Starting phenix.real_space_refine on Sat Jul 26 04:19:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xat_33098/07_2025/7xat_33098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xat_33098/07_2025/7xat_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xat_33098/07_2025/7xat_33098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xat_33098/07_2025/7xat_33098.map" model { file = "/net/cci-nas-00/data/ceres_data/7xat_33098/07_2025/7xat_33098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xat_33098/07_2025/7xat_33098.cif" } resolution = 2.85 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= 0.132 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 2, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 3} 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: 9.79, per 1000 atoms: 1.16 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: 3.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.26 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: 5.49 Time building geometry restraints manager: 4.47 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: 0.630 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.130 Process input model: 39.290 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 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:34.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.550 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.016 0.003 TRP C 63 HIS 0.006 0.002 HIS E 167 PHE 0.034 0.003 PHE B 189 TYR 0.021 0.003 TYR A 273 ARG 0.010 0.001 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.28662 ( 299) hydrogen bonds : angle 10.29236 ( 834) SS BOND : bond 0.01303 ( 4) SS BOND : angle 3.16461 ( 8) covalent geometry : bond 0.00960 ( 8629) covalent geometry : angle 0.99994 (11747) *********************** 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 : 0.946 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: 0.8321 (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: 0.7080 (t70) REVERT: E 46 GLU cc_start: 0.7975 (pt0) cc_final: 0.7600 (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: 1.2513 time to fit residues: 258.3245 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 : 0.947 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.0070 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 188 HIS B 255 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127710 restraints weight = 10048.662| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.10 r_work: 0.3307 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8633 Z= 0.129 Angle : 0.622 7.261 11755 Z= 0.335 Chirality : 0.043 0.139 1390 Planarity : 0.005 0.072 1500 Dihedral : 6.139 53.978 1235 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.87 % Allowed : 14.72 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.26 (0.22), residues: 1137 helix: -3.43 (0.19), residues: 363 sheet: -0.89 (0.28), residues: 295 loop : -1.75 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.003 0.001 HIS C 183 PHE 0.015 0.001 PHE B 189 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 299) hydrogen bonds : angle 5.75409 ( 834) SS BOND : bond 0.00643 ( 4) SS BOND : angle 2.24516 ( 8) covalent geometry : bond 0.00277 ( 8629) covalent geometry : angle 0.61968 (11747) *********************** 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 191 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.076 Fit side-chains REVERT: A 56 ILE cc_start: 0.7880 (tp) cc_final: 0.7571 (pt) REVERT: A 131 PHE cc_start: 0.8595 (m-10) cc_final: 0.8200 (m-10) REVERT: A 160 LYS cc_start: 0.7244 (mttp) cc_final: 0.6416 (mmtt) REVERT: A 272 PHE cc_start: 0.8277 (t80) cc_final: 0.8070 (t80) REVERT: C 212 ASP cc_start: 0.8593 (t70) cc_final: 0.8084 (t0) REVERT: E 43 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8286 (mmmm) REVERT: E 46 GLU cc_start: 0.8568 (pt0) cc_final: 0.8050 (pt0) REVERT: E 201 ASP cc_start: 0.7808 (t0) cc_final: 0.7557 (t0) outliers start: 16 outliers final: 8 residues processed: 185 average time/residue: 1.3667 time to fit residues: 274.6871 Evaluate side-chains 165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 100 VAL 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 31 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.9890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.183943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127326 restraints weight = 10117.103| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.09 r_work: 0.3318 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2159 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= 0.133 Angle : 0.590 7.674 11755 Z= 0.311 Chirality : 0.042 0.142 1390 Planarity : 0.004 0.071 1500 Dihedral : 5.606 55.423 1229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.04 % Allowed : 16.59 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.53 (0.23), residues: 1137 helix: -2.54 (0.23), residues: 353 sheet: -0.49 (0.29), residues: 289 loop : -1.60 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 339 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.014 