Starting phenix.real_space_refine on Sat Jun 7 03:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc7_37433/06_2025/8wc7_37433_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc7_37433/06_2025/8wc7_37433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wc7_37433/06_2025/8wc7_37433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc7_37433/06_2025/8wc7_37433.map" model { file = "/net/cci-nas-00/data/ceres_data/8wc7_37433/06_2025/8wc7_37433_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc7_37433/06_2025/8wc7_37433_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.076 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5440 2.51 5 N 1459 2.21 5 O 1577 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1856 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2523 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "R" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1984 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "S" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1769 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Y" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 384 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'VMK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.48, per 1000 atoms: 0.64 Number of scatterers: 8532 At special positions: 0 Unit cell: (87.55, 124.95, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 F 1 9.00 O 1577 8.00 N 1459 7.00 C 5440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 37.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.805A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.880A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.702A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.943A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 318 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.542A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.544A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 50 removed outlier: 3.896A pdb=" N PHE R 50 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 85 removed outlier: 3.977A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 91 through 125 removed outlier: 3.769A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA R 108 " --> pdb=" O MET R 104 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER R 109 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP R 119 " --> pdb=" O PHE R 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 130 removed outlier: 3.823A pdb=" N TYR R 130 " --> pdb=" O PRO R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 159 removed outlier: 3.993A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Proline residue: R 150 - end of helix removed outlier: 3.603A pdb=" N MET R 157 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE R 159 " --> pdb=" O PHE R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 175 removed outlier: 3.723A pdb=" N TYR R 171 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG R 172 " --> pdb=" O GLU R 168 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER R 173 " --> pdb=" O GLU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 199 through 204 removed outlier: 3.621A pdb=" N VAL R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 214 removed outlier: 3.593A pdb=" N VAL R 208 " --> pdb=" O VAL R 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR R 209 " --> pdb=" O MET R 205 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 225 removed outlier: 3.841A pdb=" N SER R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 251 Processing helix chain 'R' and resid 251 through 256 Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.725A pdb=" N CYS R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 256 through 261' Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.800A pdb=" N CYS R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP R 271 " --> pdb=" O CYS R 267 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 281 through 302 removed outlier: 3.775A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 310 removed outlier: 3.529A pdb=" N ARG R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 305 through 310' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.539A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.994A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.827A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 4.017A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.541A pdb=" N ASP A 200 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.777A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.061A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.077A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.654A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.794A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.976A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.855A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 340 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1369 1.28 - 1.41: 2300 1.41 - 1.55: 4959 1.55 - 1.68: 12 1.68 - 1.82: 80 Bond restraints: 8720 