Starting phenix.real_space_refine on Sat Aug 23 14:58:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpr_34941/08_2025/8hpr_34941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpr_34941/08_2025/8hpr_34941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpr_34941/08_2025/8hpr_34941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpr_34941/08_2025/8hpr_34941.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpr_34941/08_2025/8hpr_34941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpr_34941/08_2025/8hpr_34941.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 8071 2.51 5 N 2147 2.21 5 O 2386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12645 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2013 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 14, 'TRANS': 262} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1848 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2695 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2719 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3283 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 405} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.40, per 1000 atoms: 0.27 Number of scatterers: 12645 At special positions: 0 Unit cell: (82.82, 84.46, 169.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 6 15.00 Mg 2 11.99 O 2386 8.00 N 2147 7.00 C 8071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-1 " GLC H 1 " - " GLC H 2 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 705.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 13 sheets defined 56.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 28 through 51 removed outlier: 4.478A pdb=" N LEU A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 76 through 110 removed outlier: 4.059A pdb=" N TRP A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 191 Proline residue: A 179 - end of helix removed outlier: 3.648A pdb=" N LEU A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.943A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 214 through 237 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.603A pdb=" N TYR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 292 removed outlier: 4.384A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 removed outlier: 4.263A pdb=" N TRP B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.859A pdb=" N GLY B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.977A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 117 through 133 removed outlier: 3.644A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.570A pdb=" N ASN B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 149 removed outlier: 3.855A pdb=" N LEU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.653A pdb=" N GLU B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 removed outlier: 4.010A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 207 Proline residue: B 193 - end of helix removed outlier: 5.104A pdb=" N THR B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.759A pdb=" N ILE B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.604A pdb=" N ARG C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 81' Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.729A pdb=" N GLN C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 189 Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.115A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.698A pdb=" N ASP D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.566A pdb=" N ARG D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 189 removed outlier: 3.863A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 removed outlier: 3.554A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 3.631A pdb=" N LEU D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'E' and resid 40 through 56 removed outlier: 3.806A pdb=" N PHE E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.762A pdb=" N PHE E 199 " --> pdb=" O MET E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 276 through 286 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'E' and resid 359 through 371 Processing helix chain 'E' and resid 372 through 384 Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 414 removed outlier: 3.828A pdb=" N ASN E 414 " --> pdb=" O GLN E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 436 removed outlier: 3.653A pdb=" N VAL E 427 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 435 " --> pdb=" O MET E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 442 through 460 removed outlier: 3.659A pdb=" N GLN E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 31 removed outlier: 6.336A pdb=" N ALA C 23 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER C 12 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS C 25 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR C 10 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL C 9 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 62 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 70 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 