Starting phenix.real_space_refine on Tue Jul 29 06:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7z_29829/07_2025/8g7z_29829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7z_29829/07_2025/8g7z_29829.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/8g7z_29829/07_2025/8g7z_29829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7z_29829/07_2025/8g7z_29829.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7z_29829/07_2025/8g7z_29829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7z_29829/07_2025/8g7z_29829.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= 0.127 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 7072 2.51 5 N 1910 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11094 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4159 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4146 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 34, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1350 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 7.09, per 1000 atoms: 0.64 Number of scatterers: 11094 At special positions: 0 Unit cell: (95.45, 127.82, 151.89, 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 2072 8.00 N 1910 7.00 C 7072 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 A 901 " - " ASN A 98 " " NAG A 902 " - " ASN A 522 " " NAG B 901 " - " ASN B 98 " " NAG B 902 " - " ASN B 522 " " NAG C 502 " - " ASN C 184 " " NAG D 502 " - " ASN D 184 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 31.7% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.894A pdb=" N THR A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 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 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.997A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.508A pdb=" N MET A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.524A pdb=" N LYS A 389 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.929A pdb=" N PHE A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.665A pdb=" N GLU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.845A pdb=" N ARG A 441 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.663A pdb=" N ARG A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.548A 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 removed outlier: 3.513A pdb=" N LEU A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) 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: 3.749A pdb=" N THR B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.625A pdb=" N MET B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.539A 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 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.517A pdb=" N SER B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 316 removed outlier: 4.058A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.592A pdb=" N ARG B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 332 " --> pdb=" O CYS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.722A pdb=" N GLN B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.663A pdb=" N GLN B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.596A pdb=" N PHE B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.756A pdb=" N TYR B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.526A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 removed outlier: 4.130A pdb=" N ARG B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR B 450 " --> pdb=" O MET B 446 " (cutoff:3.500A) 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 545 Processing helix chain 'B' and resid 594 through 604 Processing helix chain 'B' and resid 605 through 608 Processing helix chain 'C' and resid 267 through 273 removed outlier: 3.869A pdb=" N ALA C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.518A 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: 5.263A pdb=" N LEU A 144 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 210 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N MET A 180 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 212 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE A 182 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LYS A 177 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR A 260 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 179 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N PHE A 262 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU A 181 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N SER A 264 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS A 286 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 259 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE A 288 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 261 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 290 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY A 263 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET A 378 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR A 481 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 380 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.718A 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: 3.680A pdb=" N VAL B 209 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL B 210 