Sorted by residual: bond pdb=" C PHE R 264 " pdb=" O PHE R 264 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.10e-02 8.26e+03 7.31e+01 bond pdb=" CA PHE R 264 " pdb=" C PHE R 264 " ideal model delta sigma weight residual 1.527 1.459 0.068 1.21e-02 6.83e+03 3.16e+01 bond pdb=" C TYR R 153 " pdb=" O TYR R 153 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.19e-02 7.06e+03 3.15e+01 bond pdb=" C LYS R 96 " pdb=" O LYS R 96 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.15e-02 7.56e+03 1.98e+01 bond pdb=" N SER R 182 " pdb=" CA SER R 182 " ideal model delta sigma weight residual 1.455 1.484 -0.029 7.00e-03 2.04e+04 1.76e+01 ... (remaining 8715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11664 2.05 - 4.10: 155 4.10 - 6.15: 26 6.15 - 8.20: 2 8.20 - 10.26: 1 Bond angle restraints: 11848 Sorted by residual: angle pdb=" C SER R 182 " pdb=" N PRO R 183 " pdb=" CA PRO R 183 " ideal model delta sigma weight residual 119.93 114.26 5.67 1.07e+00 8.73e-01 2.81e+01 angle pdb=" N PHE R 184 " pdb=" CA PHE R 184 " pdb=" C PHE R 184 " ideal model delta sigma weight residual 108.90 101.74 7.16 1.63e+00 3.76e-01 1.93e+01 angle pdb=" N ASP A 206 " pdb=" CA ASP A 206 " pdb=" C ASP A 206 " ideal model delta sigma weight residual 111.07 115.56 -4.49 1.07e+00 8.73e-01 1.76e+01 angle pdb=" O SER Y 57 " pdb=" C SER Y 57 " pdb=" N GLU Y 58 " ideal model delta sigma weight residual 122.10 126.08 -3.98 1.06e+00 8.90e-01 1.41e+01 angle pdb=" CA SER Y 57 " pdb=" C SER Y 57 " pdb=" N GLU Y 58 " ideal model delta sigma weight residual 119.26 115.05 4.21 1.14e+00 7.69e-01 1.36e+01 ... (remaining 11843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 4588 15.71 - 31.42: 390 31.42 - 47.13: 96 47.13 - 62.84: 22 62.84 - 78.55: 17 Dihedral angle restraints: 5113 sinusoidal: 1857 harmonic: 3256 Sorted by residual: dihedral pdb=" C ASP A 321 " pdb=" N ASP A 321 " pdb=" CA ASP A 321 " pdb=" CB ASP A 321 " ideal model delta harmonic sigma weight residual -122.60 -133.91 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" N ASP A 321 " pdb=" C ASP A 321 " pdb=" CA ASP A 321 " pdb=" CB ASP A 321 " ideal model delta harmonic sigma weight residual 122.80 134.04 -11.24 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " pdb=" CZ ARG B 22 " ideal model delta sinusoidal sigma weight residual 90.00 23.10 66.90 2 1.50e+01 4.44e-03 1.81e+01 ... (remaining 5110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1276 0.094 - 0.187: 69 0.187 - 0.280: 0 0.280 - 0.374: 1 0.374 - 0.467: 1 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA ASP A 321 " pdb=" N ASP A 321 " pdb=" C ASP A 321 " pdb=" CB ASP A 321 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA TYR R 153 " pdb=" N TYR R 153 " pdb=" C TYR R 153 " pdb=" CB TYR R 153 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA CYS R 181 " pdb=" N CYS R 181 " pdb=" C CYS R 181 " pdb=" CB CYS R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1344 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 264 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C PHE R 264 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE R 264 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE R 265 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 199 " 0.051 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO S 200 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO S 200 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO S 200 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 184 " 0.036 2.00e-02 2.50e+03 2.21e-02 8.57e+00 pdb=" CG PHE R 184 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE R 184 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE R 184 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE R 184 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 184 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 184 " 0.019 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1503 2.77 - 3.30: 7635 3.30 - 3.83: 13033 3.83 - 4.37: 15082 4.37 - 4.90: 27661 Nonbonded interactions: 64914 Sorted by model distance: nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 285 " pdb=" OD2 ASP A 310 " model vdw 2.281 3.040 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 228 " model vdw 2.282 3.040 nonbonded pdb=" OG SER S 17 " pdb=" O MET S 83 " model vdw 2.288 3.040 ... (remaining 64909 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 8722 Z= 0.249 Angle : 0.595 10.255 11852 Z= 0.343 Chirality : 0.045 0.467 1347 Planarity : 0.005 0.077 1505 Dihedral : 13.833 78.552 3005 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.80 % Allowed : 0.80 % Favored : 98.40 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1098 helix: 0.84 (0.30), residues: 363 sheet: 0.12 (0.32), residues: 280 loop : -1.74 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 88 HIS 0.004 0.001 HIS R 62 PHE 0.047 0.002 PHE R 264 TYR 0.016 0.001 TYR R 153 ARG 0.004 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.21167 ( 340) hydrogen bonds : angle 6.62044 ( 975) SS BOND : bond 0.00508 ( 2) SS BOND : angle 0.58800 ( 4) covalent geometry : bond 