Starting phenix.real_space_refine on Tue Mar 3 19:33:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xat_33098/03_2026/7xat_33098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xat_33098/03_2026/7xat_33098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xat_33098/03_2026/7xat_33098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xat_33098/03_2026/7xat_33098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xat_33098/03_2026/7xat_33098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xat_33098/03_2026/7xat_33098.map" } resolution = 2.85 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= 0.002 sd= 0.132 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5356 2.51 5 N 1447 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8470 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 1929 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 11, 'TRANS': 274} Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 10, 'TYR:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TRP:plan': 5, 'ASN:plan1': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 188 Chain: "B" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1591 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 4, 'GLN:plan1': 2, 'ASP:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 130 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 92 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.63, per 1000 atoms: 0.19 Number of scatterers: 8470 At special positions: 0 Unit cell: (87.74, 120.91, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1613 8.00 N 1447 7.00 C 5356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 14 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 273.4 milliseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 30.3% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 41 through 71 removed outlier: 3.961A pdb=" N VAL A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.526A pdb=" N ALA A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.196A pdb=" N GLN A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.644A pdb=" N ASN A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.579A pdb=" N VAL A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.514A pdb=" N MET A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 171 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.570A pdb=" N TYR A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 239 removed outlier: 4.171A pdb=" N LEU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.558A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.544A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.927A pdb=" N ASP A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.653A pdb=" N GLU B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.688A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.563A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.637A pdb=" N ASP B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.790A pdb=" N LEU B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.732A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 4.065A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.583A pdb=" N PHE B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 25 removed outlier: 3.636A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 25 removed outlier: 3.584A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.552A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.103A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.713A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.589A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.901A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.944A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.924A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.465A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.843A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.533A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.601A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.547A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2704 1.34 - 1.47: 2215 1.47 - 1.60: 3636 1.60 - 1.73: 0 1.73 - 1.86: 74 Bond restraints: 8629 Sorted by residual: bond pdb=" CG1 ILE C 273 " pdb=" CD1 ILE C 273 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.97e+00 bond pdb=" CG LEU C 146 " pdb=" CD2 LEU C 146 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.25e+00 bond pdb=" CG1 ILE C 338 " pdb=" CD1 ILE C 338 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.23e+00 bond pdb=" CA SER B 16 " pdb=" CB SER B 16 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.74e-02 3.30e+03 5.29e+00 ... (remaining 8624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 11263 2.22 - 4.44: 411 4.44 - 6.67: 58 6.67 - 8.89: 