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET B 180 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 212 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE B 182 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N LYS B 177 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG B 258 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 179 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS B 286 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 259 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE B 288 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 261 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN B 290 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY B 263 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 381 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET B 378 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR B 481 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 380 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LEU B 581 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE B 480 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 583 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR B 482 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 580 " --> pdb=" O ARG B 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.841A pdb=" N ARG C 112 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 263 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 114 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 261 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.927A pdb=" N ILE C 143 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL C 125 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU C 126 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 245 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG C 128 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE C 243 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 130 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 162 removed outlier: 6.733A pdb=" N LEU D 139 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D 128 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 141 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR D 242 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 195 through 197 removed outlier: 4.362A pdb=" N GLY D 116 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLY D 260 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 118 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU D 258 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N LYS D 91 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N ARG D 286 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLY D 93 " --> pdb=" O ASN D 284 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1068 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: 3.50 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3651 1.34 - 1.46: 1940 1.46 - 1.57: 5718 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 11371 Sorted by residual: bond pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N ARG D 232 " pdb=" CA ARG D 232 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.22e-02 6.72e+03 4.32e+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 3.19e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" CD ARG C 232 " pdb=" NE ARG C 232 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.40e+00 ... (remaining 11366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 15288 2.40 - 4.80: 182 4.80 - 7.20: 13 7.20 - 9.59: 2 9.59 - 11.99: 1 Bond angle restraints: 15486 Sorted by residual: angle pdb=" CB ARG C 232 " pdb=" CG ARG C 232 " pdb=" CD ARG C 232 " ideal model delta sigma weight residual 111.30 123.29 -11.99 2.30e+00 1.89e-01 2.72e+01 angle pdb=" N ASP B 440 " pdb=" CA ASP B 440 " pdb=" C ASP B 440 " ideal model delta sigma weight residual 110.06 103.75 6.31 1.43e+00 4.89e-01 1.95e+01 angle pdb=" N ASN B 522 " pdb=" CA ASN B 522 " pdb=" CB ASN B 522 " ideal model delta sigma weight residual 110.56 117.23 -6.67 1.56e+00 4.11e-01 1.83e+01 angle pdb=" N ASN B 522 " pdb=" CA ASN B 522 " pdb=" C ASN B 522 " ideal model delta sigma weight residual 110.42 104.47 5.95 1.55e+00 4.16e-01 1.47e+01 angle pdb=" C CYS A 521 " pdb=" N ASN A 522 " pdb=" CA ASN A 522 " ideal model delta sigma weight residual 122.72 117.59 5.13 1.38e+00 5.25e-01 1.38e+01 ... (remaining 15481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5921 17.17 - 34.35: 639 34.35 - 51.52: 141 51.52 - 68.69: 31 68.69 - 85.87: 12 Dihedral angle restraints: 6744 sinusoidal: 2670 harmonic: 4074 Sorted by residual: dihedral pdb=" CG ARG D 232 " pdb=" CD ARG D 232 " pdb=" NE ARG D 232 " pdb=" CZ ARG D 232 " ideal model delta sinusoidal sigma weight residual -90.00 -25.09 -64.91 2 1.50e+01 4.44e-03 1.75e+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 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA CYS B 521 " pdb=" C CYS B 521 " pdb=" N ASN B 522 " pdb=" CA ASN B 522 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1411 0.060 - 0.120: 271 0.120 - 0.180: 20 0.180 - 0.240: 1 0.240 - 0.300: 3 Chirality restraints: 1706 Sorted by residual: chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 