Starting phenix.real_space_refine on Fri Jul 3 00:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7z_29829/07_2026/8g7z_29829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7z_29829/07_2026/8g7z_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_2026/8g7z_29829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7z_29829/07_2026/8g7z_29829.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7z_29829/07_2026/8g7z_29829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7z_29829/07_2026/8g7z_29829.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} 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: {'ASN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} 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, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 2.97, per 1000 atoms: 0.27 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: 0.90 Conformation dependent library (CDL) restraints added in 407.1 milliseconds 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: 0.33 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: 1.92 Time building geometry restraints manager: 1.23 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 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 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 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.960 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 8.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG C 180 TYR 0.017 0.001 TYR C 138 PHE 0.022 0.002 PHE A 413 TRP 0.009 0.001 TRP A 538 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (11371) covalent geometry : angle 0.61467 / 0.32 (15486) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.96724 / 0.64 ( 8) hydrogen bonds : bond 0.17790 / 12.67 ( 380) hydrogen bonds : angle 7.25867 / 5.02 ( 1068) link_NAG-ASN : bond 0.00602 / 0.30 ( 6) link_NAG-ASN : angle 5.20483 / 3.15 ( 18) *********************** 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 : 0.424 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 116 average time/residue: 0.1179 time to fit residues: 19.5125 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 : 0.415 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0970 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116086 restraints weight = 13236.407| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.19 r_work: 0.3062 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11381 Z= 0.270 Angle : 0.661 12.967 15512 Z= 0.335 Chirality : 0.048 0.175 1706 Planarity : 0.004 0.040 2027 Dihedral : 5.857 50.216 1678 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.02 % Allowed : 20.00 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1411 helix: 0.18 (0.27), residues: 369 sheet: 0.22 (0.33), residues: 269 loop : -1.31 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.013 0.002 TYR A 580 PHE 0.024 0.002 PHE B 262 TRP 0.011 0.001 TRP A 122 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.27 (11371) covalent geometry : angle 0.64273 / 0.33 (15486) SS BOND : bond 0.00349 / 0.18 ( 4) SS BOND : angle 1.39152 / 0.86 ( 8) hydrogen bonds : bond 0.04534 / 3.14 ( 380) hydrogen bonds : angle 5.50391 / 3.83 ( 1068) link_NAG-ASN : bond 0.00334 / 0.16 ( 6) link_NAG-ASN : angle 4.48269 / 2.81 ( 18) *********************** 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 170 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 219 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 386 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8716 (mt-10) REVERT: B 440 ASP cc_start: 0.7816 (t0) cc_final: 0.7411 (t0) REVERT: B 454 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 527 ASP cc_start: 0.8554 (m-30) cc_final: 0.8318 (m-30) REVERT: C 271 MET cc_start: 0.7758 (mtt) cc_final: 0.7034 (tpt) outliers start: 46 outliers final: 29 residues processed: 154 average time/residue: 0.1039 time to fit residues: 23.4690 Evaluate side-chains 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 118 MET 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 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 219 LEU 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 436 THR Chi-restraints excluded: chain B residue 454 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 D residue 139 LEU 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 58 optimal weight: 6.9990 chunk 117 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107726 restraints weight = 13193.150| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.77 r_work: 0.3109 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11381 Z= 0.176 Angle : 0.596 11.606 15512 Z= 0.299 Chirality : 0.046 0.210 1706 Planarity : 0.004 0.039 2027 Dihedral : 5.296 36.748 1678 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.58 % Allowed : 20.