 (mmm160) REVERT: E 28 ASN cc_start: 0.8765 (t0) cc_final: 0.8454 (t0) REVERT: E 199 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8596 (mt-10) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 0.6345 time to fit residues: 66.8821 Evaluate side-chains 97 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 92 ARG Chi-restraints excluded: chain D residue 144 MET 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 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: 0.0270 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.070471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.052007 restraints weight = 36088.309| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.77 r_work: 0.2608 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15161 Z= 0.148 Angle : 0.462 8.730 20510 Z= 0.254 Chirality : 0.040 0.150 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.154 142.901 2409 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.70 % Allowed : 8.43 % Favored : 90.87 % 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: 1.14 (0.20), residues: 1842 helix: 1.48 (0.17), residues: 960 sheet: 0.67 (0.28), residues: 318 loop : -0.33 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 52 TYR 0.019 0.001 TYR B 41 PHE 0.006 0.001 PHE E 253 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (15161) covalent geometry : angle 0.46248 / 0.25 (20510) hydrogen bonds : bond 0.02941 / 1.89 ( 736) hydrogen bonds : angle 4.10566 / 3.04 ( 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 104 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.9073 (mtp) cc_final: 0.8813 (mtm) REVERT: B 21 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9182 (mp0) REVERT: B 112 MET cc_start: 0.8969 (mmm) cc_final: 0.8716 (tpp) REVERT: B 210 TYR cc_start: 0.9249 (m-80) cc_final: 0.9044 (m-80) REVERT: B 229 ARG cc_start: 0.7941 (mpt-90) cc_final: 0.7371 (mpt-90) REVERT: C 23 GLN cc_start: 0.9105 (tp40) cc_final: 0.8725 (tp40) REVERT: D 301 ARG cc_start: 0.8478 (mmp-170) cc_final: 0.8195 (mmm160) REVERT: E 28 ASN cc_start: 0.8758 (t0) cc_final: 0.8439 (t0) REVERT: E 199 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8555 (mt-10) REVERT: E 200 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8110 (pp30) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 0.5890 time to fit residues: 64.8823 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 : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain D 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 70 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 84 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.069526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051075 restraints weight = 36690.201| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.78 r_work: 0.2585 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15161 Z= 0.219 Angle : 0.508 8.787 20510 Z= 0.277 Chirality : 0.042 0.169 2328 Planarity : 0.003 0.030 2586 Dihedral : 12.157 142.815 2409 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.95 % Allowed : 8.49 % Favored : 90.56 % 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: 1.48 (0.17), residues: 960 sheet: 0.55 (0.28), residues: 318 loop : -0.36 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 52 TYR 0.022 0.002 TYR B 41 PHE 0.008 0.001 PHE B 123 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (15161) covalent geometry : angle 0.50822 / 0.28 (20510) hydrogen bonds : bond 0.03183 / 2.04 ( 736) hydrogen bonds : angle 4.20588 / 3.12 ( 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 104 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9169 (mp0) REVERT: B 112 MET cc_start: 0.8978 (mmm) cc_final: 0.8694 (tpp) REVERT: B 143 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8759 (pm20) REVERT: B 210 TYR cc_start: 0.9298 (m-80) cc_final: 0.9098 (m-80) REVERT: D 92 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8196 (ptt-90) REVERT: D 301 ARG cc_start: 0.8491 (mmp-170) cc_final: 0.8191 (mmm160) REVERT: E 28 ASN cc_start: 0.8756 (t0) cc_final: 0.8424 (t0) REVERT: E 199 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: E 200 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8058 (pp30) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.6144 time to fit residues: 67.6261 Evaluate side-chains 98 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 D residue 144 MET 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 198 VAL 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: 7.