0.001 TYR A 273 ARG 0.006 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 299) hydrogen bonds : angle 5.08775 ( 834) SS BOND : bond 0.00934 ( 4) SS BOND : angle 1.86864 ( 8) covalent geometry : bond 0.00303 ( 8629) covalent geometry : angle 0.58866 (11747) *********************** 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 198 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.978 Fit side-chains REVERT: A 56 ILE cc_start: 0.7896 (tp) cc_final: 0.7562 (pt) REVERT: A 131 PHE cc_start: 0.8586 (m-10) cc_final: 0.8303 (m-10) REVERT: A 160 LYS cc_start: 0.7239 (mttp) cc_final: 0.6319 (mmtt) REVERT: A 272 PHE cc_start: 0.8305 (t80) cc_final: 0.8049 (t80) REVERT: A 302 TYR cc_start: 0.8648 (m-80) cc_final: 0.8439 (m-80) REVERT: C 86 THR cc_start: 0.9206 (p) cc_final: 0.8984 (p) REVERT: C 212 ASP cc_start: 0.8584 (t70) cc_final: 0.8159 (t0) REVERT: C 214 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7720 (mmm-85) REVERT: E 46 GLU cc_start: 0.8537 (pt0) cc_final: 0.8044 (pt0) REVERT: E 65 LYS cc_start: 0.8310 (tptt) cc_final: 0.8035 (ttpt) REVERT: E 201 ASP cc_start: 0.7931 (t0) cc_final: 0.7611 (t0) outliers start: 26 outliers final: 10 residues processed: 185 average time/residue: 1.0425 time to fit residues: 207.7377 Evaluate side-chains 169 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 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 146 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 208 SER 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 30 optimal weight: 0.0000 chunk 35 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.185355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132142 restraints weight = 10079.037| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.18 r_work: 0.3327 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8633 Z= 0.107 Angle : 0.549 7.359 11755 Z= 0.290 Chirality : 0.041 0.132 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.237 56.515 1229 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.39 % Allowed : 18.81 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.07 (0.24), residues: 1137 helix: -1.97 (0.25), residues: 358 sheet: -0.36 (0.30), residues: 281 loop : -1.36 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.011 0.001 PHE B 189 TYR 0.012 0.001 TYR A 273 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 299) hydrogen bonds : angle 4.69296 ( 834) SS BOND : bond 0.00692 ( 4) SS BOND : angle 1.28381 ( 8) covalent geometry : bond 0.00235 ( 8629) covalent geometry : angle 0.54836 (11747) *********************** 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 204 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.954 Fit side-chains REVERT: A 56 ILE cc_start: 0.7948 (tp) cc_final: 0.7615 (pt) REVERT: A 127 PHE cc_start: 0.8410 (m-80) cc_final: 0.8202 (m-80) REVERT: A 131 PHE cc_start: 0.8498 (m-10) cc_final: 0.8221 (m-10) REVERT: A 154 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.8327 (mtp180) REVERT: A 160 LYS cc_start: 0.7134 (mttp) cc_final: 0.6207 (mmtt) REVERT: A 272 PHE cc_start: 0.8212 (t80) cc_final: 0.7782 (t80) REVERT: C 96 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7299 (mtt-85) REVERT: C 129 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7056 (tpt-90) REVERT: C 212 ASP cc_start: 0.8551 (t70) cc_final: 0.8125 (t0) REVERT: C 214 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7726 (mmm-85) REVERT: C 258 ASP cc_start: 0.6905 (t70) cc_final: 0.6224 (t70) REVERT: E 46 GLU cc_start: 0.8440 (pt0) cc_final: 0.7935 (pt0) REVERT: E 65 LYS cc_start: 0.8270 (tptt) cc_final: 0.7956 (ttpt) REVERT: E 89 GLU cc_start: 0.8093 (mp0) cc_final: 0.7591 (pm20) REVERT: E 93 MET cc_start: 0.8730 (ttm) cc_final: 0.8425 (ttp) REVERT: E 109 ASP cc_start: 0.8298 (p0) cc_final: 0.8012 (p0) REVERT: E 218 ARG cc_start: 0.6690 (ptp90) cc_final: 0.6377 (mtm-85) outliers start: 29 outliers final: 13 residues processed: 189 average time/residue: 1.0102 time to fit residues: 205.0364 Evaluate side-chains 175 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 208 SER 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 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124649 restraints weight = 10069.542| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.11 r_work: 0.3265 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8633 Z= 0.156 Angle : 0.582 7.873 11755 Z= 0.305 Chirality : 0.043 0.135 1390 Planarity : 0.004 0.071 1500 Dihedral : 5.275 58.735 1229 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.15 % Allowed : 20.56 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.83 (0.24), residues: 1137 helix: -1.69 (0.26), residues: 359 sheet: -0.22 (0.29), residues: 291 loop : -1.31 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.013 0.001 TYR A 273 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 299) hydrogen bonds : angle 4.67429 ( 834) SS BOND : bond 0.01066 ( 4) SS BOND : angle 1.79757 ( 8) covalent geometry : bond 0.00361 ( 8629) covalent geometry : angle 0.58026 (11747) *********************** 