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1411 helix: 0.48 (0.27), residues: 368 sheet: 0.19 (0.33), residues: 270 loop : -1.25 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.018 0.001 TYR C 138 PHE 0.021 0.002 PHE A 413 TRP 0.012 0.001 TRP A 122 HIS 0.004 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (11371) covalent geometry : angle 0.57486 / 0.29 (15486) SS BOND : bond 0.00210 / 0.11 ( 4) SS BOND : angle 1.10753 / 0.72 ( 8) hydrogen bonds : bond 0.03796 / 2.59 ( 380) hydrogen bonds : angle 5.22192 / 3.66 ( 1068) link_NAG-ASN : bond 0.00289 / 0.14 ( 6) link_NAG-ASN : angle 4.65075 / 2.86 ( 18) *********************** 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: 41 poor density : 128 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 219 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 386 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8748 (mt-10) REVERT: B 440 ASP cc_start: 0.7668 (t0) cc_final: 0.7199 (t0) REVERT: B 454 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7928 (tp) REVERT: B 527 ASP cc_start: 0.8530 (m-30) cc_final: 0.8283 (m-30) REVERT: C 271 MET cc_start: 0.7795 (mtt) cc_final: 0.7187 (tpt) outliers start: 41 outliers final: 29 residues processed: 155 average time/residue: 0.1034 time to fit residues: 23.8185 Evaluate side-chains 149 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 300 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 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 145 ASN Chi-restraints excluded: chain B residue 219 LEU 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 454 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 82 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 72 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3977 r_free = 0.3977 target = 0.170598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108490 restraints weight = 13323.006| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.80 r_work: 0.3119 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0944 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= 0.155 Angle : 0.576 9.161 15512 Z= 0.290 Chirality : 0.045 0.191 1706 Planarity : 0.004 0.039 2027 Dihedral : 5.009 28.861 1678 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.54 % Allowed : 20.61 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1411 helix: 0.66 (0.28), residues: 368 sheet: 0.19 (0.33), residues: 270 loop : -1.18 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.015 0.001 TYR C 138 PHE 0.021 0.001 PHE A 413 TRP 0.011 0.001 TRP A 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (11371) covalent geometry : angle 0.55893 / 0.29 (15486) SS BOND : bond 0.00169 / 0.09 ( 4) SS BOND : angle 1.01691 / 0.67 ( 8) hydrogen bonds : bond 0.03507 / 2.39 ( 380) hydrogen bonds : angle 5.05611 / 3.54 ( 1068) link_NAG-ASN : bond 0.00480 / 0.24 ( 6) link_NAG-ASN : angle 4.02604 / 2.51 ( 18) *********************** 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 177 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 310 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7680 (mp) REVERT: B 386 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: B 412 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7322 (m110) REVERT: B 440 ASP cc_start: 0.7637 (t0) cc_final: 0.7192 (t0) REVERT: B 527 ASP cc_start: 0.8516 (m-30) cc_final: 0.8276 (m-30) REVERT: C 131 SER cc_start: 0.9157 (p) cc_final: 0.8830 (m) REVERT: C 271 MET cc_start: 0.7787 (mtt) cc_final: 0.7187 (tpt) outliers start: 52 outliers final: 36 residues processed: 161 average time/residue: 0.1000 time to fit residues: 23.9438 Evaluate side-chains 159 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 SER 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 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 249 ILE 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 386 GLU Chi-restraints excluded: chain B residue 412 ASN 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 C residue 189 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 136 optimal weight: 0.0980 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 GLN D 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109842 restraints weight = 13188.617| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.78 r_work: 0.3135 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1079 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= 0.126 Angle : 0.547 8.291 15512 Z= 0.276 Chirality : 0.044 0.177 1706 Planarity : 0.004 0.040 2027 Dihedral : 4.735 25.846 1678 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.19 % Allowed : 20.70 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1411 helix: 0.86 (0.28), residues: 370 sheet: 0.24 (0.33), residues: 268 loop : -1.12 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 82 TYR 0.015 0.001 TYR C 138 PHE 0.021 0.001 PHE A 413 TRP 0.011 0.001 TRP A 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11371) covalent geometry : angle 0.53418 / 0.27 (15486) SS BOND : bond 0.00121 / 0.06 ( 4) SS BOND : angle 0.87220 / 0.58 ( 8) hydrogen bonds : bond 0.03208 / 2.17 ( 380) hydrogen bonds : angle 4.88198 / 3.43 ( 1068) link_NAG-ASN : bond 0.00262 / 0.12 ( 6) link_NAG-ASN : angle 3.49759 / 2.11 ( 18) *********************** 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 178 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8368 (tt0) cc_final: 0.8161 (tt0) REVERT: B 310 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7678 (mp) REVERT: B 386 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: B 412 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7278 (m110) REVERT: B 440 ASP cc_start: 0.7595 (t0) cc_final: 0.7094 (t0) REVERT: B 527 ASP cc_start: 0.8485 (m-30) cc_final: 0.8245 (m-30) REVERT: C 131 SER cc_start: 0.9121 (p) cc_final: 0.8771 (m) REVERT: C 271 MET cc_start: 0.7740 (mtt) cc_final: 0.7207 (tpt) outliers start: 48 outliers final: 38 residues processed: 164 average time/residue: 0.0980 time to fit residues: 23.9714 Evaluate side-chains 159 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 605 VAL 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 249 ILE 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 412 ASN 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 B residue 591 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 189 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 68 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108921 restraints weight = 13243.296| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.78 r_work: 0.3126 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11381 Z= 0.156 Angle : 0.568 7.860 15512 Z= 0.286 Chirality : 0.045 0.172 1706 Planarity : 0.004 0.041 2027 Dihedral : 4.722 25.763 1677 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.98 % Allowed : 20.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1411 helix: 0.82 (0.28), residues: 371 sheet: 0.20 (0.33), residues: 268 loop : -1.11 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.011 0.001 TYR A 481 PHE 0.021 0.001 PHE A 413 TRP 0.009 0.001 TRP A 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (11371) covalent geometry : angle 0.55573 / 0.28 (15486) SS BOND : bond 0.00149 / 0.08 ( 4) SS BOND : angle 1.03692 / 0.66 ( 8) hydrogen bonds : bond 0.03337 / 2.26 ( 380) hydrogen bonds : angle 4.83711 / 3.40 ( 1068) link_NAG-ASN : bond 0.00297 / 0.14 ( 6) link_NAG-ASN : angle 3.51120 / 1.95 ( 18) *********************** 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 175 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8355 (tt0) cc_final: 0.8133 (tt0) REVERT: A 454 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8081 (tp) REVERT: B 310 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7700 (mp) REVERT: B 386 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8715 (mt-10) REVERT: B 412 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7319 (m110) REVERT: B 440 ASP cc_start: 0.7638 (t0) cc_final: 0.7114 (t0) REVERT: B 527 ASP cc_start: 0.8482 (m-30) cc_final: 0.8240 (m-30) REVERT: C 131 SER cc_start: 0.9180 (p) cc_final: 0.8844 (m) REVERT: C 271 MET cc_start: 0.7802 (mtt) cc_final: 0.7265 (tpt) REVERT: D 266 LEU cc_start: 0.6150 (mt) cc_final: 0.5865 (tt) outliers start: 57 outliers final: 43 residues processed: 161 average time/residue: 0.0984 time to fit residues: 23.8286 Evaluate side-chains 162 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 360 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 SER 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 605 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 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 249 ILE 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 386 GLU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 189 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 76 optimal weight: 0.0070 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 109 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3992 r_free = 0.3992 target = 0.172907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110039 restraints weight = 13166.584| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.90 r_work: 0.3122 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11381 Z= 0.099 Angle : 0.533 7.564 15512 Z= 0.268 Chirality : 0.043 0.172 1706 Planarity : 0.003 0.039 2027 Dihedral : 4.500 27.220 1677 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.76 % Allowed : 21.83 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1411 helix: 1.12 (0.29), residues: 370 sheet: 0.27 (0.33), residues: 268 loop : -1.05 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 82 TYR 0.010 0.001 TYR A 481 PHE 0.020 0.001 PHE A 413 TRP 0.011 0.001 TRP A 122 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (11371) covalent geometry : angle 0.52251 / 0.27 (15486) SS BOND : bond 0.00074 / 0.04 ( 4) SS BOND : angle 0.76889 / 0.51 ( 8) hydrogen bonds : bond 0.02959 / 1.99 ( 380) hydrogen bonds : angle 4.72747 / 3.33 ( 1068) link_NAG-ASN : bond 0.00323 / 0.15 ( 6) link_NAG-ASN : angle 3.05873 / 1.83 ( 18) *********************** 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 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8375 (tt0) cc_final: 0.8135 (tt0) REVERT: B 310 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7638 (mp) REVERT: B 340 GLN cc_start: 0.7895 (mp10) cc_final: 0.7526 (mp10) REVERT: B 386 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8711 (mt-10) REVERT: B 412 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7221 (m110) REVERT: B 445 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 454 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7772 (tp) REVERT: B 485 HIS cc_start: 0.8822 (t70) cc_final: 