522 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ARG D 232 " pdb=" N ARG D 232 " pdb=" C ARG D 232 " pdb=" CB ARG D 232 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1703 not shown) Planarity restraints: 2033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 902 " 0.145 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" C7 NAG A 902 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 902 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG A 902 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG A 902 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 522 " 0.036 2.00e-02 2.50e+03 3.30e-02 1.36e+01 pdb=" CG ASN B 522 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 522 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 522 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B 902 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.027 2.00e-02 2.50e+03 2.59e-02 8.38e+00 pdb=" CG ASN A 98 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG A 901 " 0.030 2.00e-02 2.50e+03 ... (remaining 2030 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 29 2.37 - 3.00: 5977 3.00 - 3.64: 15981 3.64 - 4.27: 24527 4.27 - 4.90: 43266 Nonbonded interactions: 89780 Sorted by model distance: nonbonded pdb=" OD2 ASP A 362 " pdb=" NH1 ARG C 232 " model vdw 1.740 3.120 nonbonded pdb=" OG SER A 277 " pdb=" O VAL A 359 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR D 179 " pdb=" OG1 THR D 186 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR C 138 " pdb=" OD2 ASP C 158 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 119 " pdb=" O GLN C 255 " model vdw 2.194 3.040 ... (remaining 89775 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 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 553 or resid 564 through 566 or \ (resid 567 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 8 through 608 or resid 901 through 902)) selection = (chain 'B' and (resid 40 through 553 or (resid 564 and (name N or name CA or nam \ e C or name O or name CB )) or resid 565 through 608 or resid 901 through 902)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 83 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB )) or resid 168 through 289 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.120 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.004 0.043 11381 Z= 0.193 Angle : 0.640 15.345 15512 Z= 0.330 Chirality : 0.047 0.300 1706 Planarity : 0.005 0.119 2027 Dihedral : 15.128 85.865 4138 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.35 % Allowed : 21.57 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.22), residues: 1411 helix: 0.26 (0.28), residues: 352 sheet: 0.43 (0.33), residues: 270 loop : -1.20 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 538 HIS 0.005 0.001 HIS A 582 PHE 0.022 0.002 PHE A 413 TYR 0.017 0.001 TYR C 138 ARG 0.007 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 6) link_NAG-ASN : angle 5.20483 ( 18) hydrogen bonds : bond 0.17790 ( 380) hydrogen bonds : angle 7.25867 ( 1068) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.96724 ( 8) covalent geometry : bond 0.00448 (11371) covalent geometry : angle 0.61467 (15486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 116 average time/residue: 0.2486 time to fit residues: 41.3437 Evaluate side-chains 110 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 136 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 384 GLN C 103 ASN D 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112201 restraints weight = 12898.931| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.64 r_work: 0.3147 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11381 Z= 0.114 Angle : 0.558 11.882 15512 Z= 0.279 Chirality : 0.044 0.179 1706 Planarity : 0.004 0.038 2027 Dihedral : 5.568 53.986 1678 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 19.56 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1411 helix: 0.67 (0.28), residues: 368 sheet: 0.41 (0.33), residues: 271 loop : -1.17 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.004 0.001 HIS A 582 PHE 0.020 0.001 PHE A 413 TYR 0.012 0.001 TYR A 481 ARG 0.006 0.000 ARG A 492 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 6) link_NAG-ASN : angle 4.30535 ( 18) hydrogen bonds : bond 0.03683 ( 380) hydrogen bonds : angle 5.26719 ( 1068) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.79020 ( 8) covalent geometry : bond 0.00266 (11371) covalent geometry : angle 0.53829 (15486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: B 386 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8741 (mt-10) REVERT: B 454 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7868 (tp) REVERT: B 527 ASP cc_start: 0.8570 (m-30) cc_final: 0.8298 (m-30) REVERT: C 271 MET cc_start: 0.7790 (mtt) cc_final: 0.7077 (tpt) outliers start: 29 outliers final: 18 residues processed: 155 average time/residue: 0.2300 time to fit residues: 52.3204 Evaluate side-chains 139 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN D 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107871 restraints weight = 13254.898| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.78 r_work: 0.3108 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11381 Z= 0.198 