13 8.89 - 11.11: 2 Bond angle restraints: 11747 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C PHE F 11 " pdb=" N THR F 12 " pdb=" CA THR F 12 " ideal model delta sigma weight residual 120.82 126.62 -5.80 1.41e+00 5.03e-01 1.69e+01 angle pdb=" N ARG A 157 " pdb=" CA ARG A 157 " pdb=" C ARG A 157 " ideal model delta sigma weight residual 113.18 108.11 5.07 1.33e+00 5.65e-01 1.45e+01 angle pdb=" N LYS B 314 " pdb=" CA LYS B 314 " pdb=" C LYS B 314 " ideal model delta sigma weight residual 112.38 117.01 -4.63 1.22e+00 6.72e-01 1.44e+01 ... (remaining 11742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4580 16.65 - 33.29: 425 33.29 - 49.94: 78 49.94 - 66.58: 11 66.58 - 83.23: 7 Dihedral angle restraints: 5101 sinusoidal: 1767 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 167.02 -74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N PRO A 271 " pdb=" CA PRO A 271 " ideal model delta harmonic sigma weight residual 180.00 138.73 41.27 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA THR A 206 " pdb=" C THR A 206 " pdb=" N GLY A 207 " pdb=" CA GLY A 207 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 5098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1130 0.073 - 0.146: 232 0.146 - 0.219: 24 0.219 - 0.292: 3 0.292 - 0.365: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU E 174 " pdb=" CB LEU E 174 " pdb=" CD1 LEU E 174 " pdb=" CD2 LEU E 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR D 52 " pdb=" CA THR D 52 " pdb=" OG1 THR D 52 " pdb=" CG2 THR D 52 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1387 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO A 271 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 176 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO E 75 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.037 5.00e-02 4.00e+02 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1360 2.75 - 3.29: 7467 3.29 - 3.83: 14136 3.83 - 4.36: 17291 4.36 - 4.90: 29825 Nonbonded interactions: 70079 Sorted by model distance: nonbonded pdb=" O ILE A 209 " pdb=" OH TYR A 273 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.245 3.040 nonbonded pdb=" O HIS A 146 " pdb=" OG SER A 150 " model vdw 2.282 3.040 nonbonded pdb=" O ASN A 43 " pdb=" OG1 THR A 47 " model vdw 2.283 3.040 nonbonded pdb=" O SER B 228 " pdb=" OG SER B 228 " model vdw 2.302 3.040 ... (remaining 70074 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.010 0.110 8633 Z= 0.413 Angle : 1.003 11.109 11755 Z= 0.558 Chirality : 0.060 0.365 1390 Planarity : 0.007 0.086 1500 Dihedral : 13.720 83.226 2935 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.21), residues: 1137 helix: -4.60 (0.13), residues: 332 sheet: -1.16 (0.29), residues: 294 loop : -2.27 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 22 TYR 0.021 0.003 TYR A 273 PHE 0.034 0.003 PHE B 189 TRP 0.016 0.003 TRP C 63 HIS 0.006 0.002 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00960 ( 8629) covalent geometry : angle 0.99994 (11747) SS BOND : bond 0.01303 ( 4) SS BOND : angle 3.16461 ( 8) hydrogen bonds : bond 0.28662 ( 299) hydrogen bonds : angle 10.29236 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8564 (m-10) cc_final: 0.8152 (m-10) REVERT: A 160 LYS cc_start: 0.7872 (mttp) cc_final: 0.7085 (mmtt) REVERT: A 272 PHE cc_start: 0.8492 (t80) cc_final: 0.8097 (t80) REVERT: A 294 PHE cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: A 302 TYR cc_start: 0.8608 (m-80) cc_final: 0.8388 (m-80) REVERT: B 341 ASP cc_start: 0.8091 (t70) cc_final: 0.7888 (t0) REVERT: C 258 ASP cc_start: 0.7338 (t0) cc_final: 0.7081 (t70) REVERT: E 46 GLU cc_start: 0.7975 (pt0) cc_final: 0.7601 (pt0) REVERT: E 51 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (tt) REVERT: F 7 PHE cc_start: 0.7875 (t80) cc_final: 0.7608 (t80) outliers start: 7 outliers final: 3 residues processed: 194 average time/residue: 0.5296 time to fit residues: 109.1237 Evaluate side-chains 159 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 188 HIS B 346 ASN C 62 HIS C 237 ASN C 259 GLN D 24 ASN E 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125886 restraints weight = 10163.719| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.13 r_work: 0.3285 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8633 Z= 0.150 Angle : 0.636 7.752 11755 Z= 0.341 Chirality : 0.043 0.142 1390 Planarity : 0.005 0.071 1500 Dihedral : 6.193 55.168 1235 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.87 % Allowed : 15.19 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.22), residues: 1137 helix: -3.45 (0.19), residues: 363 sheet: -0.88 (0.28), residues: 297 loop : -1.73 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.012 0.001 TYR A 50 PHE 0.015 0.001 PHE B 189 TRP 0.013 0.002 TRP C 339 