Starting phenix.real_space_refine on Fri Jul 3 03:25:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1h_51766/07_2026/9h1h_51766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1h_51766/07_2026/9h1h_51766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h1h_51766/07_2026/9h1h_51766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1h_51766/07_2026/9h1h_51766.map" model { file = "/net/cci-nas-00/data/ceres_data/9h1h_51766/07_2026/9h1h_51766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1h_51766/07_2026/9h1h_51766.cif" } resolution = 3.06 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= -0.000 sd= 1.000 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 Ca 2 9.91 5 P 74 5.49 5 S 54 5.16 5 C 7228 2.51 5 N 2007 2.21 5 O 2263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 11628 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 104} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2108 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 6, 'TRANS': 279} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'HIS:plan': 4, 'GLU:plan': 9, 'TYR:plan': 2, 'PHE:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 192 Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2067 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 6, 'TRANS': 280} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 14, 'ASN:plan1': 9, 'TYR:plan': 3, 'PHE:plan': 7, 'GLN:plan1': 2, 'HIS:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 220 Chain: "D" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 104} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2108 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 6, 'TRANS': 279} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'HIS:plan': 4, 'GLU:plan': 9, 'TYR:plan': 2, 'PHE:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 192 Chain: "F" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2067 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 6, 'TRANS': 280} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 14, 'ASN:plan1': 9, 'TYR:plan': 3, 'PHE:plan': 7, 'GLN:plan1': 2, 'HIS:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 220 Chain: "G" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 523 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 537 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "J" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "K" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 3.01, per 1000 atoms: 0.26 Number of scatterers: 11628 At special positions: 0 Unit cell: (97.9, 166.1, 90.2, 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) Ca 2 19.99 S 54 16.00 P 74 15.00 O 2263 8.00 N 2007 7.00 C 7228 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: 0.99 Conformation dependent library (CDL) restraints added in 536.8 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 51.2% alpha, 15.0% beta 33 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 35 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'B' and resid 52 through 61 Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.581A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 124 Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 171 through 195 Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.520A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 4.080A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.531A pdb=" N ILE B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 262 through 279 removed outlier: 3.538A pdb=" N LYS B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.551A pdb=" N ARG C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 123 Processing helix chain 'C' and resid 126 through 137 removed outlier: 3.639A pdb=" N TYR C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.693A pdb=" N GLY C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.546A pdb=" N ALA C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 195 removed outlier: 3.618A pdb=" N SER C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 233 removed outlier: 4.000A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 removed outlier: 3.859A pdb=" N PHE C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 261 through 278 Processing helix chain 'D' and resid 18 through 35 removed outlier: 3.630A pdb=" N TYR D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'E' and resid 52 through 61 Processing helix chain 'E' and resid 87 through 96 removed outlier: 3.630A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 124 Processing helix chain 'E' and resid 126 through 139 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 171 through 195 Processing helix chain 'E' and resid 212 through 220 Processing helix chain 'E' and resid 222 through 233 removed outlier: 4.112A pdb=" N ILE E 226 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 246 removed outlier: 3.525A pdb=" N ILE E 241 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 262 through 279 removed outlier: 3.517A pdb=" N LYS E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 272 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 89 through 96 removed outlier: 4.028A pdb=" N ALA F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 123 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.582A pdb=" N TYR F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 162 removed outlier: 3.647A pdb=" N GLY F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.535A pdb=" N ALA F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 195 removed outlier: 4.062A pdb=" N MET F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 220 removed outlier: 3.643A pdb=" N GLU F 220 " --> pdb=" O SER F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 4.299A pdb=" N ILE F 226 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 227 " --> pdb=" O ARG F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 