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 187 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.901 Fit side-chains REVERT: A 131 PHE cc_start: 0.8527 (m-10) cc_final: 0.8277 (m-10) REVERT: C 96 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7393 (mtt-85) REVERT: C 129 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7141 (tpt-90) REVERT: C 212 ASP cc_start: 0.8543 (t70) cc_final: 0.8109 (t0) REVERT: C 214 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: C 258 ASP cc_start: 0.6956 (t70) cc_final: 0.6148 (t70) REVERT: E 46 GLU cc_start: 0.8451 (pt0) cc_final: 0.7960 (pt0) REVERT: E 65 LYS cc_start: 0.8278 (tptt) cc_final: 0.7967 (ttpt) REVERT: E 89 GLU cc_start: 0.8061 (mp0) cc_final: 0.7630 (pm20) REVERT: E 218 ARG cc_start: 0.6712 (ptp90) cc_final: 0.6379 (mtm-85) outliers start: 27 outliers final: 15 residues processed: 175 average time/residue: 1.1713 time to fit residues: 219.5573 Evaluate side-chains 167 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 158 SER 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 84 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 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 = 0.4090 r_free = 0.4090 target = 0.182493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125096 restraints weight = 10003.333| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.08 r_work: 0.3284 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8633 Z= 0.147 Angle : 0.583 8.881 11755 Z= 0.303 Chirality : 0.043 0.133 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.232 59.483 1229 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.86 % Allowed : 21.03 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -1.65 (0.24), residues: 1137 helix: -1.46 (0.27), residues: 361 sheet: -0.13 (0.29), residues: 291 loop : -1.27 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.014 0.001 TYR A 273 ARG 0.009 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 299) hydrogen bonds : angle 4.62522 ( 834) SS BOND : bond 0.00914 ( 4) SS BOND : angle 2.06725 ( 8) covalent geometry : bond 0.00341 ( 8629) covalent geometry : angle 0.58067 (11747) *********************** 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 189 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.005 Fit side-chains REVERT: A 56 ILE cc_start: 0.7946 (tp) cc_final: 0.7610 (pt) REVERT: A 114 ILE cc_start: 0.7125 (mp) cc_final: 0.6922 (mt) REVERT: B 184 ILE cc_start: 0.9217 (mm) cc_final: 0.8928 (tp) REVERT: B 274 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6207 (t80) REVERT: C 45 MET cc_start: 0.9023 (mtt) cc_final: 0.8568 (mtt) REVERT: C 96 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7461 (mtt-85) REVERT: C 129 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7072 (tpt-90) REVERT: C 212 ASP cc_start: 0.8549 (t70) cc_final: 0.8148 (t0) REVERT: C 214 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7823 (mmm-85) REVERT: C 258 ASP cc_start: 0.7051 (t70) cc_final: 0.6212 (t70) REVERT: E 46 GLU cc_start: 0.8488 (pt0) cc_final: 0.8021 (pt0) REVERT: E 65 LYS cc_start: 0.8280 (tptt) cc_final: 0.7981 (ttpt) REVERT: E 89 GLU cc_start: 0.8050 (mp0) cc_final: 0.7610 (pm20) REVERT: E 218 ARG cc_start: 0.6711 (ptp90) cc_final: 0.6383 (mtm-85) outliers start: 33 outliers final: 18 residues processed: 173 average time/residue: 1.4002 time to fit residues: 261.2356 Evaluate side-chains 170 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 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 196 THR 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 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 0.0020 chunk 57 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.185055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129031 restraints weight = 10145.895| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.06 r_work: 0.3323 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8633 Z= 0.110 Angle : 0.551 8.173 11755 Z= 0.287 Chirality : 0.042 0.129 1390 Planarity : 0.004 0.070 1500 Dihedral : 4.993 58.378 1229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.15 % Allowed : 21.50 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.47 (0.25), residues: 1137 helix: -1.23 (0.27), residues: 372 sheet: -0.04 (0.30), residues: 288 loop : -1.20 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.011 0.001 PHE B 189 TYR 0.013 0.001 TYR A 273 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 299) hydrogen bonds : angle 4.50228 ( 834) SS BOND : bond 0.00804 ( 4) SS BOND : angle 1.55202 ( 8) covalent geometry : bond 0.00247 ( 8629) covalent geometry : angle 0.54983 (11747) *********************** 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 183 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.951 Fit side-chains REVERT: A 127 PHE cc_start: 0.8391 (m-80) cc_final: 0.8041 (m-80) REVERT: A 131 PHE cc_start: 0.8725 (m-10) cc_final: 0.8329 (m-10) REVERT: B 184 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8953 (tp) REVERT: B 249 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8213 (tt) REVERT: B 252 