85 removed outlier: 6.232A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 219 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 261 through 264 Processing sheet with id=AA4, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.965A pdb=" N ILE C 372 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 306 " --> pdb=" O ILE C 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.967A pdb=" N ILE C 314 " --> pdb=" O HIS C 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 31 removed outlier: 5.917A pdb=" N ALA D 23 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER D 12 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS D 25 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR D 10 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE D 27 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D 9 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER D 62 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.649A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP D 163 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 85 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 261 through 264 removed outlier: 3.910A pdb=" N ILE D 282 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 292 through 293 removed outlier: 3.863A pdb=" N GLU D 366 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.998A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 60 through 66 removed outlier: 7.361A pdb=" N LEU E 88 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN E 33 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N ASP E 94 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.695A pdb=" N GLU E 139 " --> pdb=" O TRP E 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 186 690 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2377 1.32 - 1.45: 2987 1.45 - 1.57: 7465 1.57 - 1.69: 10 1.69 - 1.82: 62 Bond restraints: 12901 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.73e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.415 1.549 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 12896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 17091 3.87 - 7.74: 534 7.74 - 11.61: 8 11.61 - 15.49: 1 15.49 - 19.36: 4 Bond angle restraints: 17638 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.72 16.11 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.67 8.13 1.00e+00 1.00e+00 6.61e+01 ... (remaining 17633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 7440 24.83 - 49.66: 280 49.66 - 74.49: 23 74.49 - 99.32: 12 99.32 - 124.15: 2 Dihedral angle restraints: 7757 sinusoidal: 2875 harmonic: 4882 Sorted by residual: dihedral pdb=" CA GLU A 58 " pdb=" C GLU A 58 " pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLU D 130 " pdb=" C GLU D 130 " pdb=" N LEU D 131 " pdb=" CA LEU D 131 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS D 322 " pdb=" C LYS D 322 " pdb=" N TYR D 323 " pdb=" CA TYR D 323 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 7754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1148 0.070 - 0.140: 670 0.140 - 0.210: 218 0.210 - 0.280: 50 0.280 - 0.350: 15 Chirality restraints: 2101 Sorted by residual: chirality pdb=" C1 GLC H 1 " pdb=" C2 GLC H 1 " pdb=" O5 GLC H 1 " pdb=" O1 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.81e+01 chirality pdb=" CA TYR D 89 " pdb=" N TYR D 89 " pdb=" C TYR D 89 " pdb=" CB TYR D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PHE B 161 " pdb=" N PHE B 161 " pdb=" C PHE B 161 " pdb=" CB PHE B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2098 not shown) Planarity restraints: 2269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 97 " 0.161 2.00e-02 2.50e+03 9.03e-02 2.04e+02 pdb=" CG TRP E 97 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP E 97 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 97 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 97 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP E 97 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 97 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 97 " 0.103 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 97 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP E 97 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " 0.121 2.00e-02 2.50e+03 6.04e-02 9.12e+01 pdb=" CG TRP E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " -0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " -0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " 0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 35 " 0.103 2.00e-02 2.50e+03 5.99e-02 7.18e+01 pdb=" CG TYR E 35 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 35 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR E 35 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 35 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR E 35 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR E 35 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR E 35 " 0.103 2.00e-02 2.50e+03 ... (remaining 2266 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 