245 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 262 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.816A pdb=" N VAL A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 72 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.448A pdb=" N ILE D 72 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 44 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 7.005A pdb=" N ARG B 5 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 41 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 7 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU B 43 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 9 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL B 65 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA C 76 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL C 65 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG C 5 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU C 41 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 7 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU C 43 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 9 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 34 removed outlier: 7.661A pdb=" N LEU B 15 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 252 through 255 Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 18 removed outlier: 3.501A pdb=" N SER C 16 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 106 removed outlier: 7.025A pdb=" N ARG E 5 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU E 41 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL E 7 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU E 43 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 9 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL E 65 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA F 76 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL F 65 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ARG F 5 " --> pdb=" O ASP F 39 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU F 41 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL F 7 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU F 43 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 9 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 30 through 34 removed outlier: 7.661A pdb=" N LEU E 15 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 252 through 255 Processing sheet with id=AB2, first strand: chain 'F' and resid 14 through 18 removed outlier: 3.531A pdb=" N SER F 16 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 252 through 254 585 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2928 1.33 - 1.45: 2525 1.45 - 1.57: 6299 1.57 - 1.69: 147 1.69 - 1.81: 92 Bond restraints: 11991 Sorted by residual: bond pdb=" C3' DA H 8 " pdb=" C2' DA H 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT G 21 " pdb=" C2' DT G 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT G 18 " pdb=" C2' DT G 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.73e+00 bond pdb=" C3' DC G 8 " pdb=" C2' DC G 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.07e+00 bond pdb=" C3' DG H 25 " pdb=" O3' DG H 25 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 8.90e+00 ... (remaining 11986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 16178 1.87 - 3.73: 399 3.73 - 5.60: 44 5.60 - 7.47: 3 7.47 - 9.33: 5 Bond angle restraints: 16629 Sorted by residual: angle pdb=" CB GLN C 208 " pdb=" CG GLN C 208 " pdb=" CD GLN C 208 " ideal model delta sigma weight residual 112.60 121.27 -8.67 1.70e+00 3.46e-01 2.60e+01 angle pdb=" C ASN B 256 " pdb=" CA ASN B 256 " pdb=" CB ASN B 256 " ideal model delta sigma weight residual 117.23 110.71 6.52 1.36e+00 5.41e-01 2.30e+01 angle pdb=" C ASN E 256 " pdb=" CA ASN E 256 " pdb=" CB ASN E 256 " ideal model delta sigma weight residual 117.23 110.71 6.52 1.36e+00 5.41e-01 2.30e+01 angle pdb=" CA GLN C 208 " pdb=" CB GLN C 208 " pdb=" CG GLN C 208 " ideal model delta sigma weight residual 114.10 122.76 -8.66 2.00e+00 2.50e-01 1.88e+01 angle pdb=" N3 DT G 3 " pdb=" C4 DT G 3 " pdb=" O4 DT G 3 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 16624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 6287 29.45 - 58.91: 644 58.91 - 88.36: 19 88.36 - 117.82: 1 117.82 - 147.27: 1 Dihedral angle restraints: 6952 sinusoidal: 2918 harmonic: 4034 Sorted by residual: dihedral pdb=" C4' DG H 25 " pdb=" C3' DG H 25 " pdb=" O3' DG H 25 " pdb=" P DG H 26 " ideal model delta sinusoidal sigma weight residual 220.00 72.73 147.27 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CA ARG F 5 " pdb=" C ARG F 5 " pdb=" N THR F 6 " pdb=" CA THR F 6 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN B 237 " pdb=" C ASN B 237 " pdb=" N PHE B 238 " pdb=" CA PHE B 238 " ideal model delta harmonic sigma weight residual 180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1337 0.038 - 0.076: 458 0.076 - 0.114: 144 0.114 - 0.153: 32 0.153 - 0.191: 3 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C3' DG H 25 " pdb=" C4' DG H 25 " pdb=" O3' DG H 25 " pdb=" C2' DG H 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CG LEU B 89 " pdb=" CB LEU B 89 " pdb=" CD1 LEU B 89 " pdb=" CD2 LEU B 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CB VAL F 193 " pdb=" CA VAL F 193 " pdb=" CG1 VAL F 193 " pdb=" CG2 VAL F 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1971 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 208 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C GLN C 208 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN C 208 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE C 209 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 97 " -0.012 2.00e-02 2.50e+03 1.15e-02 3.29e+00 pdb=" CG TRP B 97 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 97 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 97 