Starting phenix.real_space_refine on Tue Jul 29 06:13:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g80_29830/07_2025/8g80_29830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g80_29830/07_2025/8g80_29830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g80_29830/07_2025/8g80_29830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g80_29830/07_2025/8g80_29830.map" model { file = "/net/cci-nas-00/data/ceres_data/8g80_29830/07_2025/8g80_29830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g80_29830/07_2025/8g80_29830.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.128 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 7055 2.51 5 N 1908 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11067 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4125 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 34, 'TRANS': 500} Chain breaks: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4150 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1353 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1353 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.68, per 1000 atoms: 0.69 Number of scatterers: 11067 At special positions: 0 Unit cell: (92.13, 128.65, 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 2064 8.00 N 1908 7.00 C 7055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1017 " - " ASN A 98 " " NAG A1018 " - " ASN A 522 " " NAG B1017 " - " ASN B 98 " " NAG B1018 " - " ASN B 522 " " NAG C1008 " - " ASN C 184 " " NAG D1008 " - " ASN D 184 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 29.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.822A pdb=" N THR A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) 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 253 Processing helix chain 'A' and resid 265 through 276 removed outlier: 4.123A pdb=" N LEU A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.873A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.679A pdb=" N LEU A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.602A pdb=" N ASP A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.972A pdb=" N LYS A 424 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.730A pdb=" N GLU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 4.802A pdb=" N THR A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.796A pdb=" N TYR A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 524 through 545 Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.807A pdb=" N HIS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.748A pdb=" N THR B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 removed outlier: 3.687A pdb=" N ALA B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.612A pdb=" N LEU B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.528A pdb=" N SER B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 316 removed outlier: 4.159A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.703A pdb=" N GLN B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.568A pdb=" N PHE B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.524A pdb=" N TYR B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.929A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 460 Processing helix chain 'B' and resid 460 through 473 removed outlier: 3.550A pdb=" N ALA B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) 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 268 through 274 Processing helix chain 'D' and resid 101 through 105 removed outlier: 4.165A pdb=" N ARG D 105 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 73 removed outlier: 5.507A pdb=" N LEU A 144 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 143 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 209 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET A 180 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A 212 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE A 182 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 179 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE A 262 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 181 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER A 264 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 259 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE A 288 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 261 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN A 290 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY A 263 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET A 378 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR A 481 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 380 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.684A pdb=" N TYR A 580 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.764A pdb=" N ARG B 50 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 73 removed outlier: 3.705A pdb=" N LEU B 146 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 144 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL B 210 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET B 180 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 212 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE B 182 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N LYS B 177 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG B 258 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 286 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 259 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE B 288 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 261 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLN B 290 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY B 263 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET B 378 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N TYR B 481 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 380 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 580 through 581 Processing sheet with id=AA7, first strand: chain 'C' and resid 158 through 162 removed outlier: 3.533A pdb=" N VAL C 127 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 143 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL C 125 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU C 126 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 245 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 128 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE C 243 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP C 130 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 195 through 197 removed outlier: 4.202A pdb=" N GLY C 116 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY C 260 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER C 118 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 258 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR C 86 