Starting phenix.real_space_refine on Sat Sep 12 23:20:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui7_64186/09_2026/9ui7_64186.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui7_64186/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ui7_64186/09_2026/9ui7_64186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui7_64186/09_2026/9ui7_64186.map" model { file = "/net/cci-nas-00/data/ceres_data/9ui7_64186/09_2026/9ui7_64186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui7_64186/09_2026/9ui7_64186.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.54, per 1000 atoms: 0.24 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: 1.70 Conformation dependent library (CDL) restraints added in 791.0 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: 2.39 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: 2.95 Time building geometry restraints manager: 2.20 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=" C1' DT H 33 " pdb=" N1 DT H 33 " ideal model delta sigma weight residual 1.468 1.596 -0.128 1.40e-02 5.10e+03 8.36e+01 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 ... (remaining 19082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.22: 25977 5.22 - 10.44: 148 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=" O4' DA I 28 " pdb=" C1' DA I 28 " pdb=" N9 DA I 28 " ideal model delta sigma weight residual 108.00 113.83 -5.83 7.00e-01 2.04e+00 6.93e+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 ... (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: 2411 0.070 - 0.140: 489 0.140 - 0.210: 53 0.210 - 0.279: 11 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.190 Find NCS groups from input model: 0.400 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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= 0.521 Angle : 1.233 26.092 26143 Z= 0.735 Chirality : 0.058 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/Z covalent geometry : bond 0.00915 / 0.52 (19087) covalent geometry : angle 1.23340 / 0.74 (26143) hydrogen bonds : bond 0.30550 / 20.22 ( 590) hydrogen bonds : angle 10.72705 / 7.40 ( 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 : 0.669 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: 0.1276 time to fit residues: 35.9350 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 : 0.673 ------------------------------------------------------------------------------- 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: 6.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 200 GLN D 206 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** F 330 ASN G 145 GLN ** G 200 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** B 188 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.105748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081068 restraints weight = 82133.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079549 restraints weight = 52131.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079950 restraints weight = 42995.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.080100 restraints weight = 36349.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080149 restraints weight = 35101.571| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 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 = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19087 Z= 0.256 Angle : 0.810 9.893 26143 Z= 0.436 Chirality : 0.048 0.407 2970 Planarity : 0.005 0.050 3082 Dihedral : 20.968 172.578 3493 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 2.34 % Allowed : 15.38 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.67 % Twisted General : 0.42 % 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: -3.82 (0.15), residues: 2170 helix: -2.63 (0.13), residues: 909 sheet: -1.96 (0.26), residues: 360 loop : -2.49 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 193 TYR 0.034 0.002 TYR C 315 PHE 0.023 0.002 PHE E 92 HIS 0.008 0.002 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.26 (19087) covalent geometry : angle 0.80950 / 0.44 (26143) hydrogen bonds : bond 0.06628 / 4.44 ( 590) hydrogen bonds : angle 7.27328 / 5.02 ( 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 165 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7316 (mmm) cc_final: 0.6676 (mmm) REVERT: E 93 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8241 (m-70) REVERT: E 278 MET cc_start: 0.2191 (mmt) cc_final: 0.0461 (ptt) REVERT: F 251 MET cc_start: 0.9165 (ttm) cc_final: 0.8925 (ttm) REVERT: G 125 MET cc_start: 0.5568 (mpp) cc_final: 0.4290 (mmt) REVERT: C 54 TYR cc_start: 0.8336 (m-10) cc_final: 0.7880 (m-80) REVERT: C 131 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8232 (m) REVERT: B 210 MET cc_start: 0.8935 (mtm) cc_final: 0.7819 (tmm) REVERT: B 326 MET cc_start: 0.7914 (tpp) cc_final: 0.7034 (mmm) outliers start: 41 outliers final: 25 residues processed: 155 average time/residue: 0.1114 time to fit residues: 28.7743 Evaluate side-chains 145 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL 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 255 LEU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 139 THR 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 A residue 218 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 230 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 104 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 HIS F 268 GLN ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.106848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.081892 restraints weight = 82521.