Starting phenix.real_space_refine on Tue Jul 29 08:33:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g81_29831/07_2025/8g81_29831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g81_29831/07_2025/8g81_29831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2025/8g81_29831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2025/8g81_29831.map" model { file = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2025/8g81_29831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2025/8g81_29831.cif" } resolution = 3.22 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= 0.001 sd= 0.119 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 38 5.16 5 C 7104 2.51 5 N 1920 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11148 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4180 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 34, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4176 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1353 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1353 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.34, per 1000 atoms: 0.75 Number of scatterers: 11148 At special positions: 0 Unit cell: (87.98, 127.82, 155.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 38 16.00 O 2084 8.00 N 1920 7.00 C 7104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1017 " - " ASN A 98 " " NAG A1018 " - " ASN A 522 " " NAG B1017 " - " ASN B 98 " " NAG B1018 " - " ASN B 522 " " NAG C1008 " - " ASN C 184 " " NAG D1008 " - " ASN D 184 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.9 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 29.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 232 through 253 removed outlier: 5.544A pdb=" N ALA A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 303 through 316 removed outlier: 4.020A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.545A pdb=" N ARG A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.670A pdb=" N LEU A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.553A pdb=" N GLN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.898A pdb=" N THR A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.562A pdb=" N TYR A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.546A pdb=" N ARG A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.611A pdb=" N ALA A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 524 through 545 Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 605 through 608 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.958A pdb=" N TYR B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.741A pdb=" N MET B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 196 " --> pdb=" O GLY B 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.579A pdb=" N SER B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 316 removed outlier: 4.020A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 Processing helix chain 'B' and resid 363 through 370 Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.748A pdb=" N PHE B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.640A pdb=" N TYR B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.824A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 447 through 460 Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 524 through 544 Processing helix chain 'B' and resid 594 through 604 Processing helix chain 'B' and resid 605 through 608 Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'D' and resid 267 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.793A pdb=" N ARG A 50 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 73 removed outlier: 4.999A pdb=" N LEU A 144 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 209 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 210 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET A 180 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU A 212 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 182 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 177 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU A 257 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL A 179 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 181 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 261 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 183 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 263 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LYS A 286 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 259 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 288 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 261 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLN A 290 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY A 263 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET A 378 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TYR A 481 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 380 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N LEU A 581 