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8629) covalent geometry : angle 0.63280 (11747) SS BOND : bond 0.00536 ( 4) SS BOND : angle 2.55939 ( 8) hydrogen bonds : bond 0.04566 ( 299) hydrogen bonds : angle 5.75605 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.286 Fit side-chains REVERT: A 56 ILE cc_start: 0.7876 (tp) cc_final: 0.7570 (pt) REVERT: A 131 PHE cc_start: 0.8565 (m-10) cc_final: 0.8141 (m-10) REVERT: A 160 LYS cc_start: 0.7189 (mttp) cc_final: 0.6380 (mmtt) REVERT: A 272 PHE cc_start: 0.8295 (t80) cc_final: 0.8087 (t80) REVERT: C 212 ASP cc_start: 0.8595 (t70) cc_final: 0.8099 (t0) REVERT: E 43 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8281 (mmmm) REVERT: E 46 GLU cc_start: 0.8597 (pt0) cc_final: 0.8084 (pt0) REVERT: E 65 LYS cc_start: 0.8369 (tptt) cc_final: 0.8133 (ttpt) REVERT: E 201 ASP cc_start: 0.7865 (t0) cc_final: 0.7608 (t0) outliers start: 16 outliers final: 9 residues processed: 184 average time/residue: 0.4813 time to fit residues: 94.5680 Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.184084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127251 restraints weight = 9951.363| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.07 r_work: 0.3280 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8633 Z= 0.154 Angle : 0.612 7.730 11755 Z= 0.322 Chirality : 0.043 0.133 1390 Planarity : 0.004 0.071 1500 Dihedral : 5.751 57.463 1229 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.92 % Allowed : 17.17 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.23), residues: 1137 helix: -2.69 (0.22), residues: 362 sheet: -0.57 (0.29), residues: 293 loop : -1.58 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.014 0.001 TYR A 273 PHE 0.013 0.001 PHE B 189 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8629) covalent geometry : angle 0.60969 (11747) SS BOND : bond 0.01124 ( 4) SS BOND : angle 2.13057 ( 8) hydrogen bonds : bond 0.03802 ( 299) hydrogen bonds : angle 5.17104 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.282 Fit side-chains REVERT: A 56 ILE cc_start: 0.7906 (tp) cc_final: 0.7575 (pt) REVERT: A 114 ILE cc_start: 0.6933 (mp) cc_final: 0.6703 (OUTLIER) REVERT: A 131 PHE cc_start: 0.8546 (m-10) cc_final: 0.8228 (m-10) REVERT: A 160 LYS cc_start: 0.7262 (mttp) cc_final: 0.6336 (mmtt) REVERT: B 243 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7777 (mmm) REVERT: B 308 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7915 (mp0) REVERT: C 129 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7159 (tpt-90) REVERT: C 212 ASP cc_start: 0.8563 (t70) cc_final: 0.8113 (t0) REVERT: C 214 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: E 43 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8283 (mmmm) REVERT: E 46 GLU cc_start: 0.8546 (pt0) cc_final: 0.8048 (pt0) REVERT: E 65 LYS cc_start: 0.8317 (tptt) cc_final: 0.8047 (ttpt) REVERT: E 201 ASP cc_start: 0.7970 (t0) cc_final: 0.7666 (t0) outliers start: 25 outliers final: 11 residues processed: 178 average time/residue: 0.4833 time to fit residues: 92.0971 Evaluate side-chains 163 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 40.0000 chunk 87 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128804 restraints weight = 10206.269| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.11 r_work: 0.3332 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8633 Z= 0.104 Angle : 0.550 7.389 11755 Z= 0.290 Chirality : 0.041 0.133 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.293 58.481 1229 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.04 % Allowed : 18.34 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.24), residues: 1137 helix: -2.06 (0.24), residues: 363 sheet: -0.39 (0.29), residues: 291 loop : -1.43 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 22 TYR 0.013 0.001 TYR A 273 PHE 0.012 0.001 PHE B 189 TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8629) covalent geometry : angle 0.54875 (11747) SS BOND : bond 0.00750 ( 4) SS BOND : angle 1.33319 ( 8) hydrogen bonds : bond 0.03089 ( 299) hydrogen bonds : angle 4.73343 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.321 Fit side-chains REVERT: A 56 ILE cc_start: 0.7970 (tp) cc_final: 0.7638 (pt) REVERT: A 131 PHE cc_start: 0.8519 (m-10) cc_final: 0.8267 (m-10) REVERT: A 160 LYS cc_start: 0.7204 (mttp) cc_final: 0.6268 (mmtt) REVERT: C 96 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7293 (mtt-85) REVERT: C 212 ASP cc_start: 0.8560 (t70) cc_final: 0.8157 (t0) REVERT: C 214 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7788 (mmm-85) REVERT: C 258 ASP cc_start: 0.7055 (t70) cc_final: 0.6377 (t70) REVERT: E 46 GLU cc_start: 0.8467 (pt0) cc_final: 0.7989 (pt0) REVERT: E 65 LYS cc_start: 0.8277 (tptt) cc_final: 0.7989 (ttpt) REVERT: E 109 ASP