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.070567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.052142 restraints weight = 36401.166| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.78 r_work: 0.2611 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15161 Z= 0.139 Angle : 0.476 10.243 20510 Z= 0.260 Chirality : 0.040 0.155 2328 Planarity : 0.003 0.030 2586 Dihedral : 11.994 142.034 2409 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.57 % Allowed : 9.00 % Favored : 90.43 % 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: 1.52 (0.17), residues: 960 sheet: 0.69 (0.28), residues: 318 loop : -0.32 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 52 TYR 0.021 0.001 TYR A 185 PHE 0.005 0.001 PHE A 120 HIS 0.003 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15161) covalent geometry : angle 0.47581 / 0.26 (20510) hydrogen bonds : bond 0.02882 / 1.86 ( 736) hydrogen bonds : angle 4.07005 / 3.02 ( 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 96 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8962 (mmm) cc_final: 0.8699 (tpp) REVERT: B 229 ARG cc_start: 0.7949 (mpt-90) cc_final: 0.7385 (mpt-90) REVERT: C 23 GLN cc_start: 0.9128 (tp40) cc_final: 0.8735 (tp40) REVERT: D 301 ARG cc_start: 0.8489 (mmp-170) cc_final: 0.8182 (mmm160) REVERT: E 28 ASN cc_start: 0.8732 (t0) cc_final: 0.8423 (t0) REVERT: E 199 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: E 200 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8093 (pp30) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.6024 time to fit residues: 62.4086 Evaluate side-chains 93 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 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: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.070761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.052285 restraints weight = 36213.006| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.79 r_work: 0.2614 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.038 15161 Z= 0.140 Angle : 0.466 9.142 20510 Z= 0.257 Chirality : 0.040 0.148 2328 Planarity : 0.003 0.030 2586 Dihedral : 11.926 141.719 2409 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.57 % Allowed : 9.19 % 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: 1.25 (0.20), residues: 1842 helix: 1.58 (0.17), residues: 960 sheet: 0.72 (0.28), residues: 318 loop : -0.30 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 52 TYR 0.023 0.001 TYR F 41 PHE 0.005 0.001 PHE F 253 HIS 0.003 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (15161) covalent geometry : angle 0.46583 / 0.26 (20510) hydrogen bonds : bond 0.02812 / 1.81 ( 736) hydrogen bonds : angle 4.02165 / 2.98 ( 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 100 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8964 (mmm) cc_final: 0.8692 (tpp) REVERT: B 229 ARG cc_start: 0.7908 (mpt-90) cc_final: 0.7691 (mpt-90) REVERT: C 23 GLN cc_start: 0.9118 (tp40) cc_final: 0.8743 (tp40) REVERT: D 92 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8567 (ptt90) REVERT: D 301 ARG cc_start: 0.8498 (mmp-170) cc_final: 0.8187 (mmm160) REVERT: E 28 ASN cc_start: 0.8726 (t0) cc_final: 0.8403 (t0) REVERT: E 200 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8110 (pp30) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.6345 time to fit residues: 69.0507 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 : 0.508 ------------------------------------------------------------------------------- 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 70 GLU 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: 0.3980 chunk 156 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3183 r_free = 0.3183 target = 0.071532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.053113 restraints weight = 36004.950| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.79 r_work: 0.2626 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15161 Z= 0.109 Angle : 0.456 10.564 20510 Z= 0.251 Chirality : 0.040 0.153 2328 Planarity : 0.003 0.030 2586 Dihedral : 11.883 140.568 2409 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.44 % Allowed : 9.63 % Favored : 89.92 % 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: 1.32 (0.20), residues: 1842 helix: 1.61 (0.17), residues: 960 sheet: 0.82 (0.29), residues: 318 loop : -0.28 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 92 TYR 0.021 0.001 TYR F 41 PHE 0.005 0.001 PHE A 120 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (15161) covalent geometry : angle 0.45552 / 0.25 (20510) hydrogen bonds : bond 0.02633 / 1.71 ( 736) hydrogen bonds : angle 3.92923 / 2.91 ( 2139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.65 seconds wall clock time: 57 minutes 39.19 seconds (3459.19 seconds total)