0.8446 (t70) REVERT: B 527 ASP cc_start: 0.8456 (m-30) cc_final: 0.8148 (m-30) REVERT: C 131 SER cc_start: 0.9149 (p) cc_final: 0.8819 (m) REVERT: C 271 MET cc_start: 0.7746 (mtt) cc_final: 0.7204 (tpt) outliers start: 43 outliers final: 29 residues processed: 159 average time/residue: 0.0952 time to fit residues: 22.9942 Evaluate side-chains 148 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 402 SER 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 B residue 70 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 192 THR 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 386 GLU Chi-restraints excluded: chain B residue 412 ASN 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 139 LEU 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 76 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 GLN D 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109309 restraints weight = 13203.763| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.89 r_work: 0.3092 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11381 Z= 0.168 Angle : 0.577 7.424 15512 Z= 0.292 Chirality : 0.045 0.169 1706 Planarity : 0.004 0.040 2027 Dihedral : 4.492 24.993 1675 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.54 % Allowed : 21.66 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.23), residues: 1411 helix: 0.98 (0.28), residues: 369 sheet: 0.25 (0.33), residues: 268 loop : -1.09 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.013 0.001 TYR B 435 PHE 0.021 0.002 PHE A 413 TRP 0.007 0.001 TRP A 538 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (11371) covalent geometry : angle 0.56804 / 0.29 (15486) SS BOND : bond 0.00150 / 0.08 ( 4) SS BOND : angle 1.00282 / 0.64 ( 8) hydrogen bonds : bond 0.03307 / 2.23 ( 380) hydrogen bonds : angle 4.78311 / 3.36 ( 1068) link_NAG-ASN : bond 0.00396 / 0.19 ( 6) link_NAG-ASN : angle 2.99911 / 1.76 ( 18) *********************** 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 169 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 117 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8413 (tt0) cc_final: 0.8186 (tt0) REVERT: A 454 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8074 (tp) REVERT: B 310 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7664 (mp) REVERT: B 340 GLN cc_start: 0.7945 (mp10) cc_final: 0.7556 (mp10) REVERT: B 386 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: B 412 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7271 (m110) REVERT: B 454 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7868 (tp) REVERT: B 485 HIS cc_start: 0.8829 (t70) cc_final: 0.8452 (t70) REVERT: B 527 ASP cc_start: 0.8498 (m-30) cc_final: 0.8213 (m-30) REVERT: C 104 ASP cc_start: 0.7874 (t0) cc_final: 0.7538 (t0) REVERT: C 131 SER cc_start: 0.9169 (p) cc_final: 0.8818 (m) REVERT: C 271 MET cc_start: 0.7767 (mtt) cc_final: 0.7230 (tpt) outliers start: 52 outliers final: 41 residues processed: 156 average time/residue: 0.0894 time to fit residues: 21.0260 Evaluate side-chains 165 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 402 SER 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 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 386 GLU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 417 LEU 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 521 CYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 130 ASP 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 68 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 118 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.171291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107831 restraints weight = 13080.581| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.88 r_work: 0.3079 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11381 Z= 0.169 Angle : 0.582 8.574 15512 Z= 0.293 Chirality : 0.045 0.168 1706 Planarity : 0.004 0.040 2027 Dihedral : 4.516 23.201 1675 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.45 % Allowed : 21.57 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1411 helix: 0.91 (0.28), residues: 371 sheet: 0.22 (0.33), residues: 268 loop : -1.12 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 82 TYR 0.013 0.001 TYR A 481 PHE 0.021 0.001 PHE A 413 TRP 0.007 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (11371) covalent geometry : angle 0.57142 / 0.29 (15486) SS BOND : bond 0.00159 / 0.08 ( 4) SS BOND : angle 1.01794 / 0.65 ( 8) hydrogen bonds : bond 0.03333 / 2.25 ( 380) hydrogen bonds : angle 4.80602 / 3.39 ( 1068) link_NAG-ASN : bond 0.00235 / 0.10 ( 6) link_NAG-ASN : angle 3.28723 / 1.73 ( 18) *********************** 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 166 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8360 (tt0) cc_final: 0.8139 (tt0) REVERT: A 446 MET cc_start: 0.8271 (tpp) cc_final: 0.8039 (tpt) REVERT: A 454 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8059 (tp) REVERT: B 310 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7614 (mp) REVERT: B 340 GLN cc_start: 0.7933 (mp10) cc_final: 0.7532 (mp10) REVERT: B 412 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7229 (m110) REVERT: B 454 