cc_start: 0.8244 (p0) cc_final: 0.7993 (p0) outliers start: 26 outliers final: 13 residues processed: 187 average time/residue: 0.4762 time to fit residues: 95.3785 Evaluate side-chains 172 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.183253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125892 restraints weight = 10150.357| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.10 r_work: 0.3297 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8633 Z= 0.134 Angle : 0.565 7.229 11755 Z= 0.297 Chirality : 0.042 0.145 1390 Planarity : 0.004 0.069 1500 Dihedral : 5.230 59.621 1229 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.74 % Allowed : 20.09 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.24), residues: 1137 helix: -1.67 (0.26), residues: 359 sheet: -0.25 (0.29), residues: 288 loop : -1.28 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.012 0.001 TYR A 273 PHE 0.012 0.001 PHE B 189 TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8629) covalent geometry : angle 0.56370 (11747) SS BOND : bond 0.00943 ( 4) SS BOND : angle 1.68273 ( 8) hydrogen bonds : bond 0.03210 ( 299) hydrogen bonds : angle 4.65187 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.308 Fit side-chains REVERT: A 56 ILE cc_start: 0.7968 (tp) cc_final: 0.7631 (pt) REVERT: A 131 PHE cc_start: 0.8538 (m-10) cc_final: 0.8308 (m-10) REVERT: B 308 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: C 96 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7327 (mtt-85) REVERT: C 129 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7056 (tpt-90) REVERT: C 212 ASP cc_start: 0.8552 (t70) cc_final: 0.8165 (t0) REVERT: C 214 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7791 (mmm-85) REVERT: C 258 ASP cc_start: 0.7057 (t70) cc_final: 0.6241 (t70) REVERT: E 46 GLU cc_start: 0.8459 (pt0) cc_final: 0.7991 (pt0) REVERT: E 65 LYS cc_start: 0.8279 (tptt) cc_final: 0.7985 (ttpt) REVERT: E 89 GLU cc_start: 0.8125 (mp0) cc_final: 0.7755 (pm20) REVERT: E 93 MET cc_start: 0.8741 (ttm) cc_final: 0.8459 (ttp) outliers start: 32 outliers final: 17 residues processed: 176 average time/residue: 0.4641 time to fit residues: 87.6401 Evaluate side-chains 171 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.185878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128487 restraints weight = 10034.186| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.14 r_work: 0.3332 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8633 Z= 0.104 Angle : 0.545 8.019 11755 Z= 0.283 Chirality : 0.041 0.134 1390 Planarity : 0.004 0.068 1500 Dihedral : 5.009 59.381 1229 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.97 % Allowed : 21.38 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.25), residues: 1137 helix: -1.32 (0.27), residues: 360 sheet: -0.04 (0.30), residues: 284 loop : -1.24 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.012 0.001 TYR A 273 PHE 0.011 0.001 PHE B 189 TRP 0.009 0.001 TRP C 169 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8629) covalent geometry : angle 0.54420 (11747) SS BOND : bond 0.00692 ( 4) SS BOND : angle 1.49346 ( 8) hydrogen bonds : bond 0.02927 ( 299) hydrogen bonds : angle 4.49450 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.301 Fit side-chains REVERT: A 131 PHE cc_start: 0.8474 (m-10) cc_final: 0.8248 (m-10) REVERT: A 154 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8353 (mmm-85) REVERT: B 252 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 274 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6265 (t80) REVERT: C 96 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7353 (mtt-85) REVERT: C 129 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6974 (tpt-90) REVERT: C 212 ASP cc_start: 0.8499 (t70) cc_final: 0.8139 (t0) REVERT: C 214 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7743 (mmm-85) REVERT: C 258 ASP cc_start: 0.6982 (t70) cc_final: 0.6160 (t70) REVERT: D 21 MET cc_start: 0.6857 (tmt) cc_final: 0.6623 (tpt) REVERT: E 46 GLU cc_start: 0.8353 (pt0) cc_final: 0.7938 (pt0) REVERT: E 65 LYS cc_start: 0.8278 (tptt) cc_final: 0.7929 (ttpt) REVERT: E 89 GLU cc_start: 0.8017 (mp0) cc_final: 0.7703 (pm20) REVERT: E 93 MET cc_start: 0.8745 (ttm) cc_final: 0.8403 (ttp) REVERT: E 218 ARG cc_start: 0.6701 (ptp90) cc_final: 0.6257 (mtm-85) outliers start: 34 outliers final: 16 residues processed: 179 average time/residue: 0.4809 time to fit residues: 92.1566 Evaluate side-chains 169 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 0.0270 chunk 105 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 255 ASN C 119 ASN C 237 ASN C 340 ASN D 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.184048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126170 restraints weight = 