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 97 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 97 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 97 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 97 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 97 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 97 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT G 12 " -0.021 2.00e-02 2.50e+03 1.03e-02 2.64e+00 pdb=" N1 DT G 12 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT G 12 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT G 12 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT G 12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT G 12 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT G 12 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DT G 12 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT G 12 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT G 12 " 0.002 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 121 2.63 - 3.20: 9898 3.20 - 3.77: 18997 3.77 - 4.33: 25590 4.33 - 4.90: 41308 Nonbonded interactions: 95914 Sorted by model distance: nonbonded pdb=" OD1 ASP A 13 " pdb="CA CA A 201 " model vdw 2.066 3.250 nonbonded pdb=" OP1 DG H 13 " pdb="CA CA A 201 " model vdw 2.197 3.250 nonbonded pdb=" OG SER A 43 " pdb="CA CA A 201 " model vdw 2.235 3.250 nonbonded pdb=" O PHE B 212 " pdb=" OG SER B 216 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR D 110 " pdb=" OE1 GLU E 44 " model vdw 2.265 3.040 ... (remaining 95909 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 'D' } ncs_group { reference = (chain 'B' and (resid 3 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 85 or (resid 86 through \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 through \ 99 or (resid 100 through 104 and (name N or name CA or name C or name O or name \ CB )) or resid 105 through 106 or (resid 107 through 108 and (name N or name CA \ or name C or name O or name CB )) or resid 109 through 117 or (resid 118 through \ 121 and (name N or name CA or name C or name O or name CB )) or (resid 122 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 or \ (resid 140 through 144 and (name N or name CA or name C or name O or name CB )) \ or resid 145 through 151 or (resid 152 through 161 and (name N or name CA or na \ me C or name O or name CB )) or (resid 162 through 172 and (name N or name CA or \ name C or name O or name CB )) or resid 173 or (resid 174 through 176 and (name \ N or name CA or name C or name O or name CB )) or resid 177 or (resid 178 and ( \ name N or name CA or name C or name O or name CB )) or resid 179 through 226 or \ (resid 227 through 228 and (name N or name CA or name C or name O or name CB )) \ or resid 229 through 231 or (resid 232 through 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 or (resid 235 through 238 and (name N o \ r name CA or name C or name O or name CB )) or resid 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 242 or (res \ id 243 through 244 and (name N or name CA or name C or name O or name CB )) or r \ esid 245 through 246 or (resid 247 and (name N or name CA or name C or name O or \ name CB )) or resid 248 through 249 or (resid 250 through 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 a \ nd (name N or name CA or name C or name O or name CB )) or resid 260 through 274 \ or (resid 275 through 276 and (name N or name CA or name C or name O or name CB \ )) or resid 277 through 285 or (resid 286 and (name N or name CA or name C or n \ ame O or name CB )) or resid 287 through 288)) selection = (chain 'C' and (resid 3 through 68 or (resid 69 through 71 and (name N or name C \ A or name C or name O or name CB )) or resid 72 through 84 or (resid 85 through \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 through \ 119 or (resid 120 through 121 and (name N or name CA or name C or name O or name \ CB )) or resid 122 through 200 or (resid 201 and (name N or name CA or name C o \ r name O or name CB )) or resid 202 through 203 or (resid 204 through 210 and (n \ ame N or name CA or name C or name O or name CB )) or resid 211 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 278 or (resid 279 through 280 and (name N or name CA or name C or name O \ or name CB )) or resid 281 through 287 or (resid 288 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'E' and (resid 3 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 85 or (resid 86 through \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 through \ 99 or (resid 100 through 104 and (name N or name CA or name C or name O or name \ CB )) or resid 105 through 106 or (resid 107 through 108 and (name N or name CA \ or name C or name O or name CB )) or resid 109 through 117 or (resid 118 through \ 121 and (name N or name CA or name C or name O or name CB )) or (resid 122 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 or \ (resid 140 through 144 and (name N or name CA or name C or name O or name CB )) \ or resid 145 through 151 or (resid 152 through 161 and (name N or name CA or na \ me C or name O or name CB )) or (resid 162 through 172 and (name N or name CA or \ name C or name O or name CB )) or resid 173 or (resid 174 through 176 and (name \ N or name CA or name C or name O or name CB )) or resid 177 or (resid 178 and ( \ name N or name CA or name C or name O or name CB )) or resid 179 through 226 or \ (resid 227 through 228 and (name N or name CA or name C or name O or name CB )) \ or resid 229 through 231 or (resid 232 through 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 or (resid 235 through 238 and (name N o \ r name CA or name C or name O or name CB )) or resid 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 242 or (res \ id 243 through 244 and (name N or name CA or name C or name O or name CB )) or r \ esid 245 through 246 or (resid 247 and (name N