505 2.74 - 3.28: 13782 3.28 - 3.82: 19862 3.82 - 4.36: 25503 4.36 - 4.90: 41089 Nonbonded interactions: 100741 Sorted by model distance: nonbonded pdb=" O GLY D 46 " pdb=" SD MET D 212 " model vdw 2.201 3.400 nonbonded pdb=" OE1 GLN C 87 " pdb="MG MG C 502 " model vdw 2.222 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 2.230 2.170 nonbonded pdb=" OG SER D 48 " pdb="MG MG D 502 " model vdw 2.241 2.170 nonbonded pdb=" NE2 GLN C 87 " pdb="MG MG C 502 " model vdw 2.256 2.250 ... (remaining 100736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 273 or (resid 274 thro \ ugh 278 and (name N or name CA or name C or name O or name CB )) or resid 279 th \ rough 327 or resid 352 through 388 or (resid 389 and (name N or name CA or name \ C or name O or name CB )) or resid 390 through 502)) selection = (chain 'D' and (resid 2 through 20 or (resid 21 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 81 or (resid 82 through \ 84 and (name N or name CA or name C or name O or name CB )) or resid 85 through \ 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or re \ sid 110 through 118 or (resid 119 through 120 and (name N or name CA or name C o \ r name O or name CB )) or resid 121 through 123 or (resid 124 through 125 and (n \ ame N or name CA or name C or name O or name CB )) or resid 126 through 130 or ( \ resid 131 through 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 143 or (resid 144 and (name N or name CA or name C or name O \ or name CB )) or resid 145 through 179 or (resid 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 232 or (resid 233 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 356 or (resi \ d 357 through 358 and (name N or name CA or name C or name O or name CB )) or re \ sid 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) o \ r resid 361 through 377 or (resid 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 386 or (resid 387 and (name N or name CA or \ name C or name O or name CB )) or resid 388 through 502)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.012 0.134 12902 Z= 0.764 Angle : 1.778 19.356 17641 Z= 1.213 Chirality : 0.096 0.350 2101 Planarity : 0.013 0.113 2269 Dihedral : 13.559 124.146 4603 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 0.64 % Allowed : 6.65 % Favored : 92.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.18), residues: 1676 helix: -1.74 (0.15), residues: 813 sheet: -0.56 (0.43), residues: 133 loop : -1.06 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 80 TYR 0.106 0.018 TYR B 23 PHE 0.080 0.012 PHE D 234 TRP 0.161 0.022 TRP E 97 HIS 0.013 0.003 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.01234 (12901) covalent geometry : angle 1.77798 (17638) hydrogen bonds : bond 0.16956 ( 690) hydrogen bonds : angle 7.98085 ( 1947) glycosidic custom : bond 0.02910 ( 1) glycosidic custom : angle 2.00096 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 395 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8793 (t80) cc_final: 0.7953 (t80) REVERT: A 137 TRP cc_start: 0.8796 (m100) cc_final: 0.8560 (m100) REVERT: A 147 TYR cc_start: 0.8611 (p90) cc_final: 0.8347 (p90) REVERT: A 180 PHE cc_start: 0.8658 (t80) cc_final: 0.8359 (t80) REVERT: A 195 ASP cc_start: 0.8221 (m-30) cc_final: 0.7995 (m-30) REVERT: A 219 ILE cc_start: 0.8959 (mt) cc_final: 0.8693 (pt) REVERT: A 233 ASP cc_start: 0.8351 (t70) cc_final: 0.8128 (t0) REVERT: A 255 SER cc_start: 0.9476 (m) cc_final: 0.9045 (t) REVERT: A 291 LYS cc_start: 0.8660 (tppp) cc_final: 0.8294 (tttt) REVERT: B 25 LEU cc_start: 0.7742 (mt) cc_final: 0.7503 (mm) REVERT: B 175 ASP cc_start: 0.7731 (m-30) cc_final: 0.7391 (m-30) REVERT: B 260 VAL cc_start: 0.8362 (t) cc_final: 0.8143 (p) REVERT: C 13 TYR cc_start: 0.8247 (m-80) cc_final: 0.7788 (m-10) REVERT: C 51 LEU cc_start: 0.9141 (tp) cc_final: 0.8492 (tp) REVERT: C 87 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: C 149 MET cc_start: 0.8817 (ttt) cc_final: 0.8582 (ttp) REVERT: C 172 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8763 (ttmm) REVERT: C 244 MET cc_start: 0.6770 (ttm) cc_final: 0.6569 (tpt) REVERT: D 92 TYR cc_start: 0.8017 (m-80) cc_final: 0.7704 (m-10) REVERT: D 198 ASP cc_start: 0.8036 (t0) cc_final: 0.7675 (t0) REVERT: D 244 MET cc_start: 0.5617 (ttm) cc_final: 0.5375 (tpp) REVERT: D 281 ASN cc_start: 0.7478 (m-40) cc_final: 0.7117 (m110) REVERT: E 315 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9214 (pp20) REVERT: E 322 ASP cc_start: 0.8902 (m-30) cc_final: 0.8684 (p0) outliers start: 8 outliers final: 3 residues processed: 400 average time/residue: 0.1344 time to fit residues: 74.3823 Evaluate side-chains 261 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 257 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain E residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 17 ASN B 118 HIS C 219 GLN C 290 HIS D 99 GLN D 164 GLN D 197 HIS D 199 GLN E 39 ASN E 49 ASN E 359 HIS E 375 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.132054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099656 restraints weight = 31016.