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 274 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6402 (t80) REVERT: C 45 MET cc_start: 0.8981 (mtt) cc_final: 0.8533 (mtt) REVERT: C 96 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7414 (mtt-85) REVERT: C 129 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7068 (tpt-90) REVERT: C 212 ASP cc_start: 0.8508 (t70) cc_final: 0.8154 (t0) REVERT: C 214 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: C 258 ASP cc_start: 0.6997 (t70) cc_final: 0.6164 (t70) REVERT: E 46 GLU cc_start: 0.8458 (pt0) cc_final: 0.7961 (pt0) REVERT: E 65 LYS cc_start: 0.8273 (tptt) cc_final: 0.7953 (ttpt) REVERT: E 89 GLU cc_start: 0.8003 (mp0) cc_final: 0.7563 (pm20) REVERT: E 93 MET cc_start: 0.8699 (ttm) cc_final: 0.8406 (ttp) REVERT: E 218 ARG cc_start: 0.6717 (ptp90) cc_final: 0.6369 (mtm-85) outliers start: 27 outliers final: 18 residues processed: 174 average time/residue: 0.9904 time to fit residues: 185.6193 Evaluate side-chains 171 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 242 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 249 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 215 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.0370 chunk 85 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 38 optimal weight: 50.0000 chunk 59 optimal weight: 0.0570 chunk 89 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.183040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124640 restraints weight = 10201.442| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.14 r_work: 0.3272 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8633 Z= 0.159 Angle : 0.591 8.267 11755 Z= 0.308 Chirality : 0.043 0.141 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.122 57.210 1229 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.62 % Allowed : 21.26 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.24), residues: 1137 helix: -1.24 (0.26), residues: 369 sheet: 0.01 (0.30), residues: 287 loop : -1.25 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.001 PHE A 92 TYR 0.016 0.001 TYR A 273 ARG 0.010 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 299) hydrogen bonds : angle 4.60442 ( 834) SS BOND : bond 0.01114 ( 4) SS BOND : angle 1.96716 ( 8) covalent geometry : bond 0.00370 ( 8629) covalent geometry : angle 0.58918 (11747) *********************** 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 183 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.972 Fit side-chains REVERT: B 184 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9049 (tp) REVERT: B 274 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6354 (t80) REVERT: C 45 MET cc_start: 0.9033 (mtt) cc_final: 0.8604 (mtt) REVERT: C 96 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7504 (mtt-85) REVERT: C 129 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7151 (tpt-90) REVERT: C 212 ASP cc_start: 0.8556 (t70) cc_final: 0.8149 (t0) REVERT: C 214 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7777 (mmm-85) REVERT: C 258 ASP cc_start: 0.7068 (t70) cc_final: 0.6192 (t70) REVERT: E 46 GLU cc_start: 0.8502 (pt0) cc_final: 0.8006 (pt0) REVERT: E 65 LYS cc_start: 0.8288 (tptt) cc_final: 0.7953 (ttpt) REVERT: E 89 GLU cc_start: 0.8035 (mp0) cc_final: 0.7584 (pm20) REVERT: E 93 MET cc_start: 0.8785 (ttm) cc_final: 0.8496 (ttp) REVERT: E 218 ARG cc_start: 0.6688 (ptp90) cc_final: 0.6364 (mtm-85) outliers start: 31 outliers final: 22 residues processed: 172 average time/residue: 1.0145 time to fit residues: 187.8753 Evaluate side-chains 174 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 B residue 184 ILE 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 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 215 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN 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 93 optimal weight: 6.9990 chunk 13 optimal weight: 0.0670 chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125488 restraints weight = 10244.609| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.14 r_work: 0.3277 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2876 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= 0.138 Angle : 0.581 8.482 11755 Z= 0.302 Chirality : 0.043 0.151 1390 Planarity : 0.004 0.071 1500 Dihedral : 5.045 56.117 1229 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.62 % Allowed : 21.26 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (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: -1.35 (0.25), residues: 1137 helix: -1.10 (0.27), residues: 369 sheet: 0.10 (0.30), residues: 284 loop : -1.21 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.016 0.001 TYR A 273 ARG 0.009 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 299) hydrogen bonds : angle 4.57160 ( 834) SS BOND : bond 0.01014 ( 4) SS BOND : angle 1.77188 ( 8) covalent geometry : bond 0.00318 ( 8629) covalent geometry : angle 0.57914 (11747) *********************** 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 185 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.142 