Starting phenix.real_space_refine on Sat May 10 17:40:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo3_42426/05_2025/8uo3_42426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo3_42426/05_2025/8uo3_42426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uo3_42426/05_2025/8uo3_42426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo3_42426/05_2025/8uo3_42426.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo3_42426/05_2025/8uo3_42426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo3_42426/05_2025/8uo3_42426.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 4187 2.51 5 N 1204 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2559 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 13, 'TRANS': 345} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2418 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 10, 'ASN:plan1': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 148 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 352 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1273 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 714 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.72 Number of scatterers: 6650 At special positions: 0 Unit cell: (82.4315, 134.493, 102.389, 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 3 15.00 Mg 1 11.99 O 1222 8.00 N 1204 7.00 C 4187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 983.2 milliseconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1858 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 49.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.187A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.797A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 4.141A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.897A pdb=" N ASP A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.587A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 4.049A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.504A pdb=" N PHE A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.888A pdb=" N GLN A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.656A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 4.033A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.772A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.016A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.715A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.758A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.798A pdb=" N ILE A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.623A pdb=" N HIS A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.775A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.619A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.690A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.003A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.438A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 46 Processing helix chain 'R' and resid 46 through 58 removed outlier: 3.844A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 4.028A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA R 76 " --> pdb=" O ILE R 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL R 81 " --> pdb=" O CYS R 77 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.973A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 172 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 198 through 208 removed outlier: 3.645A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 232 removed outlier: 3.533A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 294 removed outlier: 4.336A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 306 through 327 removed outlier: 4.921A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.543A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.789A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.082A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.523A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.761A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.797A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.769A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.751A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1376 1.33 - 1.45: 1590 1.45 - 1.57: 3754 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 6770 Sorted by residual: bond pdb=" C VAL A 375 " pdb=" O VAL A 375 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" C ARG A 374 " pdb=" O ARG A 374 " ideal model delta sigma weight residual 1.235 1.290 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N VAL R 222 " pdb=" CA VAL R 222 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N VAL R 216 " pdb=" CA VAL R 216 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N ARG A 374 " pdb=" CA ARG A 374 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.28e-02 6.10e+03 9.90e+00 ... (remaining 6765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8856 2.07 - 4.15: 362 4.15 - 6.22: 38 6.22 - 8.29: 9 8.29 - 10.36: 7 Bond angle restraints: 9272 Sorted by residual: angle pdb=" N TYR R 199 " pdb=" CA TYR R 199 " pdb=" C TYR R 199 " ideal model delta sigma weight residual 111.28 103.70 7.58 1.09e+00 8.42e-01 4.84e+01 angle pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 111.71 105.11 6.60 1.15e+00 7.56e-01 3.30e+01 angle pdb=" N ASN R 196 " pdb=" CA ASN R 196 " pdb=" C ASN R 196 " ideal model delta sigma weight residual 109.65 101.00 8.65 1.56e+00 4.11e-01 3.07e+01 angle pdb=" C THR R 164 " pdb=" N SER R 165 " pdb=" CA SER R 165 " ideal model delta sigma weight residual 122.54 113.57 8.97 1.65e+00 3.67e-01 2.96e+01 angle pdb=" C TYR R 209 " pdb=" N VAL R 210 " pdb=" CA VAL R 210 " ideal model delta sigma weight residual 120.24 116.93 3.31 6.30e-01 2.52e+00 2.76e+01 ... (remaining 9267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 3890 35.24 - 70.48: 54 70.48 - 105.71: 4 105.71 - 140.95: 3 140.95 - 176.19: 2 Dihedral angle restraints: 3953 sinusoidal: 1106 harmonic: 2847 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -71.60 176.19 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 109.41 151.46 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 174.17 129.62 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 3950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 851 0.056 - 0.111: 178 0.111 - 0.167: 56 0.167 - 0.223: 20 0.223 - 0.278: 6 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE A 382 " pdb=" N ILE A 382 " pdb=" C ILE A 382 " pdb=" CB ILE A 382 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1108 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 373 " 0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ARG A 373 " -0.077 2.00e-02 2.50e+03 pdb=" O ARG A 373 " 0.028 2.00e-02 2.50e+03 pdb=" N ARG A 374 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 195 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C THR R 195 " 0.070 2.00e-02 2.50e+03 pdb=" O THR R 195 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN R 196 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 153 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ILE R 153 " 0.064 2.00e-02 2.50e+03 pdb=" O ILE R 153 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE R 154 " -0.022 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1392 2.78 - 3.31: 6289 3.31 - 3.84: 9933 3.84 - 4.37: 10595 4.37 - 4.90: 19112 Nonbonded interactions: 47321 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 3.040 nonbonded pdb=" O ASN A 377 " pdb=" CG ARG A 380 " model vdw 2.259 3.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.271 3.040 nonbonded pdb=" O HIS R 172 " pdb=" C TRP R 173 " model vdw 2.273 3.270 nonbonded pdb=" OD1 ASP A 223 " pdb=" N VAL A 224 " model vdw 2.275 3.120 ... (remaining 47316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.380 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.006 0.055 6770 Z= 0.428 Angle : 0.871 10.363 9272 Z= 0.604 Chirality : 0.059 0.278 1111 Planarity : 0.005 0.119 1198 Dihedral : 14.929 176.189 2095 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.20 % Allowed : 0.39 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 949 helix: 2.09 (0.27), residues: 363 sheet: -1.17 (0.38), residues: 174 loop : -1.13 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 154 HIS 0.003 0.001 HIS B 183 PHE 0.024 0.001 PHE A 376 TYR 0.014 0.001 TYR R 326 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.25365 ( 316) hydrogen bonds : angle 6.87723 ( 918) covalent geometry : bond 0.00607 ( 6770) covalent geometry : angle 0.87101 ( 9272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.781 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1627 time to fit residues: 18.1073 Evaluate side-chains 66 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111818 restraints weight = 11922.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114625 restraints weight = 6691.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116202 restraints weight = 4749.259| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6770 Z= 0.164 Angle : 0.534 7.202 9272 Z= 0.290 Chirality : 0.043 0.154 1111 Planarity : 0.003 0.032 1198 Dihedral : 10.219 163.327 1054 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.79 % Allowed : 9.86 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 949 helix: 1.81 (0.26), residues: 399 sheet: -1.33 (0.38), residues: 171 loop : -1.21 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE B 241 TYR 0.013 0.001 TYR R 326 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.05694 ( 316) hydrogen bonds : angle 4.61861 ( 918) covalent geometry : bond 0.00365 ( 6770) covalent geometry : angle 0.53355 ( 9272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.703 Fit side-chains REVERT: R 194 PHE cc_start: 0.7638 (m-80) cc_final: 0.7304 (m-80) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1360 time to fit residues: 13.6615 Evaluate side-chains 66 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103755 restraints weight = 12110.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106669 restraints weight = 6556.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108592 restraints weight = 4587.412| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6770 Z= 0.147 Angle : 0.495 6.280 9272 Z= 0.270 Chirality : 0.042 0.145 1111 Planarity : 0.003 0.030 1198 Dihedral : 8.725 151.081 1054 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.99 % Allowed : 12.43 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 949 helix: 2.09 (0.26), residues: 403 sheet: -1.15 (0.38), residues: 168 loop : -1.27 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.006 0.001 HIS B 183 PHE 0.012 0.001 PHE B 241 TYR 0.017 0.001 TYR R 219 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 316) hydrogen bonds : angle 4.09424 ( 918) covalent geometry : bond 0.00337 ( 6770) covalent geometry : angle 0.49486 ( 9272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.799 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.1541 time to fit residues: 16.1664 Evaluate side-chains 61 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 173 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 82 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105807 restraints weight = 12103.