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102982 restraints weight = 17063.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105109 restraints weight = 11800.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106435 restraints weight = 9379.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107428 restraints weight = 8140.656| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12902 Z= 0.170 Angle : 0.769 8.703 17641 Z= 0.403 Chirality : 0.048 0.196 2101 Planarity : 0.005 0.045 2269 Dihedral : 8.478 62.330 1927 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.44 % Allowed : 14.25 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1676 helix: -0.06 (0.17), residues: 828 sheet: -0.60 (0.39), residues: 156 loop : -0.72 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 227 TYR 0.026 0.002 TYR C 194 PHE 0.022 0.002 PHE B 161 TRP 0.024 0.002 TRP B 12 HIS 0.008 0.002 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00362 (12901) covalent geometry : angle 0.76807 (17638) hydrogen bonds : bond 0.05202 ( 690) hydrogen bonds : angle 5.50740 ( 1947) glycosidic custom : bond 0.00545 ( 1) glycosidic custom : angle 2.54461 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8633 (t80) cc_final: 0.8288 (t80) REVERT: A 137 TRP cc_start: 0.8737 (m100) cc_final: 0.8462 (m100) REVERT: A 195 ASP cc_start: 0.8285 (m-30) cc_final: 0.8073 (m-30) REVERT: A 233 ASP cc_start: 0.8279 (t70) cc_final: 0.8039 (t0) REVERT: A 267 ASN cc_start: 0.8562 (t0) cc_final: 0.8282 (t0) REVERT: C 184 LEU cc_start: 0.9232 (tp) cc_final: 0.8828 (tp) REVERT: D 198 ASP cc_start: 0.8030 (t0) cc_final: 0.7720 (t0) REVERT: E 275 TYR cc_start: 0.7689 (m-10) cc_final: 0.7444 (m-10) REVERT: E 333 TYR cc_start: 0.9119 (t80) cc_final: 0.8914 (t80) outliers start: 43 outliers final: 22 residues processed: 308 average time/residue: 0.1178 time to fit residues: 52.4929 Evaluate side-chains 247 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 55 optimal weight: 0.7980 chunk 130 optimal weight: 0.0770 chunk 138 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 163 optimal weight: 0.3980 chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN C 367 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 176 GLN D 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.132238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.099934 restraints weight = 31262.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103300 restraints weight = 17170.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105474 restraints weight = 11893.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106717 restraints weight = 9440.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107839 restraints weight = 8218.214| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12902 Z= 0.139 Angle : 0.681 8.201 17641 Z= 0.350 Chirality : 0.046 0.211 2101 Planarity : 0.005 0.047 2269 Dihedral : 8.037 65.463 1923 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.12 % Allowed : 16.09 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1676 helix: 0.32 (0.18), residues: 826 sheet: -0.39 (0.39), residues: 162 loop : -0.70 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 64 TYR 0.018 0.002 TYR C 194 PHE 0.023 0.002 PHE B 161 TRP 0.015 0.002 TRP A 208 HIS 0.009 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00293 (12901) covalent geometry : angle 0.68022 (17638) hydrogen bonds : bond 0.04323 ( 690) hydrogen bonds : angle 5.16356 ( 1947) glycosidic custom : bond 0.00289 ( 1) glycosidic custom : angle 1.65195 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8526 (t80) cc_final: 0.8162 (t80) REVERT: A 137 TRP cc_start: 0.8696 (m100) cc_final: 0.8478 (m100) REVERT: A 147 TYR cc_start: 0.8330 (p90) cc_final: 0.8103 (p90) REVERT: A 233 ASP cc_start: 0.8321 (t70) cc_final: 0.8026 (t0) REVERT: A 262 LEU cc_start: 0.9310 (tp) cc_final: 0.8955 (tt) REVERT: B 61 PHE cc_start: 0.8605 (m-80) cc_final: 0.7933 (m-80) REVERT: B 128 MET cc_start: 0.8576 (mmt) cc_final: 0.8240 (ttm) REVERT: C 219 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 257 ARG cc_start: 0.9420 (mtt180) cc_final: 0.9093 (ptp90) REVERT: C 322 LYS cc_start: 0.8183 (mttm) cc_final: 0.7942 (mttp) REVERT: C 361 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7211 (mmm160) REVERT: D 198 ASP cc_start: 0.8078 (t0) cc_final: 0.7815 (t0) REVERT: D 361 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6927 (mmm160) REVERT: E 131 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (mt) outliers start: 39 outliers final: 24 residues processed: 270 average time/residue: 0.1180 time to fit residues: 46.1942 Evaluate side-chains 239 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 103 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 6 optimal weight: 0.0170 chunk 123 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN C 168 ASN D 176 GLN D 199 GLN D 290 HIS E 49 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096380 restraints weight = 31479.