or name CA or name C or name O or \ name CB )) or resid 248 through 249 or (resid 250 through 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 a \ nd (name N or name CA or name C or name O or name CB )) or resid 260 through 274 \ or (resid 275 through 276 and (name N or name CA or name C or name O or name CB \ )) or resid 277 through 285 or (resid 286 and (name N or name CA or name C or n \ ame O or name CB )) or resid 287 through 288)) selection = (chain 'F' and (resid 3 through 68 or (resid 69 through 71 and (name N or name C \ A or name C or name O or name CB )) or resid 72 through 84 or (resid 85 through \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 through \ 119 or (resid 120 through 121 and (name N or name CA or name C or name O or name \ CB )) or resid 122 through 200 or (resid 201 and (name N or name CA or name C o \ r name O or name CB )) or resid 202 through 203 or (resid 204 through 210 and (n \ ame N or name CA or name C or name O or name CB )) or resid 211 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 278 or (resid 279 through 280 and (name N or name CA or name C or name O \ or name CB )) or resid 281 through 287 or (resid 288 and (name N or name CA or \ name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 0.061 11991 Z= 0.300 Angle : 0.663 9.334 16629 Z= 0.463 Chirality : 0.044 0.191 1974 Planarity : 0.003 0.046 1842 Dihedral : 20.443 147.270 4332 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.06 % Allowed : 27.71 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1348 helix: 0.65 (0.20), residues: 658 sheet: 0.11 (0.40), residues: 168 loop : -0.69 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 93 TYR 0.018 0.001 TYR F 17 PHE 0.020 0.002 PHE C 24 TRP 0.030 0.002 TRP B 97 HIS 0.006 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.30 (11991) covalent geometry : angle 0.66287 / 0.46 (16629) hydrogen bonds : bond 0.16673 / 10.75 ( 665) hydrogen bonds : angle 6.07485 / 4.14 ( 1825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 262 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.8358 (m) cc_final: 0.7925 (p) REVERT: A 68 LYS cc_start: 0.8589 (mmpt) cc_final: 0.8116 (mptt) REVERT: B 191 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 220 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6386 (mp0) REVERT: B 240 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7856 (mmmt) REVERT: B 268 ASP cc_start: 0.7708 (t70) cc_final: 0.7347 (t70) REVERT: C 10 ASN cc_start: 0.7817 (t0) cc_final: 0.7152 (t0) REVERT: C 61 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7281 (tp30) REVERT: C 72 ARG cc_start: 0.7743 (mtt90) cc_final: 0.7263 (mmm-85) REVERT: C 87 SER cc_start: 0.8107 (m) cc_final: 0.7648 (p) REVERT: C 198 MET cc_start: 0.8483 (mtm) cc_final: 0.8143 (mtp) REVERT: C 256 ASN cc_start: 0.7297 (m-40) cc_final: 0.7081 (m110) REVERT: D 56 THR cc_start: 0.8399 (m) cc_final: 0.7983 (p) REVERT: D 68 LYS cc_start: 0.8657 (mmpt) cc_final: 0.8229 (mptt) REVERT: D 95 SER cc_start: 0.8655 (t) cc_final: 0.8207 (m) REVERT: E 90 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7247 (mp10) REVERT: E 191 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7020 (mm-30) REVERT: E 240 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7867 (mmmt) REVERT: E 268 ASP cc_start: 0.7571 (t0) cc_final: 0.7125 (t70) REVERT: F 18 LYS cc_start: 0.7206 (mmtm) cc_final: 0.6442 (mmmm) REVERT: F 204 LYS cc_start: 0.5944 (pttt) cc_final: 0.5289 (pttm) outliers start: 10 outliers final: 8 residues processed: 269 average time/residue: 0.1187 time to fit residues: 44.2151 Evaluate side-chains 257 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 249 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN B 12 HIS C 26 ASN C 207 ASN C 264 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 109 ASN E 12 HIS F 10 ASN F 26 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.203770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154538 restraints weight = 13460.208| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.01 r_work: 0.3546 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11991 Z= 0.256 Angle : 0.646 6.732 16629 Z= 0.356 Chirality : 0.046 0.344 1974 Planarity : 0.004 0.039 1842 Dihedral : 20.221 151.245 2306 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.41 % Allowed : 23.99 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1348 helix: 1.23 (0.20), residues: 680 sheet: 0.04 (0.40), residues: 168 loop : -0.77 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 190 TYR 0.012 0.002 TYR E 231 PHE 0.023 0.002 PHE D 12 TRP 0.009 0.001 TRP F 4 HIS 0.005 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (11991) covalent geometry : angle 0.64624 / 0.36 (16629) hydrogen bonds : bond 0.04652 / 3.07 ( 665) hydrogen bonds : angle 4.52972 / 3.13 ( 1825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.417 Fit side-chains REVERT: A 68 LYS cc_start: 0.8704 (mmpt) cc_final: 0.8413 (mptt) REVERT: B 191 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 200 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: B 220 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7142 (mp0) REVERT: B 240 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8012 (mmmt) REVERT: B 268 ASP cc_start: 0.7894 (t70) cc_final: 0.7551 (t70) REVERT: C 10 ASN cc_start: 0.8002 (t0) cc_final: 0.7552 (t0) REVERT: C 72 ARG cc_start: 0.8367 (mtt90) cc_final: 0.8006 (mmt90) REVERT: C 198 MET cc_start: 0.8598 (mtm) cc_final: 0.8271 (mtp) REVERT: C 255 TYR cc_start: 0.7211 (t80) cc_final: 0.6681 (t80) REVERT: D 39 MET cc_start: 0.8899 (ttp) cc_final: 0.8553 (ttp) REVERT: D 49 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 56 THR cc_start: 0.8565 (m) cc_final: 0.8143 (p) REVERT: D 68 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8431 (mptt) REVERT: D 95 SER cc_start: 0.8764 (t) cc_final: 0.8460 (m) REVERT: E 17 TYR cc_start: 0.8588 (t80) cc_final: 0.8242 (t80) REVERT: E 90 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7711 (mp10) REVERT: E 191 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7123 (mm-30) REVERT: E 200 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: E 240 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7952 (mmmt) REVERT: E 268 ASP cc_start: 0.7782 (t0) cc_final: 0.7388 (t70) REVERT: F 204 LYS cc_start: 0.6155 (pttt) cc_final: 0.5461 (pttm) outliers start: 51 outliers final: 34 residues processed: 291 average time/residue: 0.1158 time to fit residues: 46.7828 Evaluate side-chains 282 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 112 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 22 optimal weight: 30.