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 480 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 583 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR A 482 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 580 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.768A pdb=" N ARG B 50 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.592A pdb=" N VAL B 209 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 210 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET B 180 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 212 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE B 182 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N LYS B 177 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B 258 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 179 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS B 286 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 259 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 288 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 261 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN B 290 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY B 263 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET B 378 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TYR B 481 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 380 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU B 581 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 480 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 583 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR B 482 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 163 removed outlier: 3.913A pdb=" N ILE C 148 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE C 143 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL C 125 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 242 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 197 removed outlier: 4.151A pdb=" N GLY C 116 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLY C 260 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER C 118 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU C 258 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS C 91 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ARG C 286 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY C 93 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 195 through 197 removed outlier: 6.430A pdb=" N ARG D 112 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR D 263 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA D 114 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 261 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 162 removed outlier: 3.526A pdb=" N VAL D 127 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 143 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL D 125 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 242 " --> pdb=" O ASP D 130 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1077 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: 4.26 Time building geometry restraints manager: 3.13 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: 3169 1.33 - 1.45: 2058 1.45 - 1.57: 6136 1.57 - 1.69: 1 1.69 - 1.82: 62 Bond restraints: 11426 Sorted by residual: bond pdb=" CB PRO A 77 " pdb=" CG PRO A 77 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.44e+00 bond pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.47e+00 bond pdb=" N ARG D 232 " pdb=" CA ARG D 232 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.49e+00 bond pdb=" C ARG C 232 " pdb=" O ARG C 232 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.20e-02 6.94e+03 3.53e+00 bond pdb=" NE ARG C 232 " pdb=" CZ ARG C 232 " ideal model delta sigma weight residual 1.326 1.346 -0.020 1.10e-02 8.26e+03 3.33e+00 ... (remaining 11421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 15384 2.37 - 4.73: 159 4.73 - 7.10: 11 7.10 - 9.46: 4 9.46 - 11.83: 3 Bond angle restraints: 15561 Sorted by residual: angle pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 112.00 102.93 9.07 1.40e+00 5.10e-01 4.20e+01 angle pdb=" CA ARG C 232 " pdb=" C ARG C 232 " pdb=" O ARG C 232 " ideal model delta sigma weight residual 120.81 114.89 5.92 1.15e+00 7.56e-01 2.65e+01 angle pdb=" CB ARG C 232 " pdb=" CG ARG C 232 " pdb=" CD ARG C 232 " ideal model delta sigma weight residual 111.30 121.24 -9.94 2.30e+00 1.89e-01 1.87e+01 angle pdb=" N GLU B 392 " pdb=" CA GLU B 392 " pdb=" C GLU B 392 " ideal model delta sigma weight residual 114.56 109.40 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" CB MET D 271 " pdb=" CG MET D 271 " pdb=" SD MET D 271 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.56e+01 ... (remaining 15556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6007 17.82 - 35.64: 605 35.64 - 53.46: 135 53.46 - 71.28: 21 71.28 - 89.10: 9 Dihedral angle restraints: 6777 sinusoidal: 2687 harmonic: 4090 Sorted by residual: dihedral pdb=" CB CYS B 317 " pdb=" SG CYS B 317 