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099568 restraints weight = 17813.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101560 restraints weight = 12419.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103014 restraints weight = 9999.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103717 restraints weight = 8636.390| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12902 Z= 0.196 Angle : 0.684 8.888 17641 Z= 0.353 Chirality : 0.047 0.197 2101 Planarity : 0.005 0.049 2269 Dihedral : 7.772 71.714 1918 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.08 % Allowed : 16.41 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.20), residues: 1676 helix: 0.40 (0.18), residues: 824 sheet: -0.42 (0.37), residues: 175 loop : -0.70 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 230 TYR 0.028 0.002 TYR C 194 PHE 0.026 0.002 PHE B 161 TRP 0.018 0.002 TRP B 30 HIS 0.011 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00449 (12901) covalent geometry : angle 0.68405 (17638) hydrogen bonds : bond 0.04229 ( 690) hydrogen bonds : angle 5.20538 ( 1947) glycosidic custom : bond 0.00879 ( 1) glycosidic custom : angle 1.71390 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8588 (t80) cc_final: 0.8207 (t80) REVERT: A 137 TRP cc_start: 0.8720 (m100) cc_final: 0.8460 (m100) REVERT: A 233 ASP cc_start: 0.8431 (t70) cc_final: 0.8132 (t0) REVERT: A 262 LEU cc_start: 0.9346 (tp) cc_final: 0.8996 (tt) REVERT: B 61 PHE cc_start: 0.8647 (m-80) cc_final: 0.8047 (m-80) REVERT: B 128 MET cc_start: 0.8587 (mmt) cc_final: 0.8155 (mtp) REVERT: B 174 MET cc_start: 0.7504 (tpt) cc_final: 0.6730 (tpp) REVERT: C 47 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8629 (mtmm) REVERT: C 53 MET cc_start: 0.8720 (mtm) cc_final: 0.8312 (mtm) REVERT: C 184 LEU cc_start: 0.9107 (tp) cc_final: 0.8903 (mt) REVERT: C 244 MET cc_start: 0.6693 (ttm) cc_final: 0.6334 (mmm) REVERT: C 322 LYS cc_start: 0.8122 (mttm) cc_final: 0.7716 (mttp) REVERT: C 380 PHE cc_start: 0.8235 (m-80) cc_final: 0.7996 (m-80) REVERT: D 198 ASP cc_start: 0.8110 (t0) cc_final: 0.7790 (t0) REVERT: D 361 ARG cc_start: 0.7301 (mmm160) cc_final: 0.7043 (mmm160) REVERT: E 131 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8692 (mt) outliers start: 51 outliers final: 35 residues processed: 253 average time/residue: 0.1138 time to fit residues: 42.0803 Evaluate side-chains 250 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 139 optimal weight: 0.0010 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 142 optimal weight: 0.0170 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.0070 chunk 96 optimal weight: 0.9980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.131196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098830 restraints weight = 31232.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102247 restraints weight = 17167.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.104552 restraints weight = 11765.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.106048 restraints weight = 9209.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106804 restraints weight = 7872.317| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12902 Z= 0.124 Angle : 0.630 9.482 17641 Z= 0.319 Chirality : 0.045 0.222 2101 Planarity : 0.005 0.050 2269 Dihedral : 7.033 73.106 1918 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.64 % Allowed : 18.33 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.21), residues: 1676 helix: 0.52 (0.18), residues: 824 sheet: -0.05 (0.40), residues: 154 loop : -0.66 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.013 0.001 TYR E 333 PHE 0.020 0.001 PHE B 161 TRP 0.035 0.002 TRP B 30 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00260 (12901) covalent geometry : angle 0.62951 (17638) hydrogen bonds : bond 0.03688 ( 690) hydrogen bonds : angle 4.96836 ( 1947) glycosidic custom : bond 0.00068 ( 1) glycosidic custom : angle 1.40147 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8439 (t80) cc_final: 0.8060 (t80) REVERT: A 137 TRP cc_start: 0.8664 (m100) cc_final: 0.8448 (m100) REVERT: A 230 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7860 (tpt90) REVERT: A 233 ASP cc_start: 0.8457 (t70) cc_final: 0.8042 (t0) REVERT: A 262 LEU cc_start: 0.9302 (tp) cc_final: 0.8914 (tt) REVERT: B 61 PHE cc_start: 0.8620 (m-80) cc_final: 0.7967 (m-80) REVERT: B 128 MET cc_start: 0.8434 (mmt) cc_final: 0.8059 (mtp) REVERT: C 53 MET cc_start: 0.8749 (mtm) cc_final: 0.8360 (mtm) REVERT: C 186 ASP cc_start: 0.7021 (m-30) cc_final: 0.6492 (p0) REVERT: C 244 MET cc_start: 0.6613 (ttm) cc_final: 0.6363 (mmm) REVERT: C 282 ILE cc_start: 0.9228 (mp) cc_final: 0.8647 (mp) REVERT: D 198 ASP cc_start: 0.8147 (t0) cc_final: 0.7831 (t0) REVERT: D 361 ARG cc_start: 0.7388 (mmm160) cc_final: 0.7140 (mmm160) REVERT: E 286 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8839 (mtmm) outliers start: 33 outliers final: 19 residues processed: 269 average time/residue: 0.1205 time to fit residues: 46.8073 Evaluate side-chains 230 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 11 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094944 restraints weight = 31195.