Starting phenix.real_space_refine on Thu Feb 5 17:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui7_64186/02_2026/9ui7_64186.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui7_64186/02_2026/9ui7_64186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ui7_64186/02_2026/9ui7_64186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui7_64186/02_2026/9ui7_64186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ui7_64186/02_2026/9ui7_64186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui7_64186/02_2026/9ui7_64186.map" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 101 5.49 5 Mg 7 5.21 5 S 96 5.16 5 C 11369 2.51 5 N 3261 2.21 5 O 3811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18645 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2413 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "F" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "G" Number of atoms: 2421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 304} Conformer: "B" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 304} bond proxies already assigned to first conformer: 2446 Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "I" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT%5*END:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 440 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2387 Classifications: {'peptide': 311} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 300} Chain breaks: 1 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA G 281 " occ=0.52 ... (8 atoms not shown) pdb=" CB BALA G 281 " occ=0.48 Time building chain proxies: 4.65, per 1000 atoms: 0.25 Number of scatterers: 18645 At special positions: 0 Unit cell: (105.41, 119.52, 170.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 101 15.00 Mg 7 11.99 O 3811 8.00 N 3261 7.00 C 11369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 779.5 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3984 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 10 sheets defined 45.4% alpha, 10.9% beta 4 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 34 through 45 removed outlier: 4.061A pdb=" N VAL D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.541A pdb=" N ASN D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.815A pdb=" N CYS D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 178 removed outlier: 3.918A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 removed outlier: 4.134A pdb=" N LEU D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 213 removed outlier: 4.182A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 4.279A pdb=" N THR D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.549A pdb=" N ARG D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.707A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.639A pdb=" N GLU E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.706A pdb=" N VAL E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.776A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.643A pdb=" N ALA E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 removed outlier: 3.879A pdb=" N ASP E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.542A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 141 " --> pdb=" O CYS E 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.665A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.586A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET E 210 " --> pdb=" O GLN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 260 removed outlier: 3.716A pdb=" N HIS E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.621A pdb=" N ALA E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 removed outlier: 4.015A pdb=" N ARG F 27 " --> pdb=" O PRO F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 removed outlier: 4.300A pdb=" N LYS F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 57 through 62 removed outlier: 3.731A pdb=" N ILE F 61 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN F 62 " --> pdb=" O LYS F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 57 through 62' Processing helix chain 'F' and resid 67 through 79 removed outlier: 3.570A pdb=" N LYS F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 removed outlier: 3.911A pdb=" N PHE F 92 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.512A pdb=" N THR F 139 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 removed outlier: 3.823A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 4.007A pdb=" N THR F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 213 " --> pdb=" O ASP F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.540A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 259 removed outlier: 3.739A pdb=" N MET F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 4.039A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.872A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 54' Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.669A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 