0.00384 ( 8720) covalent geometry : angle 0.59512 (11848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.903 Fit side-chains REVERT: B 17 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 44 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7467 (mm110) REVERT: B 175 GLN cc_start: 0.8045 (mt0) cc_final: 0.7811 (mt0) REVERT: R 153 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7216 (t80) outliers start: 7 outliers final: 4 residues processed: 147 average time/residue: 0.2823 time to fit residues: 52.6936 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 153 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 268 ASN B 311 HIS R 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108651 restraints weight = 11353.201| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.36 r_work: 0.3053 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8722 Z= 0.148 Angle : 0.563 6.668 11852 Z= 0.304 Chirality : 0.044 0.155 1347 Planarity : 0.005 0.056 1505 Dihedral : 6.580 82.382 1229 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.03 % Allowed : 8.13 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1098 helix: 1.00 (0.30), residues: 365 sheet: 0.37 (0.33), residues: 271 loop : -1.79 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 88 HIS 0.006 0.001 HIS R 62 PHE 0.015 0.002 PHE A 343 TYR 0.021 0.002 TYR A 30 ARG 0.003 0.000 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 340) hydrogen bonds : angle 4.78392 ( 975) SS BOND : bond 0.00724 ( 2) SS BOND : angle 0.49031 ( 4) covalent geometry : bond 0.00342 ( 8720) covalent geometry : angle 0.56254 (11848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.084 Fit side-chains REVERT: B 17 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 44 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8220 (mm-40) outliers start: 9 outliers final: 2 residues processed: 128 average time/residue: 0.2485 time to fit residues: 42.0961 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109541 restraints weight = 11458.056| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.36 r_work: 0.3067 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8722 Z= 0.106 Angle : 0.501 6.988 11852 Z= 0.270 Chirality : 0.042 0.140 1347 Planarity : 0.004 0.058 1505 Dihedral : 5.384 82.381 1216 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.46 % Allowed : 11.11 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1098 helix: 1.13 (0.30), residues: 370 sheet: 0.56 (0.33), residues: 265 loop : -1.72 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 88 HIS 0.003 0.001 HIS R 62 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR A 30 ARG 0.002 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 340) hydrogen bonds : angle 4.36460 ( 975) SS BOND : bond 0.00642 ( 2) SS BOND : angle 0.66659 ( 4) covalent geometry : bond 0.00231 ( 8720) covalent geometry : angle 0.50113 (11848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.885 Fit side-chains REVERT: B 17 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 44 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8226 (mm110) REVERT: B 215 GLU cc_start: 0.7731 (pt0) cc_final: 0.7513 (pt0) REVERT: R 283 ASN cc_start: 0.8699 (t0) cc_final: 0.8481 (t0) outliers start: 4 outliers final: 3 residues processed: 120 average time/residue: 0.2620 time to fit residues: 40.9299 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 311 HIS R 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111705 restraints weight = 11402.551| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.20 r_work: 0.3111 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8722 Z= 0.096 Angle : 0.476 6.723 11852 Z= 0.255 Chirality : 0.041 0.145 1347 Planarity : 0.004 0.060 1505 Dihedral : 5.181 79.559 1216 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.26 % Allowed : 12.83 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1098 helix: 1.31 (0.29), residues: 369 sheet: 0.58 (0.33), residues: 266 loop : -1.69 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 88 HIS 0.003 0.001 HIS R 62 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 340) hydrogen bonds : angle 4.08792 ( 975) SS BOND : bond 0.00608 ( 2) SS BOND : angle 0.66810 ( 4) covalent geometry : bond 0.00208 ( 8720) covalent geometry : angle 0.47596 (11848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.983 Fit side-chains REVERT: A 276 GLU cc_start: 0.6069 (mm-30) cc_final: 0.5553 (mm-30) REVERT: B 17 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 44 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8150 (mm110) REVERT: B 215 GLU cc_start: 0.7719 (pt0) cc_final: 0.7498 (pt0) REVERT: B 258 ASP cc_start: 0.7080 (t0) cc_final: 0.6874 (t0) REVERT: B 259 GLN cc_start: 0.7655 (mp10) cc_final: 0.7421 (mp10) REVERT: R 60 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7195 (tt) REVERT: R 164 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6148 (pp) outliers start: 11 outliers final: 5 residues processed: 127 average time/residue: 0.2551 time to fit residues: 42.8097 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 