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual -86.00 -122.05 36.05 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA MET A 446 " pdb=" C MET A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE A 41 " pdb=" C PHE A 41 " pdb=" N PRO A 42 " pdb=" CA PRO A 42 " ideal model delta harmonic sigma weight residual 180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1529 0.075 - 0.150: 179 0.150 - 0.226: 3 0.226 - 0.301: 2 0.301 - 0.376: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" C1 NAG B1017 " pdb=" ND2 ASN B 98 " pdb=" C2 NAG B1017 " pdb=" O5 NAG B1017 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA ARG C 232 " pdb=" N ARG C 232 " pdb=" C ARG C 232 " pdb=" CB ARG C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C1 NAG B1018 " pdb=" ND2 ASN B 522 " pdb=" C2 NAG B1018 " pdb=" O5 NAG B1018 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1711 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " -0.065 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO A 77 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 375 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ASN B 375 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 375 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 376 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 549 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 550 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 550 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 550 " 0.029 5.00e-02 4.00e+02 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 126 2.63 - 3.20: 9454 3.20 - 3.76: 16797 3.76 - 4.33: 23573 4.33 - 4.90: 40156 Nonbonded interactions: 90106 Sorted by model distance: nonbonded pdb=" OE1 GLN A 370 " pdb=" NH2 ARG C 232 " model vdw 2.059 3.120 nonbonded pdb=" O LYS D 91 " pdb=" ND2 ASN D 284 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR D 119 " pdb=" O GLN D 255 " model vdw 2.218 3.040 nonbonded pdb=" O ASN B 375 " pdb=" ND2 ASN B 375 " model vdw 2.234 3.120 nonbonded pdb=" O HIS A 471 " pdb=" OG SER A 476 " model vdw 2.257 3.040 ... (remaining 90101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 608 or resid 1017 through 1018)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 27.320 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: 6.680 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.860 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.003 0.136 11436 Z= 0.137 Angle : 0.597 11.831 15587 Z= 0.306 Chirality : 0.046 0.376 1714 Planarity : 0.004 0.094 2037 Dihedral : 15.083 89.103 4161 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.69 % Allowed : 21.25 % Favored : 78.06 % 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: -0.65 (0.22), residues: 1416 helix: 0.51 (0.29), residues: 348 sheet: 0.33 (0.32), residues: 300 loop : -1.20 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 122 HIS 0.002 0.001 HIS A 582 PHE 0.020 0.001 PHE A 413 TYR 0.018 0.001 TYR C 138 ARG 0.007 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 6) link_NAG-ASN : angle 3.07171 ( 18) hydrogen bonds : bond 0.16283 ( 377) hydrogen bonds : angle 7.25778 ( 1077) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.59706 ( 8) covalent geometry : bond 0.00316 (11426) covalent geometry : angle 0.58797 (15561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7182 (mmt90) REVERT: B 440 ASP cc_start: 0.8206 (t0) cc_final: 0.7958 (t0) REVERT: B 553 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6087 (mp-120) REVERT: C 104 ASP cc_start: 0.8319 (t0) cc_final: 0.7435 (t0) REVERT: C 232 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5655 (mmm-85) REVERT: D 271 MET cc_start: 0.5511 (ppp) cc_final: 0.4932 (ptp) outliers start: 8 outliers final: 6 residues processed: 137 average time/residue: 0.2553 time to fit residues: 49.7727 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** B 340 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.172406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107279 restraints weight = 12546.857| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.85 r_work: 0.2891 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 11436 Z= 0.282 Angle : 0.667 9.544 15587 Z= 0.337 Chirality : 0.050 0.327 1714 Planarity : 0.005 0.049 2037 Dihedral : 6.763 57.245 1700 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.55 % Allowed : 19.60 % Favored : 74.85 % 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 (0.22), residues: 1416 helix: 0.59 (0.29), residues: 346 sheet: -0.08 (0.31), residues: 296 loop : -1.30 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 122 HIS 0.005 0.001 HIS B 184 PHE 0.024 0.002 PHE A 413 TYR 0.015 0.002 TYR B 481 ARG 0.005 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 6) link_NAG-ASN : angle 3.01940 ( 18) hydrogen bonds : bond 0.04429 ( 377) hydrogen bonds : angle 5.47540 ( 1077) SS BOND : bond 0.00653 ( 4) SS BOND : angle 1.19563 ( 8) covalent geometry : bond 0.00697 (11426) covalent