76 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU G 77 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.535A pdb=" N CYS G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 142 " --> pdb=" O HIS G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 178 removed outlier: 3.503A pdb=" N VAL G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 187 removed outlier: 3.636A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 214 removed outlier: 3.695A pdb=" N GLN G 202 " --> pdb=" O ASP G 198 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU G 203 " --> pdb=" O HIS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 removed outlier: 3.633A pdb=" N LEU G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 257 removed outlier: 3.760A pdb=" N HIS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 245 " --> pdb=" O ARG G 241 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG G 254 " --> pdb=" O ARG G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 294 removed outlier: 3.600A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.725A pdb=" N ARG A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.639A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.777A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.889A pdb=" N LYS A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.646A pdb=" N PHE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 4.082A pdb=" N LYS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.628A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 196 through 214 removed outlier: 4.006A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.920A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.636A pdb=" N ALA A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 4.335A pdb=" N HIS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.632A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.510A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.129A pdb=" N VAL C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.520A pdb=" N ASP C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 98 removed outlier: 3.886A pdb=" N PHE C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.160A pdb=" N HIS C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 removed outlier: 3.900A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 189 removed outlier: 3.796A pdb=" N ASP C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 214 removed outlier: 3.786A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 259 removed outlier: 3.563A pdb=" N HIS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.844A pdb=" N HIS C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 296' Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.775A pdb=" N VAL B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.524A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.685A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.751A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 196 through 210 removed outlier: 3.580A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.756A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.874A pdb=" N ARG B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.106A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 88 removed outlier: 5.348A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.024A pdb=" N GLY D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 156 through 157 removed outlier: 7.832A pdb=" N LYS D 156 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU D 219 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D 217 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.609A pdb=" N ASP D 161 " --> pdb=" O ALA D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.655A pdb=" N ALA F 190 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS F 156 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE F 220 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 217 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL F 264 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR F 123 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 329 through 330 Processing sheet with id=AA7, first strand: chain 'G' and resid 156 through 159 removed outlier: 7.653A pdb=" N LYS G 156 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU G 219 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N MET G 158 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL G 221 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA G 217 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR G 123 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE G 265 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG G 303 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 311 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 191 removed outlier: 4.203A pdb=" N ALA A 190 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 266 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.677A