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098128 restraints weight = 17465.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100150 restraints weight = 12167.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101598 restraints weight = 9722.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102495 restraints weight = 8383.259| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12902 Z= 0.191 Angle : 0.679 8.683 17641 Z= 0.344 Chirality : 0.047 0.218 2101 Planarity : 0.005 0.049 2269 Dihedral : 6.884 73.650 1918 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.16 % Allowed : 18.17 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.21), residues: 1676 helix: 0.55 (0.18), residues: 822 sheet: -0.34 (0.37), residues: 179 loop : -0.63 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 80 TYR 0.027 0.002 TYR D 194 PHE 0.024 0.002 PHE B 161 TRP 0.019 0.002 TRP B 30 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00437 (12901) covalent geometry : angle 0.67840 (17638) hydrogen bonds : bond 0.03945 ( 690) hydrogen bonds : angle 5.09092 ( 1947) glycosidic custom : bond 0.00479 ( 1) glycosidic custom : angle 2.86084 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8625 (t80) cc_final: 0.8259 (t80) REVERT: A 58 GLU cc_start: 0.6849 (tt0) cc_final: 0.6486 (tt0) REVERT: A 137 TRP cc_start: 0.8708 (m100) cc_final: 0.8401 (m100) REVERT: A 233 ASP cc_start: 0.8540 (t70) cc_final: 0.8147 (t0) REVERT: A 262 LEU cc_start: 0.9336 (tp) cc_final: 0.8975 (tt) REVERT: B 61 PHE cc_start: 0.8629 (m-80) cc_final: 0.8002 (m-80) REVERT: B 128 MET cc_start: 0.8435 (mmt) cc_final: 0.8066 (mtp) REVERT: C 53 MET cc_start: 0.8792 (mtm) cc_final: 0.8414 (mtm) REVERT: C 168 ASN cc_start: 0.9219 (m110) cc_final: 0.9017 (m-40) REVERT: C 186 ASP cc_start: 0.7044 (m-30) cc_final: 0.6661 (p0) REVERT: C 244 MET cc_start: 0.6635 (ttm) cc_final: 0.6238 (mmm) REVERT: C 361 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7229 (mmm160) REVERT: D 198 ASP cc_start: 0.8125 (t0) cc_final: 0.7775 (t0) REVERT: D 361 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7216 (mmm160) REVERT: E 286 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8857 (mtmm) outliers start: 52 outliers final: 41 residues processed: 246 average time/residue: 0.1118 time to fit residues: 40.2859 Evaluate side-chains 247 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 101 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095864 restraints weight = 31516.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099371 restraints weight = 18091.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101944 restraints weight = 11331.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102059 restraints weight = 9286.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102022 restraints weight = 8447.799| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12902 Z= 0.164 Angle : 0.664 9.840 17641 Z= 0.336 Chirality : 0.046 0.210 2101 Planarity : 0.005 0.086 2269 Dihedral : 6.690 74.164 1918 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.84 % Allowed : 19.46 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.21), residues: 1676 helix: 0.55 (0.18), residues: 823 sheet: -0.23 (0.39), residues: 164 loop : -0.71 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 98 TYR 0.025 0.002 TYR E 378 PHE 0.028 0.002 PHE A 83 TRP 0.010 0.001 TRP A 80 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00376 (12901) covalent geometry : angle 0.66301 (17638) hydrogen bonds : bond 0.03804 ( 690) hydrogen bonds : angle 5.06790 ( 1947) glycosidic custom : bond 0.00705 ( 1) glycosidic custom : angle 2.13634 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8645 (t80) cc_final: 0.8230 (t80) REVERT: A 58 GLU cc_start: 0.6942 (tt0) cc_final: 0.6589 (tt0) REVERT: A 87 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 137 TRP cc_start: 0.8725 (m100) cc_final: 0.8445 (m100) REVERT: A 233 ASP cc_start: 0.8554 (t70) cc_final: 0.8115 (t0) REVERT: A 262 LEU cc_start: 0.9330 (tp) cc_final: 0.8975 (tt) REVERT: B 61 PHE cc_start: 0.8681 (m-80) cc_final: 0.8042 (m-80) REVERT: B 128 MET cc_start: 0.8448 (mmt) cc_final: 0.8089 (mtp) REVERT: B 239 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7109 (mm-30) REVERT: C 13 TYR cc_start: 0.8359 (m-10) cc_final: 0.8157 (m-10) REVERT: C 53 MET cc_start: 0.8809 (mtm) cc_final: 0.8404 (mtm) REVERT: C 168 ASN cc_start: 0.9263 (m110) cc_final: 0.9035 (m-40) REVERT: C 186 ASP cc_start: 0.7004 (m-30) cc_final: 0.6716 (p0) REVERT: C 203 MET cc_start: 0.8988 (tpp) cc_final: 0.8689 (tpt) REVERT: C 244 MET cc_start: 0.6766 (ttm) cc_final: 0.6386 (mmm) REVERT: C 361 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7110 (mmm160) REVERT: D 198 ASP cc_start: 0.8226 (t0) cc_final: 0.7868 (t0) REVERT: D 361 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7257 (mmm160) REVERT: E 286 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8894 (mtmm) outliers start: 48 outliers final: 41 residues processed: 246 average time/residue: 0.1120 time to fit residues: 40.1867 Evaluate side-chains 254 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 126 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094871 restraints weight = 31336.