Angle : 0.602 12.398 15512 Z= 0.301 Chirality : 0.047 0.250 1706 Planarity : 0.004 0.038 2027 Dihedral : 5.188 38.652 1677 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.84 % Allowed : 19.74 % Favored : 76.42 % 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: -0.60 (0.22), residues: 1411 helix: 0.61 (0.28), residues: 370 sheet: 0.31 (0.33), residues: 270 loop : -1.19 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 122 HIS 0.005 0.001 HIS A 582 PHE 0.021 0.002 PHE A 413 TYR 0.016 0.001 TYR C 138 ARG 0.004 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 6) link_NAG-ASN : angle 4.73650 ( 18) hydrogen bonds : bond 0.03832 ( 380) hydrogen bonds : angle 5.13660 ( 1068) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.08105 ( 8) covalent geometry : bond 0.00489 (11371) covalent geometry : angle 0.57998 (15486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: B 386 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8664 (mt-10) REVERT: B 440 ASP cc_start: 0.7660 (t0) cc_final: 0.7242 (t0) REVERT: B 527 ASP cc_start: 0.8538 (m-30) cc_final: 0.8303 (m-30) REVERT: C 131 SER cc_start: 0.9157 (p) cc_final: 0.8876 (m) REVERT: C 271 MET cc_start: 0.7796 (mtt) cc_final: 0.7160 (tpt) outliers start: 44 outliers final: 29 residues processed: 153 average time/residue: 0.2114 time to fit residues: 47.8574 Evaluate side-chains 144 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR 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 513 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 139 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN C 103 ASN D 250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.171589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112192 restraints weight = 12858.938| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.67 r_work: 0.3149 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11381 Z= 0.109 Angle : 0.536 9.123 15512 Z= 0.268 Chirality : 0.044 0.177 1706 Planarity : 0.004 0.036 2027 Dihedral : 4.770 28.413 1677 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.06 % Allowed : 20.09 % Favored : 76.86 % 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: 1411 helix: 0.97 (0.28), residues: 368 sheet: 0.35 (0.33), residues: 270 loop : -1.08 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 122 HIS 0.005 0.001 HIS A 582 PHE 0.020 0.001 PHE A 413 TYR 0.012 0.001 TYR A 481 ARG 0.004 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 6) link_NAG-ASN : angle 4.05364 ( 18) hydrogen bonds : bond 0.03142 ( 380) hydrogen bonds : angle 4.91936 ( 1068) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.77429 ( 8) covalent geometry : bond 0.00259 (11371) covalent geometry : angle 0.51797 (15486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: B 310 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7696 (mp) REVERT: B 386 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8651 (mt-10) REVERT: B 527 ASP cc_start: 0.8449 (m-30) cc_final: 0.8207 (m-30) REVERT: C 131 SER cc_start: 0.9135 (p) cc_final: 0.8796 (m) REVERT: C 271 MET cc_start: 0.7783 (mtt) cc_final: 0.7140 (tpt) outliers start: 35 outliers final: 23 residues processed: 155 average time/residue: 0.2159 time to fit residues: 49.9951 Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN D 250 GLN D 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107887 restraints weight = 12923.782| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.65 r_work: 0.3094 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11381 Z= 0.236 Angle : 0.621 8.503 15512 Z= 0.315 Chirality : 0.047 0.173 1706 Planarity : 0.004 0.040 2027 Dihedral : 4.926 24.901 1677 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.28 % Allowed : 20.26 % Favored : 75.46 % 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: -0.62 (0.22), residues: 1411 helix: 0.62 (0.27), residues: 372 sheet: 0.23 (0.33), residues: 268 loop : -1.19 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 122 HIS 0.009 0.001 HIS A 582 PHE 0.022 0.002 PHE B 262 TYR 0.013 0.002 TYR B 580 ARG 0.005 0.000 ARG D 128 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 3.69760 ( 18) hydrogen bonds : bond 0.03792 ( 380) hydrogen bonds : angle 5.03907 ( 1068) SS BOND : bond 0.00263 ( 4) SS BOND : angle 1.24087 ( 8) covalent geometry : bond 0.00583 (11371) covalent geometry : angle 0.60775 (15486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: B 310 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 440 ASP cc_start: 0.7948 (t0) cc_final: 0.7703 (t70) REVERT: B 527 ASP cc_start: 0.8668 (m-30) cc_final: 0.8443 (m-30) REVERT: C 104 ASP cc_start: 0.7781 (t0) cc_final: 0.7230 (t0) REVERT: C 131 SER cc_start: 0.9142 (p) cc_final: 0.8791 (m) REVERT: C 271 MET cc_start: 0.7708 (mtt) cc_final: 0.7153 (tpt) outliers start: 49 outliers final: 37 residues processed: 159 average time/residue: 0.2250 time to fit residues: 53.4716 Evaluate side-chains 155 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN C 103 ASN D 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110469 restraints weight = 13172.355| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.78 r_work: 0.3144 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11381 Z= 0.109 Angle : 0.544 