geometry : angle 0.65892 (15561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5017 (t80) REVERT: B 446 MET cc_start: 0.7863 (tmt) cc_final: 0.7507 (tmt) REVERT: B 553 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6293 (mp-120) REVERT: B 588 ARG cc_start: 0.7083 (ttt90) cc_final: 0.5944 (mtp180) REVERT: C 232 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5434 (mtp85) REVERT: D 232 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6306 (ttm110) REVERT: D 271 MET cc_start: 0.5795 (ppp) cc_final: 0.5543 (ptp) outliers start: 64 outliers final: 43 residues processed: 165 average time/residue: 0.2411 time to fit residues: 56.6647 Evaluate side-chains 163 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 122 optimal weight: 0.0870 chunk 131 optimal weight: 40.0000 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** 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 = 0.3996 r_free = 0.3996 target = 0.177665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111946 restraints weight = 12536.659| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.96 r_work: 0.2947 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11436 Z= 0.102 Angle : 0.532 9.662 15587 Z= 0.266 Chirality : 0.044 0.269 1714 Planarity : 0.004 0.038 2037 Dihedral : 5.983 56.305 1695 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.99 % Allowed : 21.68 % Favored : 74.33 % 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: -0.55 (0.22), residues: 1416 helix: 0.88 (0.30), residues: 352 sheet: 0.03 (0.31), residues: 298 loop : -1.14 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 122 HIS 0.003 0.000 HIS C 174 PHE 0.019 0.001 PHE A 413 TYR 0.019 0.001 TYR C 138 ARG 0.003 0.000 ARG C 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 6) link_NAG-ASN : angle 2.34764 ( 18) hydrogen bonds : bond 0.03334 ( 377) hydrogen bonds : angle 4.98307 ( 1077) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.57639 ( 8) covalent geometry : bond 0.00239 (11426) covalent geometry : angle 0.52605 (15561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.4628 (t80) REVERT: B 276 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7708 (mt) REVERT: B 300 VAL cc_start: 0.8904 (m) cc_final: 0.8648 (t) REVERT: B 324 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7436 (pt0) REVERT: B 440 ASP cc_start: 0.7991 (t0) cc_final: 0.7657 (t0) REVERT: B 446 MET cc_start: 0.7533 (tmt) cc_final: 0.7042 (tmm) REVERT: B 585 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6752 (mt) REVERT: C 104 ASP cc_start: 0.8339 (t0) cc_final: 0.7453 (t0) REVERT: C 138 TYR cc_start: 0.7769 (p90) cc_final: 0.7560 (p90) REVERT: C 232 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5581 (mtp-110) REVERT: D 232 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6530 (ttm110) outliers start: 46 outliers final: 31 residues processed: 159 average time/residue: 0.2474 time to fit residues: 55.4618 Evaluate side-chains 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 500 HIS B 548 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.170322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104226 restraints weight = 12647.447| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.97 r_work: 0.2857 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 11436 Z= 0.365 Angle : 0.714 9.799 15587 Z= 0.364 Chirality : 0.052 0.277 1714 Planarity : 0.005 0.040 2037 Dihedral : 6.374 56.372 1693 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.76 % Allowed : 20.82 % Favored : 72.42 % 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: -1.07 (0.22), residues: 1416 helix: 0.45 (0.29), residues: 350 sheet: -0.40 (0.30), residues: 302 loop : -1.41 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 100 HIS 0.007 0.001 HIS B 458 PHE 0.027 0.003 PHE A 413 TYR 0.020 0.002 TYR A 580 ARG 0.008 0.001 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 6) link_NAG-ASN : angle 2.79391 ( 18) hydrogen bonds : bond 0.04385 ( 377) hydrogen bonds : angle 5.32369 ( 1077) SS BOND : bond 0.00740 ( 4) SS BOND : angle 1.46305 ( 8) covalent geometry : bond 0.00895 (11426) covalent geometry : angle 0.70791 (15561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 118 time to evaluate : 1.313 Fit side-chains REVERT: A 41 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.5127 (t80) REVERT: B 50 ARG cc_start: 0.6488 (ttp-110) cc_final: 0.6194 (mtp-110) REVERT: B 276 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7737 (mt) REVERT: B 446 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7203 (tmt) REVERT: B 553 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6109 (mp-120) REVERT: B 585 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6784 (mt) REVERT: C 232 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5597 (mtp-110) REVERT: D 232 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6657 (ttm110) outliers start: 78 outliers final: 52 residues processed: 171 average time/residue: 0.2429 time to fit