Starting phenix.real_space_refine on Fri Oct 10 14:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo3_42426/10_2025/8uo3_42426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo3_42426/10_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_42426/10_2025/8uo3_42426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo3_42426/10_2025/8uo3_42426.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo3_42426/10_2025/8uo3_42426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo3_42426/10_2025/8uo3_42426.cif" } resolution = 3.5 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= 0.021 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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, 'ARG:plan': 8, 'ASN:plan1': 6, 'GLU:plan': 24, 'ASP:plan': 20, 'PHE:plan': 5, 'TYR:plan': 2} 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: {'GLU:plan': 8, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 10, 'ASN:plan1': 5} 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, 'ARG:plan': 2, 'GLU:plan': 4, '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: {'PHE:plan': 11, 'ASN:plan1': 9, 'GLN:plan1': 6, 'TYR:plan': 5, 'ASP:plan': 4, 'HIS:plan': 4, 'TRP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 3} 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: 2.04, per 1000 atoms: 0.31 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: 0.68 Conformation dependent library (CDL) restraints added in 406.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.01 Time building geometry restraints manager: 0.85 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: 2.710 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- 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 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: 0.16 (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 ARG 0.002 0.000 ARG A 374 TYR 0.014 0.001 TYR R 326 PHE 0.024 0.001 PHE A 376 TRP 0.008 0.001 TRP A 154 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 6770) covalent geometry : angle 0.87101 ( 9272) hydrogen bonds : bond 0.25365 ( 316) hydrogen bonds : angle 6.87723 ( 918) *********************** 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 : 0.294 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.0781 time to fit residues: 8.7087 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** B 311 HIS R 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110306 restraints weight = 12078.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113072 restraints weight = 6806.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114901 restraints weight = 4826.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115915 restraints weight = 3889.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116786 restraints weight = 3402.254| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6770 Z= 0.202 Angle : 0.561 6.604 9272 Z= 0.306 Chirality : 0.044 0.160 1111 Planarity : 0.004 0.032 1198 Dihedral : 10.180 161.708 1054 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.99 % Allowed : 10.06 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.27), residues: 949 helix: 1.76 (0.26), residues: 395 sheet: -1.44 (0.38), residues: 171 loop : -1.30 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.011 0.002 TYR R 316 PHE 0.015 0.002 PHE B 241 TRP 0.009 0.001 TRP B 63 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6770) covalent geometry : angle 0.56090 ( 9272) hydrogen bonds : bond 0.05483 ( 316) hydrogen bonds : angle 4.61747 ( 918) *********************** 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 71 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.256 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.0748 time to fit residues: 7.4100 Evaluate side-chains 63 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 65 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.132359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102040 restraints weight = 12119.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104922 restraints weight = 6557.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106782 restraints weight = 4591.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108024 restraints weight = 3685.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108695 restraints weight = 3190.290| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6770 Z= 0.180 Angle : 0.521 6.317 9272 Z= 0.285 Chirality : 0.043 0.152 1111 Planarity : 0.003 0.032 1198 Dihedral : 8.954 152.380 1054 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.38 % Allowed : 12.82 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.27), residues: 949 helix: 1.91 (0.26), residues: 402 sheet: -1.41 (0.37), residues: 168 loop : -1.31 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.014 0.001 TYR R 219 PHE 0.015 0.002 PHE B 241 TRP 0.009 0.001 TRP B 63 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6770) covalent geometry : angle 0.52109 ( 9272) hydrogen bonds : bond 0.04950 ( 316) hydrogen bonds : angle 4.23065 ( 918) *********************** 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 73 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.261 Fit side-chains REVERT: R 194 PHE cc_start: 0.7480 (m-80) cc_final: 0.6938 (m-80) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.0656 time to fit residues: 6.7915 Evaluate side-chains 66 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 284 THR 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 3 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.135132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104689 restraints weight = 12180.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107646 restraints weight = 6522.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109618 restraints weight = 4533.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110710 restraints weight = 3614.