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108801 restraints weight = 6549.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110785 restraints weight = 4552.147| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6770 Z= 0.098 Angle : 0.449 5.521 9272 Z= 0.241 Chirality : 0.041 0.141 1111 Planarity : 0.003 0.028 1198 Dihedral : 7.790 141.447 1054 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.37 % Allowed : 12.43 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 949 helix: 2.24 (0.26), residues: 409 sheet: -0.93 (0.39), residues: 163 loop : -1.17 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE R 194 TYR 0.011 0.001 TYR R 219 ARG 0.002 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 316) hydrogen bonds : angle 3.75208 ( 918) covalent geometry : bond 0.00213 ( 6770) covalent geometry : angle 0.44893 ( 9272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.785 Fit side-chains REVERT: R 194 PHE cc_start: 0.7425 (m-80) cc_final: 0.6955 (m-80) outliers start: 12 outliers final: 6 residues processed: 75 average time/residue: 0.1418 time to fit residues: 15.8175 Evaluate side-chains 67 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106287 restraints weight = 11947.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109307 restraints weight = 6449.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111269 restraints weight = 4477.244| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6770 Z= 0.091 Angle : 0.437 5.749 9272 Z= 0.235 Chirality : 0.040 0.142 1111 Planarity : 0.003 0.027 1198 Dihedral : 7.281 134.690 1054 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.97 % Allowed : 13.02 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 949 helix: 2.44 (0.26), residues: 409 sheet: -0.72 (0.40), residues: 162 loop : -1.13 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.011 0.001 TYR R 219 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 316) hydrogen bonds : angle 3.59661 ( 918) covalent geometry : bond 0.00194 ( 6770) covalent geometry : angle 0.43737 ( 9272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.811 Fit side-chains REVERT: B 142 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8386 (t-170) REVERT: R 194 PHE cc_start: 0.7467 (m-80) cc_final: 0.6927 (m-80) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1419 time to fit residues: 15.5912 Evaluate side-chains 68 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 73 optimal weight: 0.0870 chunk 35 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.104878 restraints weight = 11966.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107779 restraints weight = 6475.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109739 restraints weight = 4516.883| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6770 Z= 0.117 Angle : 0.457 8.242 9272 Z= 0.244 Chirality : 0.041 0.145 1111 Planarity : 0.003 0.028 1198 Dihedral : 7.064 130.909 1054 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 14.60 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 949 helix: 2.47 (0.26), residues: 410 sheet: -0.76 (0.39), residues: 168 loop : -1.17 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.003 0.001 HIS B 183 PHE 0.012 0.001 PHE B 241 TYR 0.008 0.001 TYR A 147 ARG 0.002 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 316) hydrogen bonds : angle 3.65559 ( 918) covalent geometry : bond 0.00268 ( 6770) covalent geometry : angle 0.45719 ( 9272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.885 Fit side-chains REVERT: B 142 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8491 (t-170) REVERT: R 194 PHE cc_start: 0.7481 (m-80) cc_final: 0.6888 (m-80) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.1497 time to fit residues: 15.5619 Evaluate side-chains 71 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 326 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 10 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105359 restraints weight = 11943.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108347 restraints weight = 6473.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110312 restraints weight = 4505.012| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6770 Z= 0.106 Angle : 0.463 6.901 9272 Z= 0.247 Chirality : 0.041 0.142 1111 Planarity : 0.003 0.028 1198 Dihedral : 6.754 125.881 1054 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.37 % Allowed : 15.98 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 949 helix: 2.50 (0.26), residues: 410 sheet: -0.77 (0.39), residues: 168 loop : -1.14 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 292 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 316) hydrogen bonds : angle 3.58887 ( 918) covalent geometry : bond 0.00237 ( 6770) covalent geometry : angle 0.46273 ( 9272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.935 Fit side-chains REVERT: R 194 PHE cc_start: 0.7487 (m-80) cc_final: 0.6855 (m-80) outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.1473 time to fit residues: 16.1702 Evaluate side-chains 67 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 0.0070 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105633 restraints weight = 12033.