pdb=" N THR C 298 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 159 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 192 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.921A pdb=" N ALA B 190 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 262 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASN B 267 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET B 125 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS B 312 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 325 " --> pdb=" O CYS B 312 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4966 1.33 - 1.46: 4308 1.46 - 1.58: 9477 1.58 - 1.70: 179 1.70 - 1.83: 157 Bond restraints: 19087 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" O3A ANP B 600 " pdb=" PB ANP B 600 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" O3A ANP E 600 " pdb=" PB ANP E 600 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP A 600 " pdb=" PB ANP A 600 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.94e+01 ... (remaining 19082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.22: 25980 5.22 - 10.44: 145 10.44 - 15.66: 12 15.66 - 20.87: 1 20.87 - 26.09: 5 Bond angle restraints: 26143 Sorted by residual: angle pdb=" PB ANP B 600 " pdb=" N3B ANP B 600 " pdb=" PG ANP B 600 " ideal model delta sigma weight residual 126.95 100.86 26.09 3.00e+00 1.11e-01 7.56e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 103.37 23.58 3.00e+00 1.11e-01 6.18e+01 angle pdb=" PB ANP E 600 " pdb=" N3B ANP E 600 " pdb=" PG ANP E 600 " ideal model delta sigma weight residual 126.95 103.59 23.36 3.00e+00 1.11e-01 6.06e+01 angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 103.81 23.14 3.00e+00 1.11e-01 5.95e+01 angle pdb=" PB ANP F 600 " pdb=" N3B ANP F 600 " pdb=" PG ANP F 600 " ideal model delta sigma weight residual 126.95 103.99 22.96 3.00e+00 1.11e-01 5.86e+01 ... (remaining 26138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 10760 35.65 - 71.30: 654 71.30 - 106.95: 43 106.95 - 142.60: 5 142.60 - 178.25: 4 Dihedral angle restraints: 11466 sinusoidal: 5226 harmonic: 6240 Sorted by residual: dihedral pdb=" CA ASN E 188 " pdb=" C ASN E 188 " pdb=" N VAL E 189 " pdb=" CA VAL E 189 " ideal model delta harmonic sigma weight residual -180.00 -121.28 -58.72 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ASP E 282 " pdb=" C ASP E 282 " pdb=" N PRO E 283 " pdb=" CA PRO E 283 " ideal model delta harmonic sigma weight residual -180.00 -130.92 -49.08 0 5.00e+00 4.00e-02 9.64e+01 dihedral pdb=" CA SER F 239 " pdb=" C SER F 239 " pdb=" N ALA F 240 " pdb=" CA ALA F 240 " ideal model delta harmonic sigma weight residual -180.00 -134.80 -45.20 0 5.00e+00 4.00e-02 8.17e+01 ... (remaining 11463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2435 0.070 - 0.140: 472 0.140 - 0.210: 49 0.210 - 0.279: 8 0.279 - 0.349: 6 Chirality restraints: 2970 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' ANP F 600 " pdb=" C2' ANP F 600 " pdb=" C4' ANP F 600 " pdb=" O3' ANP F 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ANP G 600 " pdb=" C2' ANP G 600 " pdb=" C4' ANP G 600 " pdb=" O3' ANP G 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2967 not shown) Planarity restraints: 3082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 282 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C ASP E 282 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP E 282 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO E 283 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 235 " 0.014 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C ARG E 235 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG E 235 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY E 236 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 239 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C SER F 239 " -0.050 2.00e-02 2.50e+03 pdb=" O SER F 239 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA F 240 " 0.017 2.00e-02 2.50e+03 ... (remaining 3079 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 349 2.57 - 3.15: 15003 3.15 - 3.74: 32023 3.74 - 4.32: 43138 4.32 - 4.90: 67047 Nonbonded interactions: 157560 Sorted by model distance: nonbonded pdb=" O2B ANP E 600 " pdb="MG MG E 601 " model vdw 1.992 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ANP C 401 " model vdw 2.007 2.170 nonbonded pdb=" OG1 THR E 134 " pdb="MG MG E 601 " model vdw 2.024 2.170 nonbonded pdb=" O1B ANP B 600 " pdb="MG MG B 601 " model vdw 2.045 2.170 nonbonded pdb=" O1B ANP G 600 " pdb="MG MG G 601 " model vdw 2.048 2.170 ... (remaining 157555 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' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = (chain 'C' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'D' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'E' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'F' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'G' and (resid 22 through 275 or resid 283 through 