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111632 restraints weight = 3162.050| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6770 Z= 0.104 Angle : 0.457 5.384 9272 Z= 0.246 Chirality : 0.041 0.144 1111 Planarity : 0.003 0.029 1198 Dihedral : 7.955 142.850 1054 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.28), residues: 949 helix: 2.19 (0.26), residues: 405 sheet: -1.12 (0.40), residues: 153 loop : -1.21 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.012 0.001 TYR R 219 PHE 0.010 0.001 PHE B 199 TRP 0.008 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6770) covalent geometry : angle 0.45729 ( 9272) hydrogen bonds : bond 0.03507 ( 316) hydrogen bonds : angle 3.81652 ( 918) *********************** 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 81 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.281 Fit side-chains REVERT: B 142 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.8412 (t-170) REVERT: R 194 PHE cc_start: 0.7366 (m-80) cc_final: 0.6725 (m-80) outliers start: 13 outliers final: 6 residues processed: 79 average time/residue: 0.0621 time to fit residues: 7.3713 Evaluate side-chains 69 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 142 HIS 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 7 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.133014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102608 restraints weight = 12262.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105454 restraints weight = 6592.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107388 restraints weight = 4631.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108649 restraints weight = 3702.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109242 restraints weight = 3198.288| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6770 Z= 0.156 Angle : 0.500 7.875 9272 Z= 0.271 Chirality : 0.042 0.151 1111 Planarity : 0.003 0.030 1198 Dihedral : 7.803 140.034 1054 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.17 % Allowed : 13.61 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 949 helix: 2.09 (0.26), residues: 412 sheet: -1.22 (0.38), residues: 168 loop : -1.25 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.010 0.001 TYR A 163 PHE 0.015 0.001 PHE B 241 TRP 0.009 0.001 TRP B 63 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6770) covalent geometry : angle 0.50026 ( 9272) hydrogen bonds : bond 0.04032 ( 316) hydrogen bonds : angle 3.90649 ( 918) *********************** 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 76 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.340 Fit side-chains REVERT: B 142 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8549 (t-170) REVERT: R 194 PHE cc_start: 0.7507 (m-80) cc_final: 0.6770 (m-80) outliers start: 11 outliers final: 9 residues processed: 73 average time/residue: 0.0614 time to fit residues: 6.7352 Evaluate side-chains 71 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 173 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.134420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103880 restraints weight = 12218.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106864 restraints weight = 6567.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108766 restraints weight = 4559.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110032 restraints weight = 3649.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110760 restraints weight = 3154.686| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6770 Z= 0.112 Angle : 0.462 6.794 9272 Z= 0.248 Chirality : 0.041 0.144 1111 Planarity : 0.003 0.030 1198 Dihedral : 7.338 133.838 1054 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.17 % Allowed : 15.38 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.28), residues: 949 helix: 2.24 (0.26), residues: 414 sheet: -1.10 (0.39), residues: 163 loop : -1.18 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 219 TYR 0.010 0.001 TYR R 219 PHE 0.010 0.001 PHE B 241 TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6770) covalent geometry : angle 0.46161 ( 9272) hydrogen bonds : bond 0.03418 ( 316) hydrogen bonds : angle 3.71776 ( 918) *********************** 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 73 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.263 Fit side-chains REVERT: B 142 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8521 (t-170) REVERT: R 194 PHE cc_start: 0.7466 (m-80) cc_final: 0.6719 (m-80) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.0654 time to fit residues: 6.8011 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 : 0.243 ------------------------------------------------------------------------------- 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 A residue 334 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 142 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.135633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105092 restraints weight = 12035.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108006 restraints weight = 6485.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109983 restraints weight = 4540.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111098 restraints weight = 3626.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112054 restraints weight = 3159.853| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6770 Z= 0.096 Angle : 0.449 6.399 9272 Z= 0.240 Chirality : 0.041 0.158 1111 Planarity : 0.003 0.030 1198 Dihedral : 6.893 127.584 1054 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.56 % Allowed : 16.17 % 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 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: 0.63 (0.28), residues: 949 helix: 2.32 (0.26), residues: 417 sheet: -0.90 (0.41), residues: 153 loop : -1.21 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.010 0.001 TYR R 219 PHE 0.010 0.001 PHE B 199 TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6770) covalent geometry : angle 0.44918 ( 9272) hydrogen bonds : bond 0.03074 ( 316) hydrogen bonds : angle 3.58099 ( 918) *********************** 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 81 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.257 Fit side-chains REVERT: B 120 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8636 (mm) REVERT: R 194 PHE cc_start: 0.7467 (m-80) cc_final: 0.6690 (m-80) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.0582 time to fit residues: 6.7579 Evaluate side-chains 69 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain B residue 120 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 75 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.131433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101040 restraints weight = 12213.