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108641 restraints weight = 6489.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110633 restraints weight = 4504.183| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6770 Z= 0.098 Angle : 0.453 6.573 9272 Z= 0.242 Chirality : 0.040 0.141 1111 Planarity : 0.003 0.028 1198 Dihedral : 6.487 121.384 1054 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.17 % Allowed : 16.57 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 949 helix: 2.37 (0.26), residues: 420 sheet: -0.72 (0.39), residues: 168 loop : -1.16 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.005 0.001 HIS B 142 PHE 0.010 0.001 PHE R 289 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 316) hydrogen bonds : angle 3.55606 ( 918) covalent geometry : bond 0.00218 ( 6770) covalent geometry : angle 0.45319 ( 9272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.803 Fit side-chains REVERT: R 194 PHE cc_start: 0.7497 (m-80) cc_final: 0.6828 (m-80) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.1350 time to fit residues: 14.0181 Evaluate side-chains 69 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.0060 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105729 restraints weight = 12055.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108642 restraints weight = 6513.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110641 restraints weight = 4571.863| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6770 Z= 0.098 Angle : 0.452 6.292 9272 Z= 0.241 Chirality : 0.040 0.141 1111 Planarity : 0.003 0.028 1198 Dihedral : 6.240 116.769 1054 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.37 % Allowed : 16.77 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 949 helix: 2.39 (0.26), residues: 420 sheet: -0.71 (0.40), residues: 165 loop : -1.04 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.007 0.001 HIS B 142 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR R 219 ARG 0.001 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 316) hydrogen bonds : angle 3.52374 ( 918) covalent geometry : bond 0.00220 ( 6770) covalent geometry : angle 0.45218 ( 9272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.697 Fit side-chains REVERT: R 194 PHE cc_start: 0.7476 (m-80) cc_final: 0.6799 (m-80) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.1274 time to fit residues: 13.3317 Evaluate side-chains 70 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 0.5980 chunk 79 optimal weight: 0.0980 chunk 10 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107486 restraints weight = 12215.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110530 restraints weight = 6530.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112475 restraints weight = 4544.402| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6770 Z= 0.083 Angle : 0.441 6.573 9272 Z= 0.234 Chirality : 0.040 0.148 1111 Planarity : 0.003 0.028 1198 Dihedral : 5.912 110.932 1054 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.37 % Allowed : 17.16 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 949 helix: 2.52 (0.26), residues: 421 sheet: -0.67 (0.40), residues: 164 loop : -1.04 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.005 0.000 HIS B 142 PHE 0.008 0.001 PHE B 199 TYR 0.009 0.001 TYR R 219 ARG 0.001 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.02579 ( 316) hydrogen bonds : angle 3.42751 ( 918) covalent geometry : bond 0.00174 ( 6770) covalent geometry : angle 0.44115 ( 9272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.755 Fit side-chains REVERT: R 194 PHE cc_start: 0.7512 (m-80) cc_final: 0.6844 (m-80) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.1262 time to fit residues: 13.6678 Evaluate side-chains 71 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 45 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106629 restraints weight = 12061.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109635 restraints weight = 6528.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111655 restraints weight = 4521.349| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6770 Z= 0.096 Angle : 0.452 6.734 9272 Z= 0.240 Chirality : 0.041 0.182 1111 Planarity : 0.003 0.029 1198 Dihedral : 5.913 109.976 1054 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.78 % Allowed : 17.95 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 949 helix: 2.54 (0.26), residues: 422 sheet: -0.64 (0.39), residues: 170 loop : -1.10 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.006 0.001 HIS B 142 PHE 0.009 0.001 PHE B 241 TYR 0.008 0.001 TYR R 219 ARG 0.001 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 316) hydrogen bonds : angle 3.42071 ( 918) covalent geometry : bond 0.00214 ( 6770) covalent geometry : angle 0.45152 ( 9272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.57 seconds wall clock time: 42 minutes 49.11 seconds (2569.11 seconds total)