residues: 59.4915 Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 282 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN B 375 ASN B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.176355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114737 restraints weight = 12412.998| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.30 r_work: 0.2921 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11436 Z= 0.116 Angle : 0.543 9.845 15587 Z= 0.274 Chirality : 0.045 0.262 1714 Planarity : 0.004 0.039 2037 Dihedral : 5.838 55.679 1693 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.86 % Allowed : 22.81 % Favored : 72.33 % 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: -0.61 (0.22), residues: 1416 helix: 0.92 (0.30), residues: 348 sheet: -0.12 (0.31), residues: 296 loop : -1.16 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 122 HIS 0.002 0.000 HIS C 174 PHE 0.019 0.001 PHE A 413 TYR 0.011 0.001 TYR B 481 ARG 0.007 0.000 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 6) link_NAG-ASN : angle 2.18322 ( 18) hydrogen bonds : bond 0.03238 ( 377) hydrogen bonds : angle 4.87086 ( 1077) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.67763 ( 8) covalent geometry : bond 0.00275 (11426) covalent geometry : angle 0.53823 (15561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.4632 (t80) REVERT: B 50 ARG cc_start: 0.6497 (ttp-110) cc_final: 0.6193 (mtp-110) REVERT: B 276 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7699 (mt) REVERT: B 300 VAL cc_start: 0.8902 (m) cc_final: 0.8672 (t) REVERT: B 340 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7846 (mm-40) REVERT: B 440 ASP cc_start: 0.7978 (t0) cc_final: 0.7687 (t0) REVERT: B 446 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6841 (tmt) REVERT: B 585 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6721 (mt) REVERT: C 104 ASP cc_start: 0.8380 (t0) cc_final: 0.7561 (t0) REVERT: C 232 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5472 (mtp85) REVERT: D 232 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5964 (ttm110) outliers start: 56 outliers final: 37 residues processed: 171 average time/residue: 0.2395 time to fit residues: 58.6575 Evaluate side-chains 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 33 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 58 optimal weight: 0.0000 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109949 restraints weight = 12541.990| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.95 r_work: 0.2921 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11436 Z= 0.145 Angle : 0.550 9.834 15587 Z= 0.277 Chirality : 0.045 0.269 1714 Planarity : 0.004 0.038 2037 Dihedral : 5.755 55.619 1693 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.86 % Allowed : 22.98 % Favored : 72.16 % 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: -0.58 (0.22), residues: 1416 helix: 1.00 (0.30), residues: 348 sheet: -0.08 (0.31), residues: 298 loop : -1.17 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 122 HIS 0.003 0.001 HIS B 458 PHE 0.021 0.002 PHE A 413 TYR 0.018 0.001 TYR C 138 ARG 0.006 0.000 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 6) link_NAG-ASN : angle 2.11264 ( 18) hydrogen bonds : bond 0.03248 ( 377) hydrogen bonds : angle 4.84357 ( 1077) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.68846 ( 8) covalent geometry : bond 0.00353 (11426) covalent geometry : angle 0.54576 (15561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 122 time to evaluate : 1.280 Fit side-chains REVERT: A 41 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.4778 (t80) REVERT: A 56 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7184 (mmt90) REVERT: B 50 ARG cc_start: 0.6587 (ttp-110) cc_final: 0.6243 (mtp-110) REVERT: B 276 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7762 (mt) REVERT: B 300 VAL cc_start: 0.8949 (m) cc_final: 0.8720 (t) REVERT: B 440 ASP cc_start: 0.8025 (t0) cc_final: 0.7783 (t0) REVERT: B 446 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7010 (tmt) REVERT: B 585 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6744 (mt) REVERT: C 104 ASP cc_start: 0.8430 (t0) cc_final: 0.7569 (t0) REVERT: C 232 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5467 (mtp85) REVERT: D 271 MET cc_start: 0.5578 (ppp) cc_final: 0.5301 (pmm) outliers start: 56 outliers final: 39 residues processed: 160 average time/residue: 0.2580 time to fit residues: 59.2783 Evaluate side-chains 166 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109093 restraints weight = 12690.909| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.88 r_work: 0.2906 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11436 Z= 0.185 Angle : 0.576 9.826 15587 Z= 0.290 Chirality : 0.046 0.266 1714 Planarity : 0.004 0.037 2037 Dihedral : 5.654 55.470 1689 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.81 % Allowed : 22.38 % Favored : 71.81 % 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: -0.63 (0.22), residues: 1416 helix: 0.94 (0.29), residues: 350 sheet: -0.14 (0.31), residues: 298 loop : -1.19 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 244 HIS 0.004 0.001 HIS B 458 PHE 0.023 0.002 PHE A 413 TYR 0.014 0.001 TYR A 481 ARG 0.004 0.000 ARG A 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 2.12460 ( 18) hydrogen bonds : bond 0.03382 ( 377) hydrogen bonds : angle 4.88803 ( 1077) SS BOND : bond 0.00434 ( 4) SS BOND : angle 0.81056 ( 8) covalent geometry : bond 0.00454 (11426) covalent geometry : angle 0.57124 (15561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 1.412 Fit side-chains REVERT: A 41 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.4849 (t80) REVERT: A 276 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 497 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6214 (t0) REVERT: B 50 ARG cc_start: 0.6497 (ttp-110) cc_final: 0.6186 (mtp-110) REVERT: B 204 TYR cc_start: 0.7927 (t80) cc_final: 0.7560 (t80) REVERT: B 276 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 300 VAL cc_start: 0.8943 (m) cc_final: 0.8712 (t) REVERT: B 440 ASP cc_start: 0.8072 (t0) cc_final: 0.7844 (t0) REVERT: B 446 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7031 (tmt) REVERT: B 585 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6759 (mt) REVERT: C 104 ASP cc_start: 0.8433 (t0) cc_final: 0.7537 (t0) REVERT: C 232 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.5551 (mtp-110) outliers start: 67 outliers final: 53 residues processed: 168 average time/residue: 0.3074 time to fit residues: 74.5682 Evaluate side-chains 180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 120 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 375 ASN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110918 restraints weight = 12550.401| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.85 r_work: 0.2931 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11436 Z= 0.135 Angle : 0.547 9.824 15587 Z= 0.276 Chirality : 0.045 0.259 1714 Planarity : 0.004 0.037 2037 Dihedral : 5.513 55.608 1689 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.64 % Allowed : 22.55 % Favored : 71.81 % 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: -0.51 (0.22), residues: 1416 helix: 0.98 (0.29), residues: 354 sheet: -0.06 (0.31), residues: 302 loop : -1.11 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 122 HIS 0.003 0.001 HIS B 458 PHE 0.021 0.001 PHE A 413 TYR 0.013 0.001 TYR B 481 ARG 0.004 0.000 ARG C 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 6) link_NAG-ASN : angle 1.98256 ( 18) hydrogen bonds : bond 0.03179 ( 377) hydrogen bonds : angle 4.80384 ( 1077) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.62903 ( 8) covalent geometry : bond 0.00328 (11426) covalent geometry : angle 0.54323 (15561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 1.335 Fit side-chains REVERT: A 41 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.4865 (t80) REVERT: A 56 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7211 (mmt90) REVERT: A 276 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8099 (mt) REVERT: A 497 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6159 (t0) REVERT: B 50 ARG cc_start: 0.6565 (ttp-110) cc_final: 0.6207 (mtp-110) REVERT: B 276 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 300 VAL cc_start: 0.8928 (m) cc_final: 0.8705 (t) REVERT: B 440 ASP cc_start: 0.8020 (t0) cc_final: 0.7783 (t0) REVERT: B 446 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6944 (tmt) REVERT: B 585 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6752 (mt) REVERT: C 104 ASP cc_start: 0.8447 (t0) cc_final: 0.7546 (t0) REVERT: C 232 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5547 (mtp-110) REVERT: C 271 MET cc_start: 0.8241 (mtm) cc_final: 0.7680 (mtm) outliers start: 65 outliers final: 53 residues processed: 168 average time/residue: 0.3300 time to fit residues: 78.8523 Evaluate side-chains 181 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 121 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 124 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111554 restraints weight = 12482.170| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.93 r_work: 0.2933 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11436 Z= 0.115 Angle : 0.536 9.816 15587 Z= 0.271 Chirality : 0.045 0.254 1714 Planarity : 0.004 0.037 2037 Dihedral : 5.373 55.666 1689 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.38 % Allowed : 22.98 % Favored : 71.64 % 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: -0.43 (0.22), residues: 1416 helix: 1.10 (0.30), residues: 354 sheet: 0.04 (0.32), residues: 282 loop : -1.09 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 122 HIS 0.002 0.001 HIS C 174 PHE 0.020 0.001 PHE A 413 TYR 0.013 0.001 TYR C 98 ARG 0.005 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 6) link_NAG-ASN : angle 1.84689 ( 18) hydrogen bonds : bond 0.03023 ( 377) hydrogen bonds : angle 