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079999 restraints weight = 61823.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.080496 restraints weight = 49274.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.080635 restraints weight = 40433.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.080699 restraints weight = 37652.292| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19087 Z= 0.176 Angle : 0.706 9.777 26143 Z= 0.382 Chirality : 0.045 0.322 2970 Planarity : 0.004 0.059 3082 Dihedral : 20.538 170.635 3493 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.65 % Favored : 93.08 % Rotamer: Outliers : 2.68 % Allowed : 17.09 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.67 % Twisted General : 0.28 % 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: -3.02 (0.16), residues: 2170 helix: -1.79 (0.15), residues: 896 sheet: -1.74 (0.27), residues: 359 loop : -2.17 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 130 TYR 0.018 0.001 TYR G 228 PHE 0.017 0.002 PHE G 279 HIS 0.008 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (19087) covalent geometry : angle 0.70611 / 0.38 (26143) hydrogen bonds : bond 0.05068 / 3.42 ( 590) hydrogen bonds : angle 6.51172 / 4.50 ( 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 179 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.677 Fit side-chains REVERT: D 84 MET cc_start: 0.7311 (mmm) cc_final: 0.6745 (mmm) REVERT: D 211 MET cc_start: 0.8148 (mmt) cc_final: 0.7780 (mmm) REVERT: E 278 MET cc_start: 0.1744 (mmt) cc_final: 0.0182 (ptt) REVERT: G 126 PHE cc_start: 0.4634 (m-80) cc_final: 0.4394 (m-80) REVERT: A 210 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6662 (ptp) REVERT: C 54 TYR cc_start: 0.8367 (m-10) cc_final: 0.7915 (m-80) REVERT: B 210 MET cc_start: 0.8880 (mtm) cc_final: 0.7880 (tmm) outliers start: 47 outliers final: 29 residues processed: 168 average time/residue: 0.1093 time to fit residues: 30.8752 Evaluate side-chains 149 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 G residue 228 TYR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 LEU 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 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: 9.9990 chunk 182 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 159 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 93 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 202 GLN ** 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 = 0.4250 r_free = 0.4250 target = 0.106461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082932 restraints weight = 82979.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.081542 restraints weight = 58009.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.081866 restraints weight = 46988.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.082179 restraints weight = 38914.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.082209 restraints weight = 36188.556| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 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 = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2108 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= 0.195 Angle : 0.713 10.233 26143 Z= 0.379 Chirality : 0.045 0.293 2970 Planarity : 0.004 0.041 3082 Dihedral : 20.301 173.942 3491 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.66 % Favored : 92.06 % Rotamer: Outliers : 3.25 % Allowed : 19.09 % Favored : 77.66 % 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: -2.53 (0.17), residues: 2170 helix: -1.20 (0.16), residues: 887 sheet: -1.65 (0.27), residues: 361 loop : -2.05 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 193 TYR 0.019 0.002 TYR C 315 PHE 0.017 0.002 PHE G 279 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (19087) covalent geometry : angle 0.71296 / 0.38 (26143) hydrogen bonds : bond 0.04570 / 3.10 ( 590) hydrogen bonds : angle 6.26088 / 4.33 ( 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 179 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7318 (mmm) cc_final: 0.6802 (mmm) REVERT: D 211 MET cc_start: 0.8163 (mmt) cc_final: 0.7776 (mmm) REVERT: E 278 MET cc_start: 0.1954 (mmt) cc_final: 0.0451 (ptt) REVERT: G 125 MET cc_start: 0.6890 (mpp) cc_final: 0.5023 (mmm) REVERT: G 126 PHE cc_start: 0.4603 (m-80) cc_final: 0.4211 (m-80) REVERT: A 210 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6592 (ptp) REVERT: C 54 TYR cc_start: 0.8441 (m-10) cc_final: 0.8126 (m-80) REVERT: C 210 MET cc_start: 0.8043 (mtm) cc_final: 0.7826 (mtp) REVERT: C 315 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7226 (m-80) outliers start: 57 outliers final: 39 residues processed: 167 average time/residue: 0.1084 time to fit residues: 30.5164 Evaluate side-chains 158 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 210 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 128 GLU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 219 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 60 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 253 LEU 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 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 255 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 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 183 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.4250 r_free = 0.4250 target = 0.106391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.083095 restraints weight = 82030.