336)) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.030 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.009 0.156 19087 Z= 0.423 Angle : 1.208 26.092 26143 Z= 0.644 Chirality : 0.057 0.349 2970 Planarity : 0.006 0.059 3082 Dihedral : 20.698 178.248 7482 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.78 % Favored : 92.75 % Rotamer: Outliers : 0.80 % Allowed : 10.66 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.67 % Twisted General : 0.38 % 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: -4.84 (0.13), residues: 2170 helix: -4.03 (0.10), residues: 826 sheet: -2.14 (0.25), residues: 346 loop : -2.75 (0.16), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 229 TYR 0.041 0.003 TYR C 315 PHE 0.032 0.003 PHE D 126 HIS 0.012 0.002 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00895 (19087) covalent geometry : angle 1.20825 (26143) hydrogen bonds : bond 0.30550 ( 590) hydrogen bonds : angle 10.72705 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7314 (mmm) cc_final: 0.6517 (mmm) REVERT: E 25 ILE cc_start: 0.4829 (mm) cc_final: 0.4628 (mm) REVERT: F 54 TYR cc_start: 0.5915 (m-10) cc_final: 0.5455 (m-80) REVERT: F 251 MET cc_start: 0.9222 (ttm) cc_final: 0.8972 (ttm) REVERT: G 125 MET cc_start: 0.5122 (mpp) cc_final: 0.4068 (mmm) REVERT: G 211 MET cc_start: 0.2989 (tpt) cc_final: 0.2789 (tpt) outliers start: 14 outliers final: 6 residues processed: 179 average time/residue: 0.1323 time to fit residues: 36.9291 Evaluate side-chains 123 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain F residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 GLN D 272 GLN D 290 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN F 188 ASN F 200 GLN ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 GLN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 242 GLN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN B 244 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.106172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081517 restraints weight = 82212.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.080180 restraints weight = 60658.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.080563 restraints weight = 48166.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.080817 restraints weight = 40407.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080931 restraints weight = 36802.134| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19087 Z= 0.220 Angle : 0.731 10.030 26143 Z= 0.394 Chirality : 0.044 0.177 2970 Planarity : 0.005 0.063 3082 Dihedral : 20.707 175.227 3493 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Rotamer: Outliers : 2.34 % Allowed : 14.81 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.67 % Twisted General : 0.33 % 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: -3.59 (0.15), residues: 2170 helix: -2.44 (0.13), residues: 907 sheet: -1.86 (0.26), residues: 359 loop : -2.36 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 193 TYR 0.023 0.002 TYR C 315 PHE 0.020 0.002 PHE E 92 HIS 0.009 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00478 (19087) covalent geometry : angle 0.73140 (26143) hydrogen bonds : bond 0.05324 ( 590) hydrogen bonds : angle 6.80724 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7297 (mmm) cc_final: 0.6721 (mmm) REVERT: E 93 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8089 (m-70) REVERT: E 278 MET cc_start: 0.1959 (mmt) cc_final: 0.0338 (ptt) REVERT: F 158 MET cc_start: 0.5265 (mmp) cc_final: 0.4716 (mmp) REVERT: C 54 TYR cc_start: 0.8363 (m-10) cc_final: 0.7894 (m-80) REVERT: C 84 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6760 (ppp) REVERT: C 131 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.7745 (m) REVERT: B 210 MET cc_start: 0.8859 (mtm) cc_final: 0.7933 (tmm) REVERT: B 326 MET cc_start: 0.7776 (tpp) cc_final: 0.6926 (mmm) outliers start: 41 outliers final: 20 residues processed: 163 average time/residue: 0.1054 time to fit residues: 28.6646 Evaluate side-chains 142 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 176 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 104 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN E 93 HIS ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 HIS F 268 GLN ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.083255 restraints weight = 82565.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.081743 restraints weight = 60683.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082190 restraints weight = 46571.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.082299 restraints weight = 38728.