0.0370 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109854 restraints weight = 11427.515| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.21 r_work: 0.3070 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8722 Z= 0.128 Angle : 0.513 6.582 11852 Z= 0.276 Chirality : 0.043 0.149 1347 Planarity : 0.004 0.061 1505 Dihedral : 5.189 77.350 1216 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.72 % Allowed : 13.40 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1098 helix: 1.36 (0.29), residues: 369 sheet: 0.46 (0.32), residues: 273 loop : -1.59 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 88 HIS 0.005 0.001 HIS R 62 PHE 0.014 0.001 PHE A 343 TYR 0.020 0.001 TYR A 30 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 340) hydrogen bonds : angle 4.12376 ( 975) SS BOND : bond 0.00730 ( 2) SS BOND : angle 0.70011 ( 4) covalent geometry : bond 0.00299 ( 8720) covalent geometry : angle 0.51334 (11848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 267 LYS cc_start: 0.7644 (mttt) cc_final: 0.7312 (mtpt) REVERT: A 276 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5510 (mm-30) REVERT: B 17 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 42 ARG cc_start: 0.7824 (tmt170) cc_final: 0.7580 (ttt-90) REVERT: R 60 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7183 (tt) REVERT: R 164 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6185 (pp) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 0.2459 time to fit residues: 42.6339 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107909 restraints weight = 11336.766| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.25 r_work: 0.3046 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8722 Z= 0.143 Angle : 0.526 6.084 11852 Z= 0.283 Chirality : 0.043 0.157 1347 Planarity : 0.004 0.063 1505 Dihedral : 5.206 75.839 1216 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.95 % Allowed : 14.32 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1098 helix: 1.38 (0.29), residues: 368 sheet: 0.41 (0.32), residues: 279 loop : -1.55 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 88 HIS 0.005 0.001 HIS R 62 PHE 0.014 0.001 PHE A 343 TYR 0.021 0.001 TYR A 30 ARG 0.005 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 340) hydrogen bonds : angle 4.14507 ( 975) SS BOND : bond 0.00759 ( 2) SS BOND : angle 0.76329 ( 4) covalent geometry : bond 0.00339 ( 8720) covalent geometry : angle 0.52556 (11848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.890 Fit side-chains REVERT: A 267 LYS cc_start: 0.7733 (mttt) cc_final: 0.7369 (mtpt) REVERT: A 276 GLU cc_start: 0.6104 (mm-30) cc_final: 0.5607 (mm-30) REVERT: B 17 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7942 (tm-30) REVERT: R 60 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7145 (tt) REVERT: R 164 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6147 (pp) REVERT: S 246 GLU cc_start: 0.6415 (mp0) cc_final: 0.5874 (mp0) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.2488 time to fit residues: 42.7732 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110151 restraints weight = 11388.664| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.16 r_work: 0.3083 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8722 Z= 0.107 Angle : 0.489 5.754 11852 Z= 0.263 Chirality : 0.042 0.161 1347 Planarity : 0.004 0.065 1505 Dihedral : 4.869 71.697 1213 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.49 % Allowed : 15.01 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1098 helix: 1.54 (0.29), residues: 368 sheet: 0.57 (0.33), residues: 269 loop : -1.51 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 88 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.001 TYR A 30 ARG 0.004 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 340) hydrogen bonds : angle 3.99095 ( 975) SS BOND : bond 0.00658 ( 2) SS BOND : angle 0.72244 ( 4) covalent geometry : bond 0.00241 ( 8720) covalent geometry : angle 0.48923 (11848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.012 Fit side-chains REVERT: A 267 LYS cc_start: 0.7782 (mttt) cc_final: 0.7446 (mtpt) REVERT: A 276 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5579 (mm-30) REVERT: B 17 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 42 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7605 (tmt170) REVERT: B 44 GLN cc_start: 0.8340 (mm110) cc_final: 0.7804 (mm110) REVERT: R 60 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7154 (tt) REVERT: R 164 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6333 (pp) REVERT: S 246 GLU cc_start: 0.6481 (mp0) cc_final: 0.5966 (mp0) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.2770 time to fit residues: 47.2479 Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112909 restraints weight = 11469.156| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.21 r_work: 0.3126 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8722 Z= 0.090 Angle : 0.463 5.521 11852 Z= 0.248 Chirality : 0.041 0.172 1347 Planarity : 0.004 0.066 1505 Dihedral : 4.474 63.567 1213 