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.081544 restraints weight = 56389.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.081984 restraints weight = 46883.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.082140 restraints weight = 39242.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082161 restraints weight = 37208.018| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 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 = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2295 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= 0.205 Angle : 0.716 11.324 26143 Z= 0.379 Chirality : 0.045 0.291 2970 Planarity : 0.004 0.041 3082 Dihedral : 20.178 174.642 3491 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 3.30 % Allowed : 20.57 % Favored : 76.13 % 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: -2.32 (0.17), residues: 2170 helix: -0.92 (0.17), residues: 896 sheet: -1.64 (0.28), residues: 364 loop : -2.01 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 130 TYR 0.020 0.002 TYR C 315 PHE 0.016 0.002 PHE G 279 HIS 0.005 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (19087) covalent geometry : angle 0.71633 / 0.38 (26143) hydrogen bonds : bond 0.04346 / 2.94 ( 590) hydrogen bonds : angle 6.11344 / 4.22 ( 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 180 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7326 (mmm) cc_final: 0.6785 (mmm) REVERT: D 211 MET cc_start: 0.8140 (mmt) cc_final: 0.7730 (mmm) REVERT: E 278 MET cc_start: 0.1762 (mmt) cc_final: 0.0364 (ptt) REVERT: F 251 MET cc_start: 0.8969 (ttm) cc_final: 0.8700 (ttp) REVERT: G 125 MET cc_start: 0.7050 (mpp) cc_final: 0.5059 (mmm) REVERT: G 205 TYR cc_start: 0.7462 (t80) cc_final: 0.7224 (t80) REVERT: G 301 TYR cc_start: 0.5077 (t80) cc_final: 0.4791 (t80) REVERT: A 210 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6570 (ptp) REVERT: C 54 TYR cc_start: 0.8453 (m-10) cc_final: 0.8148 (m-80) REVERT: C 315 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: B 210 MET cc_start: 0.8723 (mtm) cc_final: 0.8183 (mtm) outliers start: 58 outliers final: 46 residues processed: 167 average time/residue: 0.1071 time to fit residues: 30.1395 Evaluate side-chains 164 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 99 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 220 ILE 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 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 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 G residue 109 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 210 MET 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 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 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.107091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.083772 restraints weight = 81657.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.082109 restraints weight = 58774.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.082382 restraints weight = 50965.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.082656 restraints weight = 40854.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082707 restraints weight = 36870.324| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 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 = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19087 Z= 0.156 Angle : 0.689 13.651 26143 Z= 0.362 Chirality : 0.044 0.286 2970 Planarity : 0.004 0.039 3082 Dihedral : 20.046 172.569 3491 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.06 % Favored : 92.80 % Rotamer: Outliers : 3.59 % Allowed : 21.08 % Favored : 75.33 % 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: -2.10 (0.18), residues: 2170 helix: -0.72 (0.17), residues: 890 sheet: -1.54 (0.28), residues: 362 loop : -1.90 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 130 TYR 0.018 0.001 TYR C 315 PHE 0.015 0.002 PHE E 86 HIS 0.013 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (19087) covalent geometry : angle 0.68870 / 0.36 (26143) hydrogen bonds : bond 0.04114 / 2.79 ( 590) hydrogen bonds : angle 5.91202 / 4.07 ( 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 184 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 121 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7351 (mmm) cc_final: 0.6793 (mmm) REVERT: D 211 MET cc_start: 0.8132 (mmt) cc_final: 0.7705 (mmm) REVERT: E 278 MET cc_start: 0.1596 (mmt) cc_final: 0.0260 (ptt) REVERT: F 124 GLU cc_start: 0.6599 (tp30) cc_final: 0.6235 (tp30) REVERT: F 251 MET cc_start: 0.8990 (ttm) cc_final: 0.8691 (ttt) REVERT: G 125 MET cc_start: 0.7139 (mpp) cc_final: 0.5306 (mmm) REVERT: G 205 TYR cc_start: 0.7548 (t80) cc_final: 0.7286 (t80) REVERT: A 210 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6482 (ptp) REVERT: C 54 TYR cc_start: 0.8429 (m-10) cc_final: 0.8148 (m-80) REVERT: C 210 MET cc_start: 0.7974 (mtm) cc_final: 0.7771 (mtp) REVERT: C 315 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: B 210 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (mtm) REVERT: B 326 MET cc_start: 0.7814 (tpp) cc_final: 0.6739 (mmm) outliers start: 63 outliers final: 44 residues processed: 170 average time/residue: 0.1052 time to fit residues: 30.0971 Evaluate side-chains 163 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain D residue 253 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 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 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 62 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 VAL 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 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR 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 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 126 optimal weight: 50.0000 chunk 117 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 272 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 = 0.4277 r_free = 0.4277 target = 0.107900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.082509 restraints weight = 82084.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081569 restraints weight = 52514.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082260 restraints weight = 43375.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082165 restraints weight = 35326.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.082316 restraints weight = 34800.825| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19087 Z= 0.129 Angle : 0.668 11.961 26143 Z= 0.351 Chirality : 0.044 0.279 2970 Planarity : 0.003 0.037 3082 Dihedral : 19.912 170.777 3491 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.55 % Favored : 93.31 % Rotamer: Outliers : 3.02 % Allowed : 21.71 % Favored : 75.27 % 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: -1.95 (0.18), residues: 2170 helix: -0.57 (0.17), residues: 904 sheet: -1.47 (0.28), residues: 362 loop : -1.87 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 130 TYR 0.014 0.001 TYR C 315 PHE 0.012 0.002 PHE G 279 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (19087) covalent geometry : angle 0.66807 / 0.35 (26143) hydrogen bonds : bond 0.03917 / 2.69 ( 590) hydrogen bonds : angle 5.72010 / 3.93 ( 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 180 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7356 (mmm) cc_final: 0.6815 (mmm) REVERT: D 211 MET cc_start: 0.8110 (mmt) cc_final: 0.7727 (mmm) REVERT: E 158 MET cc_start: 0.7276 (tpp) cc_final: 0.6844 (mmm) REVERT: E 278 MET cc_start: 0.1211 (mmt) cc_final: 0.0023 (ptt) REVERT: F 124 GLU cc_start: 0.6762 (tp30) cc_final: 0.6485 (tp30) REVERT: F 251 MET cc_start: 0.9119 (ttm) cc_final: 0.8767 (ttt) REVERT: G 125 MET cc_start: 0.7304 (mpp) cc_final: 0.5739 (mmm) REVERT: G 205 TYR cc_start: 0.7681 (t80) cc_final: 0.7431 (t80) REVERT: A 210 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6557 (ptp) REVERT: C 54 TYR cc_start: 0.8405 (m-10) cc_final: 0.8165 (m-80) REVERT: C 315 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: B 210 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8194 (mtm) REVERT: B 326 MET cc_start: 0.7879 (tpp) cc_final: 0.6718 (mmm) outliers start: 53 outliers final: 44 residues processed: 166 average time/residue: 0.1050 time to fit residues: 29.5893 Evaluate side-chains 167 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 212 VAL 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 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 259 PHE 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 312 CYS Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 210 MET 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 252 LEU 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 104 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 172 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 105 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 108 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.106832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.083478 restraints weight = 81540.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.081629 restraints weight = 57504.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082026 restraints weight = 49088.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082209 restraints weight = 39803.