10245.646| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.15 r_work: 0.3297 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8633 Z= 0.135 Angle : 0.572 8.081 11755 Z= 0.298 Chirality : 0.042 0.135 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.052 58.589 1229 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.86 % Allowed : 22.08 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.25), residues: 1137 helix: -1.24 (0.27), residues: 363 sheet: -0.00 (0.30), residues: 283 loop : -1.19 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.014 0.001 TYR A 273 PHE 0.011 0.001 PHE B 189 TRP 0.012 0.001 TRP C 339 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8629) covalent geometry : angle 0.56998 (11747) SS BOND : bond 0.00980 ( 4) SS BOND : angle 1.90557 ( 8) hydrogen bonds : bond 0.03108 ( 299) hydrogen bonds : angle 4.54995 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.309 Fit side-chains REVERT: B 274 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6253 (t80) REVERT: C 45 MET cc_start: 0.9040 (mtt) cc_final: 0.8541 (mtt) REVERT: C 96 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7470 (mtt-85) REVERT: C 129 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7058 (tpt-90) REVERT: C 212 ASP cc_start: 0.8534 (t70) cc_final: 0.8157 (t0) REVERT: C 214 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7726 (mmm-85) REVERT: C 258 ASP cc_start: 0.7018 (t70) cc_final: 0.6176 (t70) REVERT: E 46 GLU cc_start: 0.8396 (pt0) cc_final: 0.7941 (pt0) REVERT: E 65 LYS cc_start: 0.8271 (tptt) cc_final: 0.7936 (ttpt) REVERT: E 89 GLU cc_start: 0.8072 (mp0) cc_final: 0.7756 (pm20) REVERT: E 93 MET cc_start: 0.8782 (ttm) cc_final: 0.8510 (ttp) REVERT: E 218 ARG cc_start: 0.6733 (ptp90) cc_final: 0.6339 (mtm-85) outliers start: 33 outliers final: 18 residues processed: 172 average time/residue: 0.4598 time to fit residues: 84.8813 Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 14 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 255 ASN C 237 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.184511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127257 restraints weight = 10086.163| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.11 r_work: 0.3314 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8633 Z= 0.117 Angle : 0.564 8.345 11755 Z= 0.293 Chirality : 0.042 0.145 1390 Planarity : 0.004 0.070 1500 Dihedral : 4.980 58.091 1229 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.15 % Allowed : 22.31 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.25), residues: 1137 helix: -1.11 (0.27), residues: 369 sheet: 0.03 (0.30), residues: 282 loop : -1.14 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.014 0.001 TYR A 273 PHE 0.011 0.001 PHE B 189 TRP 0.008 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8629) covalent geometry : angle 0.56254 (11747) SS BOND : bond 0.00822 ( 4) SS BOND : angle 1.54377 ( 8) hydrogen bonds : bond 0.02988 ( 299) hydrogen bonds : angle 4.49832 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.247 Fit side-chains REVERT: A 127 PHE cc_start: 0.8354 (m-80) cc_final: 0.7996 (m-80) REVERT: A 131 PHE cc_start: 0.8711 (m-10) cc_final: 0.8320 (m-10) REVERT: A 248 LYS cc_start: 0.5377 (mtmt) cc_final: 0.4989 (mtmt) REVERT: B 192 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7891 (mtpp) REVERT: B 274 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6508 (t80) REVERT: C 45 MET cc_start: 0.9010 (mtt) cc_final: 0.8541 (mtt) REVERT: C 96 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7516 (mtt-85) REVERT: C 129 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7012 (tpt-90) REVERT: C 212 ASP cc_start: 0.8515 (t70) cc_final: 0.8156 (t0) REVERT: C 214 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7739 (mmm-85) REVERT: C 258 ASP cc_start: 0.7012 (t70) cc_final: 0.6147 (t70) REVERT: E 46 GLU cc_start: 0.8378 (pt0) cc_final: 0.7915 (pt0) REVERT: E 65 LYS cc_start: 0.8345 (tptt) cc_final: 0.7974 (ttpt) REVERT: E 83 MET cc_start: 0.8296 (mtm) cc_final: 0.7995 (mpp) REVERT: E 89 GLU cc_start: 0.8023 (mp0) cc_final: 0.7729 (pm20) REVERT: E 93 MET cc_start: 0.8763 (ttm) cc_final: 0.8494 (ttp) outliers start: 27 outliers final: 19 residues processed: 172 average time/residue: 0.4632 time to fit residues: 85.4993 Evaluate side-chains 168 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 0.0040 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 255 ASN C 237 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125553 restraints weight = 10117.304| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.14 r_work: 0.3276 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8633 Z= 0.146 Angle : 0.590 8.214 11755 Z= 0.307 Chirality : 0.043 0.155 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.047 