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.92 % Allowed : 15.46 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1098 helix: 1.77 (0.29), residues: 360 sheet: 0.57 (0.32), residues: 279 loop : -1.53 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 88 HIS 0.002 0.001 HIS S 35 PHE 0.009 0.001 PHE A 189 TYR 0.009 0.001 TYR A 30 ARG 0.004 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 340) hydrogen bonds : angle 3.79566 ( 975) SS BOND : bond 0.00540 ( 2) SS BOND : angle 0.65316 ( 4) covalent geometry : bond 0.00195 ( 8720) covalent geometry : angle 0.46315 (11848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.917 Fit side-chains REVERT: A 267 LYS cc_start: 0.7738 (mttt) cc_final: 0.7440 (mtpt) REVERT: A 276 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5622 (mm-30) REVERT: B 17 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7935 (tm-30) REVERT: R 60 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7175 (tt) outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.3039 time to fit residues: 50.8802 Evaluate side-chains 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 83 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110670 restraints weight = 11515.926| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.34 r_work: 0.3089 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8722 Z= 0.096 Angle : 0.487 7.647 11852 Z= 0.259 Chirality : 0.041 0.172 1347 Planarity : 0.004 0.065 1505 Dihedral : 4.357 58.527 1213 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.80 % Allowed : 16.38 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1098 helix: 1.84 (0.29), residues: 360 sheet: 0.59 (0.32), residues: 280 loop : -1.48 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 88 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.008 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 340) hydrogen bonds : angle 3.76838 ( 975) SS BOND : bond 0.00577 ( 2) SS BOND : angle 0.65852 ( 4) covalent geometry : bond 0.00211 ( 8720) covalent geometry : angle 0.48706 (11848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 267 LYS cc_start: 0.7728 (mttt) cc_final: 0.7422 (mtpt) REVERT: A 276 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5694 (mm-30) REVERT: B 17 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7938 (tm-30) REVERT: R 60 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7228 (tt) outliers start: 7 outliers final: 6 residues processed: 120 average time/residue: 0.2545 time to fit residues: 40.7808 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 25 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111354 restraints weight = 11357.073| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.21 r_work: 0.3095 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8722 Z= 0.104 Angle : 0.507 11.772 11852 Z= 0.266 Chirality : 0.041 0.172 1347 Planarity : 0.004 0.063 1505 Dihedral : 4.320 54.577 1213 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.92 % Allowed : 16.49 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1098 helix: 1.87 (0.29), residues: 360 sheet: 0.57 (0.32), residues: 280 loop : -1.50 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 88 HIS 0.003 0.001 HIS R 62 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR A 30 ARG 0.007 0.000 ARG Y 27 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 340) hydrogen bonds : angle 3.79134 ( 975) SS BOND : bond 0.00625 ( 2) SS BOND : angle 0.68905 ( 4) covalent geometry : bond 0.00233 ( 8720) covalent geometry : angle 0.50729 (11848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 267 LYS cc_start: 0.7717 (mttt) cc_final: 0.7435 (mtpt) REVERT: A 276 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5839 (mm-30) REVERT: B 17 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 286 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8241 (mp) REVERT: R 60 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7223 (tt) outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.2645 time to fit residues: 41.3468 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110572 restraints weight = 11468.713| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.20 r_work: 0.3081 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8722 Z= 0.113 Angle : 0.521 10.549 11852 Z= 0.275 Chirality : 0.042 0.170 1347 Planarity : 0.004 0.063 1505 Dihedral : 4.351 51.816 1213 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.92 % Allowed : 16.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1098 helix: 1.74 (0.29), residues: 366 sheet: 0.51 (0.32), residues: 282 loop : -1.52 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 88 HIS 0.004 0.001 HIS R 62 PHE 0.011 0.001 PHE A 343 TYR 0.017 0.001 TYR A 30 ARG 0.012 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 340) hydrogen bonds : angle 3.84491 ( 975) SS BOND : bond 0.00646 ( 2) SS BOND : angle 0.69178 ( 4) covalent geometry : bond 0.00258 ( 8720) covalent geometry : angle 0.52043 (11848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5366.91 seconds wall clock time: 93 minutes 26.52 seconds (5606.52 seconds total)