8.179 15512 Z= 0.274 Chirality : 0.044 0.173 1706 Planarity : 0.004 0.040 2027 Dihedral : 4.664 25.275 1677 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.06 % Allowed : 21.40 % Favored : 75.55 % 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: -0.42 (0.22), residues: 1411 helix: 0.94 (0.28), residues: 370 sheet: 0.28 (0.33), residues: 268 loop : -1.11 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 122 HIS 0.006 0.001 HIS A 582 PHE 0.020 0.001 PHE A 413 TYR 0.020 0.001 TYR C 138 ARG 0.005 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 6) link_NAG-ASN : angle 3.48343 ( 18) hydrogen bonds : bond 0.03138 ( 380) hydrogen bonds : angle 4.85087 ( 1068) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.83843 ( 8) covalent geometry : bond 0.00262 (11371) covalent geometry : angle 0.53129 (15486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8414 (tt0) cc_final: 0.8022 (tt0) REVERT: A 454 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8083 (tp) REVERT: B 310 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 440 ASP cc_start: 0.7591 (t0) cc_final: 0.7343 (t70) REVERT: B 527 ASP cc_start: 0.8449 (m-30) cc_final: 0.8230 (m-30) REVERT: C 131 SER cc_start: 0.9188 (p) cc_final: 0.8849 (m) REVERT: C 271 MET cc_start: 0.7791 (mtt) cc_final: 0.7233 (tpt) outliers start: 35 outliers final: 28 residues processed: 152 average time/residue: 0.1982 time to fit residues: 45.5407 Evaluate side-chains 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR 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 119 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110578 restraints weight = 13253.781| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.91 r_work: 0.3113 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11381 Z= 0.120 Angle : 0.551 7.947 15512 Z= 0.276 Chirality : 0.044 0.174 1706 Planarity : 0.004 0.038 2027 Dihedral : 4.505 27.763 1675 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.41 % Allowed : 21.22 % Favored : 75.37 % 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: -0.34 (0.23), residues: 1411 helix: 1.07 (0.28), residues: 370 sheet: 0.28 (0.33), residues: 268 loop : -1.07 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 PHE 0.020 0.001 PHE A 413 TYR 0.017 0.001 TYR C 138 ARG 0.006 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 6) link_NAG-ASN : angle 3.16980 ( 18) hydrogen bonds : bond 0.03081 ( 380) hydrogen bonds : angle 4.73857 ( 1068) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.86847 ( 8) covalent geometry : bond 0.00292 (11371) covalent geometry : angle 0.54081 (15486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8392 (tt0) cc_final: 0.8160 (tt0) REVERT: A 454 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8057 (tp) REVERT: B 310 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7663 (mp) REVERT: B 340 GLN cc_start: 0.7948 (mp10) cc_final: 0.7584 (mp10) REVERT: B 485 HIS cc_start: 0.8830 (t70) cc_final: 0.8435 (t70) REVERT: B 527 ASP cc_start: 0.8477 (m-30) cc_final: 0.8193 (m-30) REVERT: C 131 SER cc_start: 0.9169 (p) cc_final: 0.8823 (m) REVERT: C 271 MET cc_start: 0.7744 (mtt) cc_final: 0.7179 (tpt) outliers start: 39 outliers final: 32 residues processed: 150 average time/residue: 0.2059 time to fit residues: 46.5588 Evaluate side-chains 154 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR 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 32 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 78 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN D 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111442 restraints weight = 13167.937| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.91 r_work: 0.3124 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11381 Z= 0.112 Angle : 0.541 7.837 15512 Z= 0.273 Chirality : 0.043 0.170 1706 Planarity : 0.004 0.038 2027 Dihedral : 4.338 24.833 1675 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.76 % Allowed : 21.22 % Favored : 75.02 % 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: -0.26 (0.23), residues: 1411 helix: 1.24 (0.29), residues: 366 sheet: 0.29 (0.33), residues: 268 loop : -1.05 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 PHE 0.020 0.001 PHE A 413 TYR 0.018 0.001 TYR C 138 ARG 0.006 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 3.20281 ( 18) hydrogen bonds : bond 0.02964 ( 380) hydrogen bonds : angle 4.68151 ( 1068) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.80841 ( 8) covalent geometry : bond 0.00270 (11371) covalent geometry : angle 0.52964 (15486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8424 (tt0) cc_final: 0.8175 (tt0) REVERT: A 454 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 310 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 340 GLN cc_start: 0.7887 (mp10) cc_final: 0.7543 (mp10) REVERT: B 485 HIS cc_start: 0.8819 (t70) cc_final: 0.8459 (t70) REVERT: B 527 ASP cc_start: 0.8447 (m-30) cc_final: 0.8169 (m-30) REVERT: C 131 SER cc_start: 0.9164 (p) cc_final: 0.8829 (m) REVERT: C 271 MET cc_start: 0.7753 (mtt) cc_final: 0.7202 (tpt) outliers start: 43 outliers final: 36 residues processed: 145 average time/residue: 0.2024 time to fit residues: 44.3218 Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 