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN F 34 HIS F 112 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158436 restraints weight = 13605.650| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.15 r_work: 0.3586 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11991 Z= 0.139 Angle : 0.545 6.961 16629 Z= 0.307 Chirality : 0.042 0.329 1974 Planarity : 0.003 0.039 1842 Dihedral : 20.257 149.951 2299 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.56 % Allowed : 25.48 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1348 helix: 1.56 (0.20), residues: 678 sheet: -0.13 (0.40), residues: 158 loop : -0.73 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.014 0.001 TYR C 255 PHE 0.015 0.002 PHE F 77 TRP 0.007 0.001 TRP E 106 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (11991) covalent geometry : angle 0.54516 / 0.31 (16629) hydrogen bonds : bond 0.03941 / 2.60 ( 665) hydrogen bonds : angle 4.24714 / 2.93 ( 1825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.419 Fit side-chains REVERT: A 49 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8463 (mt) REVERT: A 68 LYS cc_start: 0.8666 (mmpt) cc_final: 0.8335 (mptt) REVERT: A 100 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 17 TYR cc_start: 0.8415 (t80) cc_final: 0.8067 (t80) REVERT: B 191 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 200 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: B 220 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7047 (mp0) REVERT: B 240 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7937 (mmmt) REVERT: B 268 ASP cc_start: 0.7730 (t70) cc_final: 0.7499 (t70) REVERT: C 10 ASN cc_start: 0.7989 (t0) cc_final: 0.7539 (t0) REVERT: C 72 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7730 (mmt90) REVERT: C 198 MET cc_start: 0.8545 (mtm) cc_final: 0.8227 (mtp) REVERT: D 26 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8510 (mtm110) REVERT: D 39 MET cc_start: 0.8843 (ttp) cc_final: 0.8491 (ttp) REVERT: D 56 THR cc_start: 0.8515 (m) cc_final: 0.8117 (p) REVERT: D 68 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8406 (mptt) REVERT: D 95 SER cc_start: 0.8690 (t) cc_final: 0.8276 (m) REVERT: E 17 TYR cc_start: 0.8520 (t80) cc_final: 0.8161 (t80) REVERT: E 90 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7679 (mp10) REVERT: E 191 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7047 (mm-30) REVERT: E 240 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8002 (mmmt) REVERT: F 204 LYS cc_start: 0.6120 (pttt) cc_final: 0.5457 (pttm) outliers start: 43 outliers final: 30 residues processed: 279 average time/residue: 0.1232 time to fit residues: 47.2673 Evaluate side-chains 277 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN D 93 ASN F 90 GLN F 112 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.199920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150371 restraints weight = 13604.852| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.02 r_work: 0.3527 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11991 Z= 0.292 Angle : 0.670 7.044 16629 Z= 0.363 Chirality : 0.047 0.344 1974 Planarity : 0.004 0.041 1842 Dihedral : 20.594 150.210 2297 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.05 % Allowed : 23.57 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1348 helix: 1.53 (0.20), residues: 680 sheet: -0.15 (0.44), residues: 136 loop : -0.99 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 190 TYR 0.019 0.002 TYR C 255 PHE 0.024 0.003 PHE F 77 TRP 0.019 0.002 TRP F 4 HIS 0.007 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 (11991) covalent geometry : angle 0.67023 / 0.36 (16629) hydrogen bonds : bond 0.04593 / 2.98 ( 665) hydrogen bonds : angle 4.28471 / 2.93 ( 1825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8661 (mt) REVERT: A 68 LYS cc_start: 0.8766 (mmpt) cc_final: 0.8410 (mptt) REVERT: A 100 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 17 TYR cc_start: 0.8625 (t80) cc_final: 0.8278 (t80) REVERT: B 191 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 200 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: B 220 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7025 (mp0) REVERT: B 240 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7992 (mmmt) REVERT: B 268 ASP cc_start: 0.8032 (t70) cc_final: 0.7599 (t70) REVERT: C 10 ASN cc_start: 0.8109 (t0) cc_final: 0.7656 (t0) REVERT: C 20 ASN cc_start: 0.8445 (t0) cc_final: 0.8217 (t0) REVERT: C 213 ASN cc_start: 0.7478 (t0) cc_final: 0.7275 (t0) REVERT: D 38 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 49 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 56 THR cc_start: 0.8630 (m) cc_final: 0.8145 (p) REVERT: D 68 LYS cc_start: 0.8792 (mmpt) cc_final: 0.8491 (mmtm) REVERT: D 95 SER cc_start: 0.8795 (t) cc_final: 0.8424 (m) REVERT: E 17 TYR cc_start: 0.8613 (t80) cc_final: 0.8288 (t80) REVERT: E 90 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7774 (mp10) REVERT: E 191 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7029 (mm-30) REVERT: E 240 LYS cc_start: 0.8288 (mmtm) cc_final: 