4.75607 ( 1077) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.62050 ( 8) covalent geometry : bond 0.00278 (11426) covalent geometry : angle 0.53294 (15561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 1.917 Fit side-chains REVERT: A 41 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.4786 (t80) REVERT: A 56 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7175 (mmt90) REVERT: A 497 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6188 (t0) REVERT: B 50 ARG cc_start: 0.6508 (ttp-110) cc_final: 0.6154 (mtp-110) REVERT: B 143 TYR cc_start: 0.8171 (m-80) cc_final: 0.7646 (m-80) REVERT: B 276 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 300 VAL cc_start: 0.8876 (m) cc_final: 0.8664 (t) REVERT: B 440 ASP cc_start: 0.7983 (t0) cc_final: 0.7696 (t0) REVERT: B 446 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6861 (tmt) REVERT: B 585 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6677 (mt) REVERT: C 104 ASP cc_start: 0.8435 (t0) cc_final: 0.7545 (t0) REVERT: C 232 ARG cc_start: 0.6238 (OUTLIER) cc_final: 0.5598 (mtp180) REVERT: C 271 MET cc_start: 0.8232 (mtm) cc_final: 0.7720 (mtm) outliers start: 62 outliers final: 46 residues processed: 167 average time/residue: 0.3405 time to fit residues: 83.7356 Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111696 restraints weight = 12478.129| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.94 r_work: 0.2936 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11436 Z= 0.120 Angle : 0.551 9.807 15587 Z= 0.276 Chirality : 0.045 0.253 1714 Planarity : 0.004 0.037 2037 Dihedral : 5.182 55.640 1686 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.77 % Allowed : 23.42 % Favored : 71.81 % 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: -0.41 (0.22), residues: 1416 helix: 1.11 (0.30), residues: 354 sheet: 0.07 (0.32), residues: 282 loop : -1.07 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 122 HIS 0.002 0.001 HIS B 458 PHE 0.020 0.001 PHE A 413 TYR 0.011 0.001 TYR B 481 ARG 0.005 0.000 ARG C 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 6) link_NAG-ASN : angle 1.81624 ( 18) hydrogen bonds : bond 0.03054 ( 377) hydrogen bonds : angle 4.76795 ( 1077) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.66638 ( 8) covalent geometry : bond 0.00289 (11426) covalent geometry : angle 0.54758 (15561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 1.253 Fit side-chains REVERT: A 41 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.4815 (t80) REVERT: A 56 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7176 (mmt90) REVERT: A 276 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8054 (mt) REVERT: A 497 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6197 (t0) REVERT: B 50 ARG cc_start: 0.6529 (ttp-110) cc_final: 0.6177 (mtp-110) REVERT: B 143 TYR cc_start: 0.8159 (m-80) cc_final: 0.7640 (m-80) REVERT: B 276 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 300 VAL cc_start: 0.8891 (m) cc_final: 0.8679 (t) REVERT: B 386 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: B 440 ASP cc_start: 0.8005 (t0) cc_final: 0.7721 (t0) REVERT: B 446 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6866 (tmt) REVERT: B 585 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6669 (mt) REVERT: C 104 ASP cc_start: 0.8439 (t0) cc_final: 0.7539 (t0) REVERT: C 232 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5581 (mtp180) REVERT: C 271 MET cc_start: 0.8196 (mtm) cc_final: 0.7662 (mtm) outliers start: 55 outliers final: 45 residues processed: 155 average time/residue: 0.2389 time to fit residues: 53.1695 Evaluate side-chains 173 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 127 optimal weight: 40.0000 chunk 98 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.178025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112661 restraints weight = 12382.633| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.93 r_work: 0.2953 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11436 Z= 0.102 Angle : 0.541 9.805 15587 Z= 0.272 Chirality : 0.044 0.251 1714 Planarity : 0.004 0.036 2037 Dihedral : 5.132 55.650 1686 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.68 % Allowed : 23.33 % Favored : 71.99 % 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: -0.37 (0.22), residues: 1416 helix: 1.16 (0.30), residues: 354 sheet: 0.11 (0.32), residues: 282 loop : -1.05 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 122 HIS 0.002 0.000 HIS C 174 PHE 0.019 0.001 PHE A 413 TYR 0.011 0.001 TYR C 98 ARG 0.005 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 6) link_NAG-ASN : angle 1.76363 ( 18) hydrogen bonds : bond 0.02967 ( 377) hydrogen bonds : angle 4.73197 ( 1077) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.65296 ( 8) covalent geometry : bond 0.00240 (11426) covalent geometry : angle 0.53814 (15561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7159.74 seconds wall clock time: 129 minutes 11.69 seconds (7751.69 seconds total)