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.082272 restraints weight = 37260.858| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 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 = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19087 Z= 0.183 Angle : 0.701 12.509 26143 Z= 0.366 Chirality : 0.044 0.276 2970 Planarity : 0.004 0.038 3082 Dihedral : 19.884 174.154 3491 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.57 % Favored : 92.29 % Rotamer: Outliers : 3.19 % Allowed : 22.22 % Favored : 74.59 % 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: -1.83 (0.18), residues: 2170 helix: -0.43 (0.17), residues: 891 sheet: -1.49 (0.28), residues: 363 loop : -1.79 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 235 TYR 0.017 0.001 TYR C 315 PHE 0.015 0.002 PHE E 86 HIS 0.005 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (19087) covalent geometry : angle 0.70057 / 0.37 (26143) hydrogen bonds : bond 0.03947 / 2.71 ( 590) hydrogen bonds : angle 5.73016 / 3.94 ( 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 178 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 122 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: D 84 MET cc_start: 0.7352 (mmm) cc_final: 0.6824 (mmm) REVERT: D 211 MET cc_start: 0.8131 (mmt) cc_final: 0.7681 (mmm) REVERT: E 158 MET cc_start: 0.7299 (tpp) cc_final: 0.6904 (mmm) REVERT: E 278 MET cc_start: 0.1426 (mmt) cc_final: 0.0174 (ptt) REVERT: F 124 GLU cc_start: 0.6716 (tp30) cc_final: 0.6461 (tp30) REVERT: F 251 MET cc_start: 0.8981 (ttm) cc_final: 0.8645 (ttt) REVERT: F 265 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8628 (tp) REVERT: G 125 MET cc_start: 0.7373 (mpp) cc_final: 0.5518 (mmm) REVERT: G 205 TYR cc_start: 0.7535 (t80) cc_final: 0.7274 (t80) REVERT: A 210 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6533 (ptp) REVERT: C 54 TYR cc_start: 0.8417 (m-10) cc_final: 0.8176 (m-80) REVERT: C 315 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: B 210 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8230 (mtm) outliers start: 56 outliers final: 49 residues processed: 165 average time/residue: 0.1052 time to fit residues: 29.1978 Evaluate side-chains 171 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 210 MET Chi-restraints excluded: chain E residue 212 VAL 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 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 259 PHE Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 265 ILE 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 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 210 MET 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 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR 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 104 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 172 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 163 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.4238 r_free = 0.4238 target = 0.105739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.081611 restraints weight = 81822.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.079640 restraints weight = 60946.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080079 restraints weight = 48747.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.080108 restraints weight = 41638.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.080299 restraints weight = 38182.610| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 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 = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2756 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= 0.232 Angle : 0.746 11.880 26143 Z= 0.389 Chirality : 0.046 0.279 2970 Planarity : 0.004 0.041 3082 Dihedral : 19.931 176.593 3491 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.79 % Rotamer: Outliers : 3.08 % Allowed : 23.13 % Favored : 73.79 % 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: -1.83 (0.18), residues: 2170 helix: -0.45 (0.17), residues: 900 sheet: -1.46 (0.29), residues: 353 loop : -1.80 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 95 TYR 0.023 0.002 TYR C 315 PHE 0.021 0.002 PHE E 86 HIS 0.007 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (19087) covalent geometry : angle 0.74573 / 0.39 (26143) hydrogen bonds : bond 0.04161 / 2.84 ( 590) hydrogen bonds : angle 5.84984 / 4.02 ( 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 173 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7335 (mmm) cc_final: 0.6793 (mmm) REVERT: E 158 MET cc_start: 0.7300 (tpp) cc_final: 0.6958 (mmm) REVERT: E 278 MET cc_start: 0.1297 (mmt) cc_final: 0.0097 (ptt) REVERT: F 124 GLU cc_start: 0.6865 (tp30) cc_final: 0.6335 (tp30) REVERT: F 251 MET cc_start: 0.9043 (ttm) cc_final: 0.8703 (ttt) REVERT: F 265 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8641 (tp) REVERT: G 125 MET cc_start: 0.7460 (mpp) cc_final: 0.5626 (mmm) REVERT: G 205 TYR cc_start: 0.7666 (t80) cc_final: 0.7405 (t80) REVERT: A 210 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6639 (ptp) REVERT: C 54 TYR cc_start: 0.8466 (m-10) cc_final: 0.8211 (m-80) REVERT: C 315 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: B 326 MET cc_start: 0.7870 (tpp) cc_final: 0.6566 (mmm) outliers start: 54 outliers final: 46 residues processed: 161 average time/residue: 0.1050 time to fit residues: 28.4947 Evaluate side-chains 167 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR 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 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 265 ILE 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 210 MET 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 219 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR 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 104 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 221 VAL 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: 20.0000 chunk 160 optimal weight: 0.0000 chunk 220 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 127 optimal weight: 40.0000 chunk 94 optimal weight: 50.0000 chunk 197 optimal weight: 2.9990 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 GLN ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.105631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.081972 restraints weight = 81695.