Fit side-chains REVERT: A 272 PHE cc_start: 0.8229 (t80) cc_final: 0.7883 (t80) REVERT: B 274 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6460 (t80) REVERT: C 45 MET cc_start: 0.9031 (mtt) cc_final: 0.8611 (mtt) REVERT: C 96 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7529 (mtt-85) REVERT: C 129 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7134 (tpt-90) REVERT: C 212 ASP cc_start: 0.8539 (t70) cc_final: 0.8107 (t0) REVERT: C 214 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7766 (mmm-85) REVERT: C 258 ASP cc_start: 0.7026 (t70) cc_final: 0.6135 (t70) REVERT: E 46 GLU cc_start: 0.8478 (pt0) cc_final: 0.7951 (pt0) REVERT: E 65 LYS cc_start: 0.8241 (tptt) cc_final: 0.7883 (ttpt) REVERT: E 89 GLU cc_start: 0.8039 (mp0) cc_final: 0.7600 (pm20) REVERT: E 93 MET cc_start: 0.8769 (ttm) cc_final: 0.8470 (ttp) REVERT: E 218 ARG cc_start: 0.6702 (ptp90) cc_final: 0.6352 (mtm-85) outliers start: 31 outliers final: 25 residues processed: 175 average time/residue: 1.2592 time to fit residues: 237.2407 Evaluate side-chains 181 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 B residue 37 LEU Chi-restraints excluded: chain B residue 48 THR 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 215 GLU 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 186 GLN 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 2 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 101 optimal weight: 0.4980 chunk 90 optimal weight: 0.0270 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 B 255 ASN C 119 ASN C 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127211 restraints weight = 10065.090| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.13 r_work: 0.3298 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3025 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= 0.120 Angle : 0.568 8.680 11755 Z= 0.296 Chirality : 0.042 0.195 1390 Planarity : 0.004 0.069 1500 Dihedral : 4.933 55.220 1229 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.92 % Allowed : 22.31 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.23 (0.25), residues: 1137 helix: -0.94 (0.27), residues: 365 sheet: 0.11 (0.30), residues: 283 loop : -1.16 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.011 0.001 PHE B 189 TYR 0.010 0.001 TYR E 190 ARG 0.008 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 299) hydrogen bonds : angle 4.53083 ( 834) SS BOND : bond 0.00873 ( 4) SS BOND : angle 1.51570 ( 8) covalent geometry : bond 0.00272 ( 8629) covalent geometry : angle 0.56665 (11747) ********************** 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 187 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.956 Fit side-chains REVERT: A 272 PHE cc_start: 0.8257 (t80) cc_final: 0.7896 (t80) REVERT: B 192 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7875 (mtpp) REVERT: B 252 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 45 MET cc_start: 0.8997 (mtt) cc_final: 0.8567 (mtt) REVERT: C 96 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: C 129 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7079 (tpt-90) REVERT: C 212 ASP cc_start: 0.8516 (t70) cc_final: 0.8118 (t0) REVERT: C 214 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: C 258 ASP cc_start: 0.7051 (t70) cc_final: 0.6166 (t70) REVERT: E 46 GLU cc_start: 0.8459 (pt0) cc_final: 0.7947 (pt0) REVERT: E 65 LYS cc_start: 0.8264 (tptt) cc_final: 0.7913 (ttpt) REVERT: E 89 GLU cc_start: 0.8021 (mp0) cc_final: 0.7559 (pm20) REVERT: E 93 MET cc_start: 0.8746 (ttm) cc_final: 0.8447 (ttp) outliers start: 25 outliers final: 19 residues processed: 179 average time/residue: 1.2120 time to fit residues: 233.7430 Evaluate side-chains 179 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 252 SER 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 215 GLU 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 47 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 104 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.181549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124815 restraints weight = 10155.220| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.33 r_work: 0.3232 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8633 Z= 0.204 Angle : 0.639 9.029 11755 Z= 0.332 Chirality : 0.045 0.184 1390 Planarity : 0.004 0.070 1500 Dihedral : 4.975 36.743 1227 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.80 % Allowed : 23.01 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.28 (0.24), residues: 1137 helix: -0.97 (0.27), residues: 366 sheet: 0.05 (0.30), residues: 286 loop : -1.19 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS B 213 PHE 0.012 0.002 PHE B 189 TYR 0.016 0.002 TYR C 59 ARG 0.005 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 299) hydrogen bonds : angle 4.72206 ( 834) SS BOND : bond 0.01346 ( 4) SS BOND : angle 2.22220 ( 8) covalent geometry : bond 0.00479 ( 8629) covalent geometry : angle 0.63619 (11747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9206.41 seconds wall clock time: 166 minutes 8.72 seconds (9968.72 seconds total)