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098117 restraints weight = 17501.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100226 restraints weight = 12147.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101637 restraints weight = 9645.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102514 restraints weight = 8318.690| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12902 Z= 0.166 Angle : 0.665 9.443 17641 Z= 0.337 Chirality : 0.046 0.233 2101 Planarity : 0.005 0.100 2269 Dihedral : 6.381 75.420 1918 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.00 % Allowed : 19.86 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1676 helix: 0.54 (0.18), residues: 824 sheet: -0.30 (0.39), residues: 170 loop : -0.70 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 230 TYR 0.028 0.002 TYR E 378 PHE 0.024 0.002 PHE D 380 TRP 0.011 0.001 TRP A 175 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00380 (12901) covalent geometry : angle 0.66420 (17638) hydrogen bonds : bond 0.03813 ( 690) hydrogen bonds : angle 5.06119 ( 1947) glycosidic custom : bond 0.00829 ( 1) glycosidic custom : angle 2.50899 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8633 (t80) cc_final: 0.8184 (t80) REVERT: A 58 GLU cc_start: 0.6946 (tt0) cc_final: 0.6610 (tt0) REVERT: A 137 TRP cc_start: 0.8718 (m100) cc_final: 0.8446 (m100) REVERT: A 219 ILE cc_start: 0.8855 (mm) cc_final: 0.8433 (mt) REVERT: A 233 ASP cc_start: 0.8555 (t70) cc_final: 0.8107 (t0) REVERT: A 262 LEU cc_start: 0.9343 (tp) cc_final: 0.8985 (tt) REVERT: B 61 PHE cc_start: 0.8628 (m-80) cc_final: 0.8007 (m-80) REVERT: B 128 MET cc_start: 0.8459 (mmt) cc_final: 0.8100 (mtp) REVERT: B 209 ASP cc_start: 0.7905 (t70) cc_final: 0.7666 (t0) REVERT: C 13 TYR cc_start: 0.8384 (m-10) cc_final: 0.7889 (m-10) REVERT: C 53 MET cc_start: 0.8770 (mtm) cc_final: 0.8550 (mtm) REVERT: C 244 MET cc_start: 0.6676 (ttm) cc_final: 0.6375 (mmm) REVERT: C 361 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7221 (mmm160) REVERT: D 198 ASP cc_start: 0.8125 (t0) cc_final: 0.7793 (t0) REVERT: D 361 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7273 (mmm160) outliers start: 50 outliers final: 46 residues processed: 251 average time/residue: 0.1170 time to fit residues: 42.8962 Evaluate side-chains 258 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 150 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 168 ASN D 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098047 restraints weight = 31312.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101447 restraints weight = 17176.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103694 restraints weight = 11820.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105172 restraints weight = 9303.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105982 restraints weight = 7974.556| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12902 Z= 0.124 Angle : 0.671 11.985 17641 Z= 0.333 Chirality : 0.046 0.216 2101 Planarity : 0.005 0.076 2269 Dihedral : 6.016 73.348 1918 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.28 % Allowed : 20.90 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1676 helix: 0.60 (0.18), residues: 831 sheet: -0.03 (0.38), residues: 171 loop : -0.72 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 98 TYR 0.030 0.001 TYR E 378 PHE 0.026 0.001 PHE A 83 TRP 0.016 0.001 TRP A 175 HIS 0.004 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00267 (12901) covalent geometry : angle 0.67090 (17638) hydrogen bonds : bond 0.03558 ( 690) hydrogen bonds : angle 4.96532 ( 1947) glycosidic custom : bond 0.00375 ( 1) glycosidic custom : angle 1.50541 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8505 (t80) cc_final: 0.8101 (t80) REVERT: A 137 TRP cc_start: 0.8691 (m100) cc_final: 0.8461 (m100) REVERT: A 173 GLU cc_start: 0.8232 (tp30) cc_final: 0.8012 (tp30) REVERT: A 181 MET cc_start: 0.8889 (ptm) cc_final: 0.8662 (ptt) REVERT: A 219 ILE cc_start: 0.8773 (mm) cc_final: 0.8348 (mt) REVERT: A 230 ARG cc_start: 0.8085 (tpt170) cc_final: 0.7648 (tpt170) REVERT: A 233 ASP cc_start: 0.8543 (t70) cc_final: 0.8063 (t0) REVERT: A 262 LEU cc_start: 0.9288 (tp) cc_final: 0.8888 (tt) REVERT: A 292 ILE cc_start: 0.8486 (mm) cc_final: 0.8281 (tt) REVERT: B 61 PHE cc_start: 0.8581 (m-80) cc_final: 0.7953 (m-80) REVERT: B 128 MET cc_start: 0.8276 (mmt) cc_final: 0.7927 (mtp) REVERT: B 209 ASP cc_start: 0.7572 (t70) cc_final: 0.7318 (t0) REVERT: C 13 TYR cc_start: 0.8334 (m-10) cc_final: 0.7807 (m-10) REVERT: C 53 MET cc_start: 0.8782 (mtm) cc_final: 0.8533 (mtt) REVERT: C 244 MET cc_start: 0.6734 (ttm) cc_final: 0.6448 (mmm) REVERT: C 269 MET cc_start: 0.8529 (ptt) cc_final: 0.7881 (pmm) REVERT: C 353 ILE cc_start: 0.9123 (mm) cc_final: 0.8536 (tp) REVERT: C 361 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7256 (mmm160) REVERT: D 198 ASP cc_start: 0.8118 (t0) cc_final: 0.7786 (t0) REVERT: D 268 HIS cc_start: 0.9222 (m-70) cc_final: 0.8801 (m90) REVERT: D 361 ARG cc_start: 0.7574 (mmm160) cc_final: 0.7319 (mmm160) REVERT: E 286 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8884 (mtmm) outliers start: 41 outliers final: 36 residues processed: 259 average time/residue: 0.1215 time to fit residues: 45.4688 Evaluate side-chains 253 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 14 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 0.0060 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.130018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097470 restraints weight = 31723.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100927 restraints weight = 17474.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103126 restraints weight = 12025.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104346 restraints weight = 9519.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105478 restraints weight = 8290.493| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12902 Z= 0.126 Angle : 0.676 11.674 17641 Z= 0.334 Chirality : 0.046 0.348 2101 Planarity : 0.005 0.063 2269 Dihedral : 5.929 72.936 1918 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 21.46 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.21), residues: 1676 helix: 0.58 (0.18), residues: 833 sheet: 0.08 (0.39), residues: 171 loop : -0.68 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 66 TYR 0.031 0.001 TYR E 378 PHE 0.022 0.001 PHE D 380 TRP 0.017 0.001 TRP A 175 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00277 (12901) covalent geometry : angle 0.67599 (17638) hydrogen bonds : bond 0.03487 ( 690) hydrogen bonds : angle 4.94609 ( 1947) glycosidic custom : bond 0.00586 ( 1) glycosidic custom : angle 1.71187 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8499 (t80) cc_final: 0.8099 (t80) REVERT: A 137 TRP cc_start: 0.8693 (m100) cc_final: 0.8465 (m100) REVERT: A 219 ILE cc_start: 0.8766 (mm) cc_final: 0.8375 (mt) REVERT: A 233 ASP cc_start: 0.8558 (t70) cc_final: 0.8042 (t0) REVERT: A 262 LEU cc_start: 0.9282 (tp) cc_final: 0.8880 (tt) REVERT: A 292 ILE cc_start: 0.8492 (mm) cc_final: 0.8277 (tt) REVERT: B 61 PHE cc_start: 0.8569 (m-80) cc_final: 0.7973 (m-80) REVERT: B 128 MET cc_start: 0.8276 (mmt) cc_final: 0.7950 (mtp) REVERT: C 13 TYR cc_start: 0.8356 (m-10) cc_final: 0.7896 (m-10) REVERT: C 53 MET cc_start: 0.8774 (mtm) cc_final: 0.8510 (mtt) REVERT: C 219 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 244 MET cc_start: 0.6632 (ttm) cc_final: 0.6313 (mmm) REVERT: C 269 MET cc_start: 0.8579 (ptt) cc_final: 0.8062 (pmm) REVERT: C 353 ILE cc_start: 0.9122 (mm) cc_final: 0.8539 (tp) REVERT: C 361 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7262 (mmm160) REVERT: C 367 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8643 (tp-100) REVERT: D 198 ASP cc_start: 0.8136 (t0) cc_final: 0.7803 (t0) REVERT: D 268 HIS cc_start: 0.9220 (m-70) cc_final: 0.8809 (m90) REVERT: D 361 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7319 (mmm160) REVERT: E 286 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8885 (mtmm) outliers start: 34 outliers final: 33 residues processed: 249 average time/residue: 0.1144 time to fit residues: 41.9132 Evaluate side-chains 248 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 TYR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN C 176 GLN D 176 GLN E 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095677 restraints weight = 31664.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099021 restraints weight = 17477.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101209 restraints weight = 12075.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102639 restraints weight = 9531.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103404 restraints weight = 8195.708| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12902 Z= 0.155 Angle : 0.688 10.911 17641 Z= 0.341 Chirality : 0.047 0.399 2101 Planarity : 0.005 0.059 2269 Dihedral : 6.009 73.750 1918 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.28 % Allowed : 21.46 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.21), residues: 1676 helix: 0.60 (0.18), residues: 844 sheet: 0.07 (0.39), residues: 170 loop : -0.71 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 66 TYR 0.032 0.002 TYR E 378 PHE 0.030 0.002 PHE A 83 TRP 0.014 0.001 TRP A 175 HIS 0.004 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00356 (12901) covalent geometry : angle 0.68756 (17638) hydrogen bonds : bond 0.03623 ( 690) hydrogen bonds : angle 4.96993 ( 1947) glycosidic custom : bond 0.00862 ( 1) glycosidic custom : angle 2.09233 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2588.91 seconds wall clock time: 45 minutes 24.68 seconds (2724.68 seconds total)