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.079880 restraints weight = 64815.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.080377 restraints weight = 51360.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.080537 restraints weight = 41129.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.080580 restraints weight = 38887.186| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 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 = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19087 Z= 0.244 Angle : 0.769 14.530 26143 Z= 0.400 Chirality : 0.046 0.280 2970 Planarity : 0.004 0.044 3082 Dihedral : 19.965 176.576 3491 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.58 % Favored : 91.28 % Rotamer: Outliers : 3.02 % Allowed : 23.48 % Favored : 73.50 % 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: -1.90 (0.18), residues: 2170 helix: -0.47 (0.17), residues: 904 sheet: -1.56 (0.28), residues: 356 loop : -1.84 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 241 TYR 0.024 0.002 TYR C 315 PHE 0.028 0.002 PHE G 126 HIS 0.007 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (19087) covalent geometry : angle 0.76851 / 0.40 (26143) hydrogen bonds : bond 0.04206 / 2.88 ( 590) hydrogen bonds : angle 5.93744 / 4.07 ( 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: 53 poor density : 122 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.7337 (mmm) cc_final: 0.6805 (mmm) REVERT: E 158 MET cc_start: 0.7277 (tpp) cc_final: 0.6954 (mmm) REVERT: E 278 MET cc_start: 0.1307 (mmt) cc_final: 0.0088 (ptt) REVERT: F 124 GLU cc_start: 0.6836 (tp30) cc_final: 0.6212 (tp30) REVERT: F 251 MET cc_start: 0.9006 (ttm) cc_final: 0.8700 (ttt) REVERT: F 265 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8596 (tp) REVERT: G 125 MET cc_start: 0.7585 (mpp) cc_final: 0.5624 (mmm) REVERT: G 205 TYR cc_start: 0.7628 (t80) cc_final: 0.7362 (t80) REVERT: A 210 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6591 (ptp) REVERT: C 54 TYR cc_start: 0.8455 (m-10) cc_final: 0.8208 (m-80) REVERT: C 315 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: B 210 MET cc_start: 0.8345 (mtm) cc_final: 0.7928 (mtm) REVERT: B 326 MET cc_start: 0.7870 (tpp) cc_final: 0.6489 (mmm) outliers start: 53 outliers final: 49 residues processed: 162 average time/residue: 0.1088 time to fit residues: 29.9394 Evaluate side-chains 172 residues out of total 1756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 212 VAL 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 142 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 265 ILE 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 87 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 210 MET 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 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 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 104 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 221 VAL 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 8 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.4242 r_free = 0.4242 target = 0.105985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.081057 restraints weight = 81626.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079747 restraints weight = 53308.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.080415 restraints weight = 46680.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.080406 restraints weight = 37908.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.080527 restraints weight = 35034.243| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19087 Z= 0.215 Angle : 0.740 12.873 26143 Z= 0.385 Chirality : 0.045 0.278 2970 Planarity : 0.004 0.042 3082 Dihedral : 19.907 175.529 3489 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.75 % Favored : 92.11 % Rotamer: Outliers : 3.13 % Allowed : 23.42 % Favored : 73.45 % 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: -1.84 (0.18), residues: 2170 helix: -0.40 (0.17), residues: 903 sheet: -1.50 (0.28), residues: 353 loop : -1.85 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 130 TYR 0.022 0.002 TYR C 315 PHE 0.016 0.002 PHE E 86 HIS 0.006 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (19087) covalent geometry : angle 0.73954 / 0.39 (26143) hydrogen bonds : bond 0.04122 / 2.82 ( 590) hydrogen bonds : angle 5.84761 / 4.00 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.79 seconds wall clock time: 54 minutes 2.29 seconds (3242.29 seconds total)