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7865 (tp) REVERT: B 527 ASP cc_start: 0.8489 (m-30) cc_final: 0.8249 (m-30) REVERT: C 104 ASP cc_start: 0.7850 (t0) cc_final: 0.7504 (t0) REVERT: C 131 SER cc_start: 0.9169 (p) cc_final: 0.8806 (m) REVERT: C 271 MET cc_start: 0.7762 (mtt) cc_final: 0.7229 (tpt) outliers start: 51 outliers final: 42 residues processed: 153 average time/residue: 0.0865 time to fit residues: 20.1935 Evaluate side-chains 160 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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 402 SER 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 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 412 ASN Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 454 LEU 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 C residue 261 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 130 ASP 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 87 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 127 optimal weight: 0.0050 chunk 124 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3972 r_free = 0.3972 target = 0.172463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109148 restraints weight = 13186.545| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.88 r_work: 0.3093 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11381 Z= 0.129 Angle : 0.558 8.018 15512 Z= 0.282 Chirality : 0.044 0.169 1706 Planarity : 0.004 0.039 2027 Dihedral : 4.366 22.153 1675 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.76 % Allowed : 22.10 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1411 helix: 1.06 (0.28), residues: 370 sheet: 0.23 (0.33), residues: 268 loop : -1.09 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 82 TYR 0.011 0.001 TYR A 481 PHE 0.020 0.001 PHE A 413 TRP 0.010 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (11371) covalent geometry : angle 0.55092 / 0.28 (15486) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.88394 / 0.58 ( 8) hydrogen bonds : bond 0.03123 / 2.10 ( 380) hydrogen bonds : angle 4.70893 / 3.30 ( 1068) link_NAG-ASN : bond 0.00321 / 0.15 ( 6) link_NAG-ASN : angle 2.63963 / 1.58 ( 18) ********************** 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 160 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8358 (tt0) cc_final: 0.8127 (tt0) REVERT: A 446 MET cc_start: 0.8281 (tpp) cc_final: 0.8052 (tpt) REVERT: A 454 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8020 (tp) REVERT: B 310 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7613 (mp) REVERT: B 340 GLN cc_start: 0.7871 (mp10) cc_final: 0.7483 (mp10) REVERT: B 412 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7212 (m110) REVERT: B 445 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 454 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7817 (tp) REVERT: B 485 HIS cc_start: 0.8822 (t70) cc_final: 0.8432 (t70) REVERT: B 527 ASP cc_start: 0.8486 (m-30) cc_final: 0.8196 (m-30) REVERT: C 104 ASP cc_start: 0.7871 (t0) cc_final: 0.7478 (t0) REVERT: C 131 SER cc_start: 0.9161 (p) cc_final: 0.8795 (m) REVERT: C 271 MET cc_start: 0.7781 (mtt) cc_final: 0.7254 (tpt) outliers start: 43 outliers final: 36 residues processed: 150 average time/residue: 0.0919 time to fit residues: 20.6677 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 : 0.392 ------------------------------------------------------------------------------- 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 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 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 402 SER 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 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 412 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 130 ASP 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 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 548 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 = 0.3958 r_free = 0.3958 target = 0.171153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109418 restraints weight = 13071.808| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.79 r_work: 0.3091 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1399 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= 0.135 Angle : 0.560 7.935 15512 Z= 0.283 Chirality : 0.044 0.168 1706 Planarity : 0.004 0.039 2027 Dihedral : 4.358 21.308 1675 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.02 % Allowed : 21.92 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1411 helix: 1.05 (0.28), residues: 371 sheet: 0.20 (0.33), residues: 268 loop : -1.08 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 82 TYR 0.011 0.001 TYR A 481 PHE 0.020 0.001 PHE A 413 TRP 0.009 0.001 TRP A 122 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 (11371) covalent geometry : angle 0.55050 / 0.28 (15486) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 0.89111 / 0.58 ( 8) hydrogen bonds : bond 0.03125 / 2.10 ( 380) hydrogen bonds : angle 4.68949 / 3.29 ( 1068) link_NAG-ASN : bond 0.00278 / 0.13 ( 6) link_NAG-ASN : angle 2.96576 / 1.64 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2801.78 seconds wall clock time: 48 minutes 46.63 seconds (2926.63 seconds total)