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.082407 restraints weight = 36265.697| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19087 Z= 0.169 Angle : 0.666 9.335 26143 Z= 0.355 Chirality : 0.043 0.172 2970 Planarity : 0.004 0.043 3082 Dihedral : 20.320 174.714 3491 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.60 % Favored : 93.26 % Rotamer: Outliers : 3.02 % Allowed : 18.12 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.67 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.17), residues: 2170 helix: -1.44 (0.16), residues: 891 sheet: -1.75 (0.27), residues: 366 loop : -2.05 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 130 TYR 0.017 0.001 TYR C 315 PHE 0.016 0.002 PHE G 279 HIS 0.008 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00372 (19087) covalent geometry : angle 0.66613 (26143) hydrogen bonds : bond 0.04408 ( 590) hydrogen bonds : angle 6.13214 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7298 (mmm) cc_final: 0.6721 (mmm) REVERT: E 278 MET cc_start: 0.1811 (mmt) cc_final: 0.0401 (ptt) REVERT: G 125 MET cc_start: 0.7143 (mpp) cc_final: 0.5221 (mmm) REVERT: G 126 PHE cc_start: 0.4619 (m-80) cc_final: 0.3994 (m-80) REVERT: C 54 TYR cc_start: 0.8402 (m-10) cc_final: 0.8088 (m-80) outliers start: 53 outliers final: 33 residues processed: 172 average time/residue: 0.1052 time to fit residues: 30.3884 Evaluate side-chains 154 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 89 optimal weight: 20.0000 chunk 182 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 93 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.106212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083028 restraints weight = 83052.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.081049 restraints weight = 59500.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081565 restraints weight = 47094.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081696 restraints weight = 39233.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.081827 restraints weight = 37065.111| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19087 Z= 0.207 Angle : 0.692 10.804 26143 Z= 0.365 Chirality : 0.043 0.164 2970 Planarity : 0.004 0.044 3082 Dihedral : 20.214 176.052 3491 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.71 % Favored : 92.16 % Rotamer: Outliers : 3.30 % Allowed : 19.49 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2170 helix: -0.96 (0.16), residues: 899 sheet: -1.67 (0.27), residues: 367 loop : -1.95 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 130 TYR 0.023 0.002 TYR C 315 PHE 0.016 0.002 PHE D 86 HIS 0.006 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00458 (19087) covalent geometry : angle 0.69161 (26143) hydrogen bonds : bond 0.04140 ( 590) hydrogen bonds : angle 5.93788 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7373 (mmm) cc_final: 0.6830 (mmm) REVERT: E 158 MET cc_start: 0.7201 (tpp) cc_final: 0.6825 (mmm) REVERT: E 278 MET cc_start: 0.1475 (mmt) cc_final: 0.0198 (ptt) REVERT: F 300 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7859 (pp) REVERT: G 125 MET cc_start: 0.7282 (mpp) cc_final: 0.5334 (mmm) REVERT: G 301 TYR cc_start: 0.5198 (t80) cc_final: 0.4913 (t80) REVERT: C 54 TYR cc_start: 0.8422 (m-10) cc_final: 0.8137 (m-80) REVERT: C 84 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6786 (ppp) REVERT: C 315 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: B 210 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8256 (mtm) outliers start: 58 outliers final: 39 residues processed: 166 average time/residue: 0.1046 time to fit residues: 29.3303 Evaluate side-chains 158 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 183 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN A 200 GLN A 206 GLN A 244 HIS ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** 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 = 0.4237 r_free = 0.4237 target = 0.105720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.081656 restraints weight = 81839.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079530 restraints weight = 58875.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.079849 restraints weight = 47175.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079955 restraints weight = 41483.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.080050 restraints weight = 39659.509| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19087 Z= 0.228 Angle : 0.702 10.043 26143 Z= 0.369 Chirality : 0.043 0.169 2970 Planarity : 0.004 0.044 3082 Dihedral : 20.173 178.036 3491 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.75 % Favored : 92.11 % Rotamer: Outliers : 3.93 % Allowed : 20.06 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2170 helix: -0.77 (0.17), residues: 907 sheet: -1.65 (0.28), residues: 363 loop : -1.95 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 250 TYR 0.023 0.002 TYR C 315 PHE 0.020 0.002 PHE E 86 HIS 0.011 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00504 (19087) covalent geometry : angle 0.70203 (26143) hydrogen bonds : bond 0.04116 ( 590) hydrogen bonds : angle 5.89443 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 120 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7378 (mmm) cc_final: 0.6819 (mmm) REVERT: E 158 MET cc_start: 0.7149 (tpp) cc_final: 0.6836 (mmm) REVERT: E 278 MET cc_start: 0.1277 (mmt) cc_final: 0.0073 (ptt) REVERT: G 125 MET cc_start: 0.7532 (mpp) cc_final: 0.5730 (mmm) REVERT: G 205 TYR cc_start: 0.7658 (t80) cc_final: 0.7391 (t80) REVERT: G 326 MET cc_start: 0.3922 (tmm) cc_final: 0.3721 (tmm) REVERT: C 54 TYR cc_start: 0.8484 (m-10) cc_final: 0.8195 (m-80) REVERT: C 84 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6823 (ppp) REVERT: C 315 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: B 210 MET cc_start: 0.8794 (mtm) cc_final: 0.8066 (mtm) REVERT: B 326 MET cc_start: 0.7864 (tpp) cc_final: 0.6804 (mmm) outliers start: 69 outliers final: 52 residues processed: 174 average time/residue: 0.1082 time to fit residues: 31.5646 Evaluate side-chains 171 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** 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 = 0.4269 r_free = 0.4269 target = 0.107357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.083990 restraints weight = 81453.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.082662 restraints weight = 54232.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083095 restraints weight = 43628.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.083285 restraints weight = 36534.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.083324 restraints weight = 34480.361| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19087 Z= 0.138 Angle : 0.630 10.545 26143 Z= 0.331 Chirality : 0.042 0.195 2970 Planarity : 0.003 0.039 3082 Dihedral : 19.907 179.450 3491 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 2.96 % Allowed : 22.17 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.18), residues: 2170 helix: -0.40 (0.18), residues: 892 sheet: -1.46 (0.28), residues: 357 loop : -1.79 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 130 TYR 0.013 0.001 TYR C 315 PHE 0.012 0.002 PHE D 126 HIS 0.005 0.001 HIS F 294 Details of bonding type rmsd covalent geometry : bond 0.00311 (19087) covalent geometry : angle 0.62984 (26143) hydrogen bonds : bond 0.03632 ( 590) hydrogen bonds : angle 5.47690 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7377 (mmm) cc_final: 0.6809 (mmm) REVERT: E 278 MET cc_start: 0.1289 (mmt) cc_final: 0.0172 (ptt) REVERT: F 124 GLU cc_start: 0.6812 (tp30) cc_final: 0.6288 (tp30) REVERT: F 251 MET cc_start: 0.8990 (ttm) cc_final: 0.8640 (ttt) REVERT: G 125 MET cc_start: 0.7470 (mpp) cc_final: 0.5785 (mmm) REVERT: G 205 TYR cc_start: 0.7570 (t80) cc_final: 0.7334 (t80) REVERT: A 251 MET cc_start: 0.6403 (mmm) cc_final: 0.6159 (mmm) REVERT: C 54 TYR cc_start: 0.8359 (m-10) cc_final: 0.8149 (m-80) REVERT: C 84 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6815 (ppp) REVERT: C 315 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: B 210 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: B 326 MET cc_start: 0.7718 (tpp) cc_final: 0.6669 (mmm) outliers start: 52 outliers final: 41 residues processed: 177 average time/residue: 0.1041 time to fit residues: 31.4027 Evaluate side-chains 166 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 195 optimal weight: 0.4980 chunk 20 optimal weight: 0.0270 overall best weight: 2.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** 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 = 0.4257 r_free = 0.4257 target = 0.106681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.084269 restraints weight = 82245.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.082398 restraints weight = 59284.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082855 restraints weight = 48458.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083338 restraints weight = 38233.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083351 restraints weight = 34211.600| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19087 Z= 0.179 Angle : 0.667 13.514 26143 Z= 0.347 Chirality : 0.042 0.172 2970 Planarity : 0.004 0.042 3082 Dihedral : 19.876 179.100 3489 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.71 % Favored : 92.16 % Rotamer: Outliers : 3.65 % Allowed : 22.56 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2170 helix: -0.34 (0.18), residues: 899 sheet: -1.42 (0.28), residues: 355 loop : -1.73 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 130 TYR 0.019 0.001 TYR C 315 PHE 0.013 0.002 PHE D 126 HIS 0.004 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00400 (19087) covalent geometry : angle 0.66666 (26143) hydrogen bonds : bond 0.03772 ( 590) hydrogen bonds : angle 5.53863 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7370 (mmm) cc_final: 0.6829 (mmm) REVERT: D 278 MET cc_start: 0.2826 (tpp) cc_final: 0.2572 (tpp) REVERT: E 274 ASP cc_start: 0.7245 (m-30) cc_final: 0.6496 (p0) REVERT: E 278 MET cc_start: 0.1370 (mmt) cc_final: 0.0205 (ptt) REVERT: F 124 GLU cc_start: 0.6871 (tp30) cc_final: 0.6549 (tp30) REVERT: F 251 MET cc_start: 0.8948 (ttm) cc_final: 0.8592 (ttt) REVERT: F 300 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7796 (pp) REVERT: G 125 MET cc_start: 0.7500 (mpp) cc_final: 0.5696 (mmm) REVERT: G 205 TYR cc_start: 0.7526 (t80) cc_final: 0.7258 (t80) REVERT: G 301 TYR cc_start: 0.5164 (t80) cc_final: 0.4685 (t80) REVERT: A 251 MET cc_start: 0.6498 (mmm) cc_final: 0.6210 (mmm) REVERT: C 54 TYR cc_start: 0.8385 (m-10) cc_final: 0.8155 (m-80) REVERT: C 84 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6854 (ppp) REVERT: C 315 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: B 210 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8153 (mtm) outliers start: 64 outliers final: 51 residues processed: 174 average time/residue: 0.1064 time to fit residues: 31.1246 Evaluate side-chains 176 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 105 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.107177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.083803 restraints weight = 81678.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081584 restraints weight = 64482.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.082019 restraints weight = 48573.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.082595 restraints weight = 40004.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.082644 restraints weight = 36160.979| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19087 Z= 0.158 Angle : 0.660 13.627 26143 Z= 0.342 Chirality : 0.042 0.166 2970 Planarity : 0.003 0.038 3082 Dihedral : 19.760 178.659 3489 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.74 % Favored : 93.12 % Rotamer: Outliers : 3.76 % Allowed : 23.02 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2170 helix: -0.17 (0.18), residues: 891 sheet: -1.41 (0.28), residues: 357 loop : -1.71 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 130 TYR 0.016 0.001 TYR C 315 PHE 0.013 0.002 PHE D 126 HIS 0.005 0.001 HIS F 294 Details of bonding type rmsd covalent geometry : bond 0.00355 (19087) covalent geometry : angle 0.65963 (26143) hydrogen bonds : bond 0.03666 ( 590) hydrogen bonds : angle 5.40562 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 129 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7361 (mmm) cc_final: 0.6747 (mmm) REVERT: D 235 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (tpt90) REVERT: E 274 ASP cc_start: 0.7212 (m-30) cc_final: 0.6654 (p0) REVERT: E 278 MET cc_start: 0.1079 (mmt) cc_final: 0.0004 (ptt) REVERT: F 124 GLU cc_start: 0.6994 (tp30) cc_final: 0.6689 (tp30) REVERT: F 300 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7812 (pp) REVERT: G 125 MET cc_start: 0.7699 (mpp) cc_final: 0.6061 (mmm) REVERT: G 205 TYR cc_start: 0.7696 (t80) cc_final: 0.7448 (t80) REVERT: G 301 TYR cc_start: 0.5457 (t80) cc_final: 0.4964 (t80) REVERT: A 251 MET cc_start: 0.6252 (mmm) cc_final: 0.6013 (mmm) REVERT: C 54 TYR cc_start: 0.8372 (m-10) cc_final: 0.8158 (m-80) REVERT: C 84 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6857 (ppp) REVERT: C 315 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: C 326 MET cc_start: 0.8147 (tpp) cc_final: 0.7911 (tpp) REVERT: B 210 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8145 (mtm) REVERT: B 326 MET cc_start: 0.7630 (tpp) cc_final: 0.6691 (mmm) outliers start: 66 outliers final: 54 residues processed: 177 average time/residue: 0.1081 time to fit residues: 31.7419 Evaluate side-chains 184 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 163 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN D 290 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN A 244 HIS ** C 294 HIS ** 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 = 0.4214 r_free = 0.4214 target = 0.104361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.079724 restraints weight = 82663.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.078467 restraints weight = 63859.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.078746 restraints weight = 47281.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.079147 restraints weight = 42742.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.079175 restraints weight = 38491.770| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 19087 Z= 0.314 Angle : 0.809 12.518 26143 Z= 0.419 Chirality : 0.046 0.162 2970 Planarity : 0.005 0.051 3082 Dihedral : 20.062 177.406 3489 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.28 % Favored : 90.54 % Rotamer: Outliers : 3.76 % Allowed : 24.10 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 2170 helix: -0.52 (0.17), residues: 921 sheet: -1.50 (0.29), residues: 346 loop : -1.94 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 235 TYR 0.032 0.002 TYR C 315 PHE 0.019 0.002 PHE D 327 HIS 0.012 0.002 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00686 (19087) covalent geometry : angle 0.80881 (26143) hydrogen bonds : bond 0.04426 ( 590) hydrogen bonds : angle 5.99893 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7325 (mmm) cc_final: 0.6701 (mmm) REVERT: D 235 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7792 (tpt90) REVERT: E 278 MET cc_start: 0.0942 (mmt) cc_final: -0.0055 (ptt) REVERT: F 251 MET cc_start: 0.9080 (ttm) cc_final: 0.8707 (ttt) REVERT: F 300 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7957 (pp) REVERT: G 125 MET cc_start: 0.7777 (mpp) cc_final: 0.5895 (mmm) REVERT: G 205 TYR cc_start: 0.7699 (t80) cc_final: 0.7452 (t80) REVERT: G 301 TYR cc_start: 0.5487 (t80) cc_final: 0.5244 (t80) REVERT: A 251 MET cc_start: 0.6334 (mmm) cc_final: 0.6052 (mmm) REVERT: C 54 TYR cc_start: 0.8480 (m-10) cc_final: 0.8238 (m-80) REVERT: C 315 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: C 326 MET cc_start: 0.8207 (tpp) cc_final: 0.7976 (tpp) REVERT: B 326 MET cc_start: 0.7807 (tpp) cc_final: 0.6724 (mmm) outliers start: 66 outliers final: 47 residues processed: 167 average time/residue: 0.1102 time to fit residues: 30.5755 Evaluate side-chains 166 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 32 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** 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 = 0.4128 r_free = 0.4128 target = 0.102890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.075585 restraints weight = 81306.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.075295 restraints weight = 54461.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.075565 restraints weight = 38874.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.075802 restraints weight = 34373.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.075960 restraints weight = 32136.384| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 19087 Z= 0.261 Angle : 0.770 12.177 26143 Z= 0.397 Chirality : 0.045 0.232 2970 Planarity : 0.004 0.050 3082 Dihedral : 19.991 179.439 3487 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.98 % Favored : 91.88 % Rotamer: Outliers : 3.19 % Allowed : 24.56 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.18), residues: 2170 helix: -0.47 (0.17), residues: 905 sheet: -1.60 (0.28), residues: 352 loop : -1.89 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 310 TYR 0.025 0.002 TYR C 315 PHE 0.016 0.002 PHE D 126 HIS 0.008 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00577 (19087) covalent geometry : angle 0.77004 (26143) hydrogen bonds : bond 0.04207 ( 590) hydrogen bonds : angle 5.89045 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7546 (mmm) cc_final: 0.6874 (mmm) REVERT: D 235 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7797 (tpt90) REVERT: D 278 MET cc_start: 0.3226 (tpt) cc_final: 0.3006 (tpp) REVERT: E 278 MET cc_start: 0.1115 (mmt) cc_final: 0.0055 (ptt) REVERT: F 124 GLU cc_start: 0.7558 (tp30) cc_final: 0.6806 (tp30) REVERT: F 300 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8240 (pp) REVERT: G 125 MET cc_start: 0.7900 (mpp) cc_final: 0.6123 (mmm) REVERT: G 205 TYR cc_start: 0.7764 (t80) cc_final: 0.7515 (t80) REVERT: G 301 TYR cc_start: 0.5643 (t80) cc_final: 0.5348 (t80) REVERT: A 251 MET cc_start: 0.6211 (mmm) cc_final: 0.5944 (mmm) REVERT: C 54 TYR cc_start: 0.8618 (m-10) cc_final: 0.8383 (m-80) REVERT: C 315 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: C 326 MET cc_start: 0.8365 (tpp) cc_final: 0.8063 (tpp) REVERT: B 210 MET cc_start: 0.8777 (mtm) cc_final: 0.8105 (mtm) REVERT: B 326 MET cc_start: 0.8152 (tpp) cc_final: 0.7044 (mmm) outliers start: 56 outliers final: 48 residues processed: 163 average time/residue: 0.1086 time to fit residues: 29.5371 Evaluate side-chains 169 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN C 200 GLN ** C 294 HIS ** 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 = 0.4267 r_free = 0.4267 target = 0.106983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.084057 restraints weight = 82073.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.082444 restraints weight = 57505.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.082897 restraints weight = 47143.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.082925 restraints weight = 39346.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.083133 restraints weight = 37279.393| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19087 Z= 0.141 Angle : 0.691 14.350 26143 Z= 0.352 Chirality : 0.042 0.186 2970 Planarity : 0.003 0.040 3082 Dihedral : 19.753 177.992 3487 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.92 % Favored : 92.94 % Rotamer: Outliers : 3.19 % Allowed : 24.50 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.18), residues: 2170 helix: -0.10 (0.18), residues: 878 sheet: -1.51 (0.28), residues: 356 loop : -1.69 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 310 TYR 0.014 0.001 TYR E 205 PHE 0.014 0.002 PHE G 248 HIS 0.006 0.001 HIS F 294 Details of bonding type rmsd covalent geometry : bond 0.00324 (19087) covalent geometry : angle 0.69106 (26143) hydrogen bonds : bond 0.03773 ( 590) hydrogen bonds : angle 5.47120 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.31 seconds wall clock time: 52 minutes 10.02 seconds (3130.02 seconds total)