0.8008 (mmmt) REVERT: E 268 ASP cc_start: 0.7987 (t70) cc_final: 0.7426 (t70) REVERT: F 204 LYS cc_start: 0.6211 (pttt) cc_final: 0.5532 (pttm) outliers start: 57 outliers final: 40 residues processed: 294 average time/residue: 0.1210 time to fit residues: 49.4562 Evaluate side-chains 298 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.203501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155434 restraints weight = 13391.944| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.94 r_work: 0.3575 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11991 Z= 0.141 Angle : 0.554 6.799 16629 Z= 0.308 Chirality : 0.042 0.332 1974 Planarity : 0.003 0.043 1842 Dihedral : 20.567 149.833 2297 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.52 % Allowed : 23.78 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1348 helix: 1.76 (0.21), residues: 678 sheet: -0.38 (0.41), residues: 158 loop : -0.92 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.017 0.001 TYR C 255 PHE 0.021 0.002 PHE F 209 TRP 0.016 0.001 TRP F 4 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11991) covalent geometry : angle 0.55375 / 0.31 (16629) hydrogen bonds : bond 0.03652 / 2.40 ( 665) hydrogen bonds : angle 4.05512 / 2.76 ( 1825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 68 LYS cc_start: 0.8645 (mmpt) cc_final: 0.8274 (mptt) REVERT: A 100 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7118 (tm-30) REVERT: B 17 TYR cc_start: 0.8494 (t80) cc_final: 0.8151 (t80) REVERT: B 22 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8356 (tp) REVERT: B 191 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7020 (mm-30) REVERT: B 200 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: B 220 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7106 (mp0) REVERT: B 240 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7926 (mmmt) REVERT: B 268 ASP cc_start: 0.7846 (t70) cc_final: 0.7536 (t70) REVERT: C 10 ASN cc_start: 0.7991 (t0) cc_final: 0.7572 (t0) REVERT: C 20 ASN cc_start: 0.8565 (t0) cc_final: 0.8113 (t0) REVERT: C 204 LYS cc_start: 0.6112 (ptpt) cc_final: 0.5111 (pttm) REVERT: D 56 THR cc_start: 0.8581 (m) cc_final: 0.8113 (p) REVERT: D 68 LYS cc_start: 0.8768 (mmpt) cc_final: 0.8434 (mptt) REVERT: D 95 SER cc_start: 0.8754 (t) cc_final: 0.8341 (m) REVERT: E 17 TYR cc_start: 0.8547 (t80) cc_final: 0.8240 (t80) REVERT: E 22 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8386 (tp) REVERT: E 90 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7732 (mp10) REVERT: E 191 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6940 (mm-30) REVERT: E 240 LYS cc_start: 0.8285 (mmtm) cc_final: 0.8059 (mmmt) REVERT: E 268 ASP cc_start: 0.7707 (t70) cc_final: 0.7307 (t70) REVERT: F 204 LYS cc_start: 0.6142 (pttt) cc_final: 0.5497 (pttm) outliers start: 52 outliers final: 39 residues processed: 297 average time/residue: 0.1169 time to fit residues: 48.5223 Evaluate side-chains 294 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 130 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 213 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.204381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.156142 restraints weight = 13497.069| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.02 r_work: 0.3572 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11991 Z= 0.141 Angle : 0.549 6.973 16629 Z= 0.304 Chirality : 0.042 0.331 1974 Planarity : 0.003 0.048 1842 Dihedral : 20.513 149.754 2297 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.67 % Allowed : 24.20 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1348 helix: 1.85 (0.21), residues: 678 sheet: -0.33 (0.41), residues: 158 loop : -0.90 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 93 TYR 0.019 0.001 TYR C 255 PHE 0.016 0.002 PHE F 209 TRP 0.017 0.001 TRP F 4 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11991) covalent geometry : angle 0.54946 / 0.30 (16629) hydrogen bonds : bond 0.03505 / 2.31 ( 665) hydrogen bonds : angle 3.96393 / 2.71 ( 1825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8645 (mmpt) cc_final: 0.8315 (mptt) REVERT: B 17 TYR cc_start: 0.8494 (t80) cc_final: 0.8158 (t80) REVERT: B 90 GLN cc_start: 0.8285 (mp10) cc_final: 0.7918 (mp10) REVERT: B 191 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 200 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: B 220 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7240 (mp0) REVERT: B 240 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7935 (mmmt) REVERT: B 252 THR cc_start: 0.7579 (m) cc_final: 0.6811 (p) REVERT: C 10 ASN cc_start: 0.7981 (t0) cc_final: 0.7565 (t0) REVERT: C 198 MET cc_start: 0.8493 (mtm) cc_final: 0.8208 (mtp) REVERT: C 204 LYS cc_start: 0.6091 (ptpt) cc_final: 0.5052 (pttm) REVERT: D 49 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8518 (mt) REVERT: D 56 THR cc_start: 0.8602 (m) cc_final: 0.8132 (p) REVERT: D 68 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8469 (mptt) REVERT: D 93 ASN cc_start: 0.8612 (t0) cc_final: 0.8203 (t0) REVERT: D 95 SER cc_start: 0.8837 (t) cc_final: 0.8407 (m) REVERT: E 17 TYR cc_start: 0.8540 (t80) cc_final: 0.8170 (t80) REVERT: E 90 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7798 (mp10) REVERT: E 191 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7015 (mm-30) REVERT: E 240 LYS cc_start: 0.8260 (mmtm) cc_final: 0.8059 (mmmt) REVERT: E 268 ASP cc_start: 0.7752 (t70) cc_final: 0.7429 (t70) REVERT: F 204 LYS cc_start: 0.6111 (pttt) cc_final: 0.5487 (pttm) outliers start: 44 outliers final: 32 residues processed: 279 average time/residue: 0.1137 time to fit residues: 43.9505 Evaluate side-chains 278 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.204895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156323 restraints weight = 13532.759| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.95 