56.989 1229 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.04 % Allowed : 23.25 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.24), residues: 1137 helix: -1.07 (0.27), residues: 367 sheet: 0.04 (0.30), residues: 284 loop : -1.18 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.010 0.001 TYR E 103 PHE 0.012 0.001 PHE A 92 TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8629) covalent geometry : angle 0.58810 (11747) SS BOND : bond 0.01053 ( 4) SS BOND : angle 1.88338 ( 8) hydrogen bonds : bond 0.03172 ( 299) hydrogen bonds : angle 4.55197 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.293 Fit side-chains REVERT: A 131 PHE cc_start: 0.8706 (m-10) cc_final: 0.8356 (m-10) REVERT: B 192 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7819 (mtpp) REVERT: B 274 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6304 (t80) REVERT: C 45 MET cc_start: 0.9047 (mtt) cc_final: 0.8606 (mtt) REVERT: C 96 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7480 (mtt-85) REVERT: C 129 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7037 (tpt-90) REVERT: C 212 ASP cc_start: 0.8539 (t70) cc_final: 0.8108 (t0) REVERT: C 214 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7714 (mmm-85) REVERT: C 258 ASP cc_start: 0.7042 (t70) cc_final: 0.6143 (t70) REVERT: E 46 GLU cc_start: 0.8418 (pt0) cc_final: 0.7930 (pt0) REVERT: E 65 LYS cc_start: 0.8268 (tptt) cc_final: 0.7899 (ttpt) REVERT: E 89 GLU cc_start: 0.8054 (mp0) cc_final: 0.7717 (pm20) REVERT: E 93 MET cc_start: 0.8774 (ttm) cc_final: 0.8495 (ttp) REVERT: E 218 ARG cc_start: 0.6700 (ptp90) cc_final: 0.6302 (mtm-85) outliers start: 26 outliers final: 24 residues processed: 177 average time/residue: 0.4725 time to fit residues: 89.3983 Evaluate side-chains 182 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 213 HIS C 237 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.187037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129937 restraints weight = 10070.291| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.14 r_work: 0.3340 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8633 Z= 0.101 Angle : 0.550 8.335 11755 Z= 0.288 Chirality : 0.042 0.166 1390 Planarity : 0.004 0.069 1500 Dihedral : 4.853 56.705 1229 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.45 % Allowed : 23.71 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.25), residues: 1137 helix: -0.76 (0.27), residues: 373 sheet: 0.01 (0.30), residues: 280 loop : -1.03 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.011 0.001 TYR A 50 PHE 0.010 0.001 PHE B 189 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8629) covalent geometry : angle 0.54947 (11747) SS BOND : bond 0.00642 ( 4) SS BOND : angle 1.19800 ( 8) hydrogen bonds : bond 0.02882 ( 299) hydrogen bonds : angle 4.42045 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.304 Fit side-chains REVERT: B 192 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7858 (mtpp) REVERT: B 252 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8302 (p) REVERT: C 96 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7536 (mtt-85) REVERT: C 129 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6993 (tpt-90) REVERT: C 212 ASP cc_start: 0.8480 (t70) cc_final: 0.8131 (t0) REVERT: C 214 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7728 (mmm-85) REVERT: C 258 ASP cc_start: 0.6984 (t70) cc_final: 0.6097 (t70) REVERT: E 46 GLU cc_start: 0.8331 (pt0) cc_final: 0.7882 (pt0) REVERT: E 89 GLU cc_start: 0.8021 (mp0) cc_final: 0.7735 (pm20) REVERT: E 93 MET cc_start: 0.8707 (ttm) cc_final: 0.8424 (ttp) outliers start: 21 outliers final: 14 residues processed: 176 average time/residue: 0.4547 time to fit residues: 85.9576 Evaluate side-chains 169 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127477 restraints weight = 10024.429| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.13 r_work: 0.3303 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8633 Z= 0.127 Angle : 0.574 8.342 11755 Z= 0.300 Chirality : 0.042 0.171 1390 Planarity : 0.004 0.073 1500 Dihedral : 4.625 36.473 1227 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.99 % Allowed : 25.12 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1137 helix: -0.61 (0.27), residues: 374 sheet: 0.06 (0.30), residues: 279 loop : -1.05 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.013 0.001 TYR C 59 PHE 0.011 0.001 PHE B 189 TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8629) covalent geometry : angle 0.57311 (11747) SS BOND : bond 0.00902 ( 4) SS BOND : angle 1.60042 ( 8) hydrogen bonds : bond 0.03015 ( 299) hydrogen bonds : angle 4.44775 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3770.35 seconds wall clock time: 64 minutes 42.59 seconds (3882.59 seconds total)