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103812 restraints weight = 6616.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105718 restraints weight = 4663.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106919 restraints weight = 3746.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107510 restraints weight = 3253.086| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6770 Z= 0.211 Angle : 0.543 6.387 9272 Z= 0.295 Chirality : 0.044 0.155 1111 Planarity : 0.003 0.031 1198 Dihedral : 7.300 130.368 1054 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.37 % Allowed : 17.75 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.28), residues: 949 helix: 1.94 (0.26), residues: 422 sheet: -1.14 (0.39), residues: 168 loop : -1.47 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.011 0.001 TYR B 111 PHE 0.019 0.002 PHE B 241 TRP 0.011 0.001 TRP B 63 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 6770) covalent geometry : angle 0.54312 ( 9272) hydrogen bonds : bond 0.04517 ( 316) hydrogen bonds : angle 4.03686 ( 918) *********************** 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: 12 poor density : 60 time to evaluate : 0.280 Fit side-chains REVERT: B 120 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8768 (mm) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.0597 time to fit residues: 6.1881 Evaluate side-chains 67 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 120 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 34 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.135439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104987 restraints weight = 12133.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107900 restraints weight = 6541.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109886 restraints weight = 4567.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110850 restraints weight = 3639.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111916 restraints weight = 3198.362| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6770 Z= 0.093 Angle : 0.458 6.316 9272 Z= 0.246 Chirality : 0.040 0.141 1111 Planarity : 0.003 0.062 1198 Dihedral : 6.631 121.694 1054 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 18.15 % 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 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: 0.45 (0.28), residues: 949 helix: 2.09 (0.26), residues: 427 sheet: -0.99 (0.41), residues: 158 loop : -1.28 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 380 TYR 0.009 0.001 TYR R 219 PHE 0.011 0.001 PHE B 292 TRP 0.007 0.001 TRP B 99 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6770) covalent geometry : angle 0.45820 ( 9272) hydrogen bonds : bond 0.03080 ( 316) hydrogen bonds : angle 3.64597 ( 918) *********************** 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 71 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.258 Fit side-chains REVERT: B 120 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8629 (mm) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.0645 time to fit residues: 6.5155 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 : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 120 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 6.9990 chunk 73 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.135532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105104 restraints weight = 12118.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108034 restraints weight = 6521.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110012 restraints weight = 4537.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111127 restraints weight = 3624.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112057 restraints weight = 3155.993| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2503 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= 0.097 Angle : 0.455 6.438 9272 Z= 0.243 Chirality : 0.040 0.142 1111 Planarity : 0.003 0.049 1198 Dihedral : 6.348 116.492 1054 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.38 % Allowed : 18.54 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.28), residues: 949 helix: 2.34 (0.26), residues: 418 sheet: -0.82 (0.40), residues: 163 loop : -1.17 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 219 TYR 0.009 0.001 TYR R 219 PHE 0.010 0.001 PHE B 199 TRP 0.007 0.001 TRP R 313 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6770) covalent geometry : angle 0.45477 ( 9272) hydrogen bonds : bond 0.03014 ( 316) hydrogen bonds : angle 3.56659 ( 918) ********************** 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 70 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.189 Fit side-chains REVERT: B 45 MET cc_start: 0.8651 (ptt) cc_final: 0.8391 (ptt) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.0643 time to fit residues: 6.5515 Evaluate side-chains 68 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 80 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.134344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103956 restraints weight = 12048.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106902 restraints weight = 6534.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108796 restraints weight = 4548.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110059 restraints weight = 3639.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110748 restraints weight = 3147.184| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6770 Z= 0.117 Angle : 0.468 6.528 9272 Z= 0.251 Chirality : 0.041 0.143 1111 Planarity : 0.003 0.041 1198 Dihedral : 6.350 115.234 1054 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.18 % Allowed : 18.54 % 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 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: 0.54 (0.28), residues: 949 helix: 2.21 (0.27), residues: 420 sheet: -0.76 (0.42), residues: 152 loop : -1.34 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 219 TYR 0.009 0.001 TYR R 219 PHE 0.012 0.001 PHE B 241 TRP 0.006 0.001 TRP R 313 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6770) covalent geometry : angle 0.46789 ( 9272) hydrogen bonds : bond 0.03277 ( 316) hydrogen bonds : angle 3.62007 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.05 seconds wall clock time: 24 minutes 2.99 seconds (1442.99 seconds total)