r_work: 0.3580 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11991 Z= 0.152 Angle : 0.560 7.955 16629 Z= 0.309 Chirality : 0.042 0.331 1974 Planarity : 0.004 0.052 1842 Dihedral : 20.514 149.739 2295 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.10 % Allowed : 24.42 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1348 helix: 1.87 (0.21), residues: 678 sheet: -0.27 (0.41), residues: 158 loop : -0.94 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 93 TYR 0.018 0.001 TYR C 255 PHE 0.017 0.002 PHE F 77 TRP 0.028 0.002 TRP C 4 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11991) covalent geometry : angle 0.55996 / 0.31 (16629) hydrogen bonds : bond 0.03509 / 2.31 ( 665) hydrogen bonds : angle 3.92918 / 2.69 ( 1825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 68 LYS cc_start: 0.8620 (mmpt) cc_final: 0.8273 (mptt) REVERT: B 17 TYR cc_start: 0.8524 (t80) cc_final: 0.8205 (t80) REVERT: B 22 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8343 (tp) REVERT: B 90 GLN cc_start: 0.8139 (mp10) cc_final: 0.7815 (mp10) REVERT: B 191 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 200 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: B 220 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7158 (mp0) REVERT: B 240 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7969 (mmmt) REVERT: C 10 ASN cc_start: 0.8023 (t0) cc_final: 0.7581 (t0) REVERT: C 61 GLU cc_start: 0.7648 (tt0) cc_final: 0.7333 (tt0) REVERT: C 198 MET cc_start: 0.8496 (mtm) cc_final: 0.8218 (mtp) REVERT: C 204 LYS cc_start: 0.5903 (ptpt) cc_final: 0.4923 (pttm) REVERT: D 49 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8524 (mt) REVERT: D 56 THR cc_start: 0.8572 (m) cc_final: 0.8081 (p) REVERT: D 68 LYS cc_start: 0.8756 (mmpt) cc_final: 0.8465 (mmtm) REVERT: D 95 SER cc_start: 0.8812 (t) cc_final: 0.8312 (m) REVERT: E 17 TYR cc_start: 0.8532 (t80) cc_final: 0.8155 (t80) REVERT: E 22 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8388 (tp) REVERT: E 90 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7750 (mp10) REVERT: E 191 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6985 (mm-30) REVERT: E 268 ASP cc_start: 0.7772 (t70) cc_final: 0.7384 (t70) outliers start: 48 outliers final: 39 residues processed: 282 average time/residue: 0.1175 time to fit residues: 45.7983 Evaluate side-chains 290 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN B 112 GLN C 62 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.203608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154755 restraints weight = 13500.764| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.98 r_work: 0.3568 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11991 Z= 0.164 Angle : 0.573 9.476 16629 Z= 0.314 Chirality : 0.042 0.329 1974 Planarity : 0.004 0.055 1842 Dihedral : 20.546 149.829 2295 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.41 % Allowed : 24.31 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1348 helix: 1.92 (0.21), residues: 676 sheet: -0.18 (0.41), residues: 168 loop : -0.92 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 93 TYR 0.015 0.001 TYR C 255 PHE 0.017 0.002 PHE F 77 TRP 0.028 0.002 TRP C 4 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11991) covalent geometry : angle 0.57261 / 0.31 (16629) hydrogen bonds : bond 0.03549 / 2.34 ( 665) hydrogen bonds : angle 3.93178 / 2.69 ( 1825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (mt) REVERT: A 68 LYS cc_start: 0.8656 (mmpt) cc_final: 0.8292 (mptt) REVERT: B 17 TYR cc_start: 0.8563 (t80) cc_final: 0.8230 (t80) REVERT: B 22 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 90 GLN cc_start: 0.8166 (mp10) cc_final: 0.7900 (mp10) REVERT: B 191 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 200 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: B 220 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7171 (mp0) REVERT: B 240 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7949 (mmmt) REVERT: C 10 ASN cc_start: 0.8029 (t0) cc_final: 0.7594 (t0) REVERT: C 198 MET cc_start: 0.8499 (mtm) cc_final: 0.8176 (mtp) REVERT: D 49 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (mt) REVERT: D 56 THR cc_start: 0.8568 (m) cc_final: 0.8075 (p) REVERT: D 68 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8441 (mptt) REVERT: D 95 SER cc_start: 0.8760 (t) cc_final: 0.8367 (m) REVERT: D 100 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7087 (mm-30) REVERT: E 17 TYR cc_start: 0.8554 (t80) cc_final: 0.8193 (t80) REVERT: E 22 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8428 (tp) REVERT: E 90 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7787 (mp10) REVERT: E 191 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7000 (mm-30) REVERT: E 268 ASP cc_start: 0.7805 (t70) cc_final: 0.7405 (t70) REVERT: F 198 MET cc_start: 0.8023 (mtp) cc_final: 0.7715 (mtm) outliers start: 51 outliers final: 43 residues processed: 288 average time/residue: 0.1139 time to fit residues: 45.7350 Evaluate side-chains 297 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.199376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150468 restraints weight = 13338.708| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.95 r_work: 0.3511 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11991 Z= 0.285 Angle : 0.672 8.327 16629 Z= 0.361 Chirality : 0.046 0.335 1974 Planarity : 0.004 0.047 1842 Dihedral : 20.728 150.662 2295 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.52 % Allowed : 24.31 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1348 helix: 1.78 (0.21), residues: 678 sheet: -0.31 (0.40), residues: 166 loop : -1.00 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 93 TYR 0.014 0.002 TYR C 255 PHE 0.023 0.003 PHE A 12 TRP 0.032 0.002 TRP C 4 HIS 0.007 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.28 (11991) covalent