576 LYS Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR 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 119 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 chunk 34 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 101 optimal weight: 0.0980 chunk 16 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110409 restraints weight = 13130.972| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.90 r_work: 0.3109 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11381 Z= 0.109 Angle : 0.539 7.532 15512 Z= 0.271 Chirality : 0.043 0.169 1706 Planarity : 0.004 0.038 2027 Dihedral : 4.273 23.549 1675 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.41 % Allowed : 21.83 % Favored : 74.76 % 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: -0.22 (0.23), residues: 1411 helix: 1.30 (0.29), residues: 364 sheet: 0.28 (0.33), residues: 268 loop : -1.03 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 PHE 0.019 0.001 PHE A 413 TYR 0.009 0.001 TYR A 481 ARG 0.007 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 6) link_NAG-ASN : angle 3.27774 ( 18) hydrogen bonds : bond 0.02912 ( 380) hydrogen bonds : angle 4.65720 ( 1068) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.77569 ( 8) covalent geometry : bond 0.00263 (11371) covalent geometry : angle 0.52796 (15486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8378 (tt0) cc_final: 0.8108 (tt0) REVERT: A 454 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7998 (tp) REVERT: B 310 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7607 (mp) REVERT: B 340 GLN cc_start: 0.7834 (mp10) cc_final: 0.7472 (mp10) REVERT: B 485 HIS cc_start: 0.8785 (t70) cc_final: 0.8399 (t70) REVERT: B 527 ASP cc_start: 0.8429 (m-30) cc_final: 0.8144 (m-30) REVERT: C 131 SER cc_start: 0.9149 (p) cc_final: 0.8810 (m) REVERT: C 271 MET cc_start: 0.7727 (mtt) cc_final: 0.7184 (tpt) outliers start: 39 outliers final: 35 residues processed: 142 average time/residue: 0.2284 time to fit residues: 48.9369 Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.172450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109058 restraints weight = 13207.400| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.88 r_work: 0.3090 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11381 Z= 0.150 Angle : 0.564 12.536 15512 Z= 0.284 Chirality : 0.045 0.208 1706 Planarity : 0.004 0.038 2027 Dihedral : 4.341 24.689 1675 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.49 % Allowed : 21.83 % Favored : 74.67 % 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: -0.34 (0.23), residues: 1411 helix: 1.07 (0.28), residues: 371 sheet: 0.24 (0.33), residues: 268 loop : -1.06 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 PHE 0.021 0.001 PHE A 413 TYR 0.011 0.001 TYR A 481 ARG 0.007 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 6) link_NAG-ASN : angle 3.72661 ( 18) hydrogen bonds : bond 0.03100 ( 380) hydrogen bonds : angle 4.67957 ( 1068) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.94157 ( 8) covalent geometry : bond 0.00371 (11371) covalent geometry : angle 0.54914 (15486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8414 (tt0) cc_final: 0.8134 (tt0) REVERT: A 454 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8006 (tp) REVERT: B 310 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 340 GLN cc_start: 0.7835 (mp10) cc_final: 0.7465 (mp10) REVERT: B 485 HIS cc_start: 0.8815 (t70) cc_final: 0.8415 (t70) REVERT: B 527 ASP cc_start: 0.8477 (m-30) cc_final: 0.8192 (m-30) REVERT: C 131 SER cc_start: 0.9158 (p) cc_final: 0.8815 (m) REVERT: C 271 MET cc_start: 0.7736 (mtt) cc_final: 0.7198 (tpt) outliers start: 40 outliers final: 36 residues processed: 144 average time/residue: 0.2598 time to fit residues: 55.6610 Evaluate side-chains 150 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 121 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR 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 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 117 optimal weight: 0.0770 chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111909 restraints weight = 13025.429| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.89 r_work: 0.3125 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11381 Z= 0.092 Angle : 0.539 12.124 15512 Z= 0.267 Chirality : 0.044 0.267 1706 Planarity : 0.004 0.040 2027 Dihedral : 4.462 36.641 1675 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.88 % Allowed : 22.62 % Favored : 74.50 % 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: -0.17 (0.23), residues: 1411 helix: 1.26 (0.29), residues: 372 sheet: 0.34 (0.33), residues: 268 loop : -0.99 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 PHE 0.019 0.001 PHE A 413 TYR 0.009 0.001 TYR A 481 ARG 0.007 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 6) link_NAG-ASN : angle 4.62762 ( 18) hydrogen bonds : bond 0.02765 ( 380) hydrogen bonds : angle 4.57990 ( 1068) SS BOND : bond 0.00066 ( 4) SS BOND : angle 0.72030 ( 8) covalent geometry : bond 0.00214 (11371) covalent geometry : angle 0.51590 (15486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6650.81 seconds wall clock time: 116 minutes 49.53 seconds (7009.53 seconds total)