geometry : angle 0.67171 / 0.36 (16629) hydrogen bonds : bond 0.04353 / 2.83 ( 665) hydrogen bonds : angle 4.10821 / 2.81 ( 1825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 68 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8481 (mptt) REVERT: B 17 TYR cc_start: 0.8694 (t80) cc_final: 0.8315 (t80) REVERT: B 22 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8372 (tp) REVERT: B 90 GLN cc_start: 0.8299 (mp10) cc_final: 0.8013 (mp10) REVERT: B 191 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 200 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: B 220 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7245 (mp0) REVERT: B 240 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8033 (mmmt) REVERT: C 10 ASN cc_start: 0.8052 (t0) cc_final: 0.7716 (t0) REVERT: C 25 ARG cc_start: 0.7368 (tmm160) cc_final: 0.7127 (tmm160) REVERT: C 61 GLU cc_start: 0.7923 (tt0) cc_final: 0.7700 (tt0) REVERT: D 38 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8528 (mp) REVERT: D 49 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8639 (mt) REVERT: D 56 THR cc_start: 0.8617 (m) cc_final: 0.8140 (p) REVERT: D 68 LYS cc_start: 0.8840 (mmpt) cc_final: 0.8551 (mmtm) REVERT: D 93 ASN cc_start: 0.8678 (t0) cc_final: 0.8218 (t0) REVERT: D 95 SER cc_start: 0.8900 (t) cc_final: 0.8560 (m) REVERT: E 17 TYR cc_start: 0.8713 (t80) cc_final: 0.8347 (t80) REVERT: E 90 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7969 (mp10) REVERT: E 191 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7087 (mm-30) REVERT: E 268 ASP cc_start: 0.7935 (t70) cc_final: 0.7425 (t70) outliers start: 52 outliers final: 44 residues processed: 288 average time/residue: 0.1078 time to fit residues: 43.6362 Evaluate side-chains 302 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.200937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152831 restraints weight = 13461.298| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.00 r_work: 0.3537 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11991 Z= 0.207 Angle : 0.617 8.137 16629 Z= 0.336 Chirality : 0.044 0.327 1974 Planarity : 0.004 0.053 1842 Dihedral : 20.761 150.680 2295 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.31 % Allowed : 24.63 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1348 helix: 1.78 (0.21), residues: 678 sheet: -0.35 (0.40), residues: 166 loop : -0.98 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 93 TYR 0.015 0.002 TYR C 255 PHE 0.020 0.002 PHE F 77 TRP 0.036 0.002 TRP C 4 HIS 0.005 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (11991) covalent geometry : angle 0.61739 / 0.34 (16629) hydrogen bonds : bond 0.03877 / 2.55 ( 665) hydrogen bonds : angle 4.04115 / 2.76 ( 1825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.433 Fit side-chains REVERT: A 49 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8611 (mt) REVERT: A 68 LYS cc_start: 0.8728 (mmpt) cc_final: 0.8374 (mptt) REVERT: B 17 TYR cc_start: 0.8660 (t80) cc_final: 0.8287 (t80) REVERT: B 22 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 90 GLN cc_start: 0.8264 (mp10) cc_final: 0.8015 (mp10) REVERT: B 191 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 200 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: B 220 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7202 (mp0) REVERT: B 240 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8036 (mmmt) REVERT: C 25 ARG cc_start: 0.7330 (tmm160) cc_final: 0.7058 (tmm160) REVERT: D 38 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8524 (mp) REVERT: D 39 MET cc_start: 0.8726 (ttp) cc_final: 0.8412 (ttp) REVERT: D 49 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8596 (mt) REVERT: D 56 THR cc_start: 0.8587 (m) cc_final: 0.8095 (p) REVERT: D 68 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8532 (mmtm) REVERT: D 95 SER cc_start: 0.8848 (t) cc_final: 0.8348 (p) REVERT: E 17 TYR cc_start: 0.8674 (t80) cc_final: 0.8305 (t80) REVERT: E 22 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8396 (tp) REVERT: E 90 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7942 (mp10) REVERT: E 191 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7038 (mm-30) REVERT: E 268 ASP cc_start: 0.7838 (t70) cc_final: 0.7372 (t70) REVERT: F 18 LYS cc_start: 0.7123 (tppt) cc_final: 0.6489 (tttp) REVERT: F 25 ARG cc_start: 0.7394 (tmm160) cc_final: 0.7066 (tmm160) REVERT: F 198 MET cc_start: 0.8273 (mtp) cc_final: 0.8063 (mtm) outliers start: 50 outliers final: 39 residues processed: 282 average time/residue: 0.1062 time to fit residues: 42.0626 Evaluate side-chains 297 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 6 MET Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 249 PHE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN C 62 ASN C 207 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.202644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154821 restraints weight = 13409.636| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.93 r_work: 0.3561 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11991 Z= 0.155 Angle : 0.581 7.721 16629 Z= 0.319 Chirality : 0.042 0.324 1974 Planarity : 0.004 0.054 1842 Dihedral : 20.685 150.564 2295 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.35 % Allowed : 25.48 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1348 helix: 1.89 (0.21), residues: 676 sheet: -0.41 (0.40), residues: 172 loop : -0.88 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 93 TYR 0.023 0.001 TYR B 82 PHE 0.018 0.002 PHE F 77 TRP 0.060 0.002 TRP C 4 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11991) covalent geometry : angle 0.58142 / 0.32 (16629) hydrogen bonds : bond 0.03558 / 2.35 ( 665) hydrogen bonds : angle 3.92315 / 2.68 ( 1825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2873.07 seconds wall clock time: 49 minutes 56.23 seconds (2996.23 seconds total)