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN C 284 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 10.257A pdb=" N GLY C 92 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N VAL C 282 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N GLY C 94 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N ALA C 280 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 162 removed outlier: 3.590A pdb=" N VAL D 127 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE D 143 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL D 125 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 242 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 195 through 197 removed outlier: 4.181A pdb=" N GLY D 116 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 5.190A 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: 5.436A pdb=" N LEU D 258 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N LYS D 91 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N ARG D 286 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY D 93 " --> pdb=" O ASN D 284 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 3.21 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: 3646 1.34 - 1.46: 2271 1.46 - 1.58: 5363 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 11342 Sorted by residual: bond pdb=" C1 NAG A1017 " pdb=" O5 NAG A1017 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" N ARG D 232 " pdb=" CA ARG D 232 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.24e-02 6.50e+03 4.98e+00 bond pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.23e-02 6.61e+03 3.43e+00 bond pdb=" C1 NAG B1018 " pdb=" C2 NAG B1018 " ideal model delta sigma weight residual 1.532 1.562 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG C1008 " pdb=" O5 NAG C1008 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 11337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 15281 2.27 - 4.53: 151 4.53 - 6.79: 14 6.79 - 9.06: 0 9.06 - 11.32: 1 Bond angle restraints: 15447 Sorted by residual: angle pdb=" C ARG C 232 " pdb=" CA ARG C 232 " pdb=" CB ARG C 232 " ideal model delta sigma weight residual 110.22 121.54 -11.32 1.67e+00 3.59e-01 4.60e+01 angle pdb=" C ARG D 232 " pdb=" CA ARG D 232 " pdb=" CB ARG D 232 " ideal model delta sigma weight residual 110.29 116.71 -6.42 1.64e+00 3.72e-01 1.53e+01 angle pdb=" C ARG C 232 " pdb=" N GLN C 233 " pdb=" CA GLN C 233 " ideal model delta sigma weight residual 122.87 129.13 -6.26 1.61e+00 3.86e-01 1.51e+01 angle pdb=" C GLY C 201 " pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta sigma weight residual 122.30 118.27 4.03 1.35e+00 5.49e-01 8.90e+00 angle pdb=" CD ARG C 232 " pdb=" NE ARG C 232 " pdb=" CZ ARG C 232 " ideal model delta sigma weight residual 124.40 128.34 -3.94 1.40e+00 5.10e-01 7.91e+00 ... (remaining 15442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5930 17.65 - 35.30: 626 35.30 - 52.95: 148 52.95 - 70.59: 16 70.59 - 88.24: 10 Dihedral angle restraints: 6730 sinusoidal: 2663 harmonic: 4067 Sorted by residual: 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 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" C ARG C 232 " pdb=" N ARG C 232 " pdb=" CA ARG C 232 " pdb=" CB ARG C 232 " ideal model delta harmonic sigma weight residual -122.60 -133.82 11.22 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA MET A 446 " pdb=" C MET A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1349 0.050 - 0.100: 274 0.100 - 0.151: 79 0.151 - 0.201: 2 0.201 - 0.251: 1 Chirality restraints: 1705 Sorted by residual: chirality pdb=" CA ARG C 232 " pdb=" N ARG C 232 " pdb=" C ARG C 232 " pdb=" CB ARG C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+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 2.32 0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" C1 NAG A1018 " pdb=" ND2 ASN A 522 " pdb=" C2 NAG A1018 " pdb=" O5 NAG A1018 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1702 not shown) Planarity restraints: 2027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1018 " 0.129 2.00e-02 2.50e+03 1.07e-01 1.43e+02 pdb=" C7 NAG A1018 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG A1018 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG A1018 " -0.172 2.00e-02 2.50e+03 pdb=" O7 NAG A1018 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.002 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" CG ASN A 98 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG A1017 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 522 " 0.006 2.00e-02 2.50e+03 3.04e-02 1.16e+01 pdb=" CG ASN B 522 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 522 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 522 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG B1018 " 0.031 2.00e-02 2.50e+03 ... (remaining 2024 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 172 2.67 - 3.23: 9997 3.23 - 3.78: 16712 3.78 - 4.34: 23199 4.34 - 4.90: 39378 Nonbonded interactions: 89458 Sorted by model distance: nonbonded pdb=" O3 NAG A1018 " pdb=" O7 NAG A1018 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" OD1 ASP C 111 " model vdw 2.226 3.040 nonbonded pdb=" O3 NAG B1018 " pdb=" O7 NAG B1018 " model vdw 2.242 3.040 nonbonded pdb=" ND2 ASN B 232 " pdb=" OD2 ASP B 356 " model vdw 2.243 3.120 nonbonded pdb=" O SER A 280 " pdb=" OG SER A 280 " model vdw 2.269 3.040 ... (remaining 89453 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' selection = (chain 'B' and (resid 40 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 150 or resid 175 through 357 or (r \ esid 358 and (name N or name CA or name C or name O or name CB )) or resid 359 t \ hrough 553 or (resid 564 through 565 and (name N or name CA or name C or name O \ or name CB )) or resid 566 through 608 or resid 1017 through 1018)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.130 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11352 Z= 0.127 Angle : 0.605 23.338 15473 Z= 0.294 Chirality : 0.044 0.251 1705 Planarity : 0.004 0.107 2021 Dihedral : 15.050 88.242 4128 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.35 % Allowed : 22.44 % Favored : 77.21 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1409 helix: 0.59 (0.29), residues: 348 sheet: 0.17 (0.33), residues: 285 loop : -1.04 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 122 HIS 0.004 0.001 HIS B 582 PHE 0.018 0.001 PHE B 565 TYR 0.014 0.001 TYR B 481 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 6) link_NAG-ASN : angle 8.24632 ( 18) hydrogen bonds : bond 0.16389 ( 369) hydrogen bonds : angle 7.25353 ( 1059) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.73254 ( 8) covalent geometry : bond 0.00272 (11342) covalent geometry : angle 0.53593 (15447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.4378 (mtt180) outliers start: 4 outliers final: 2 residues processed: 126 average time/residue: 0.2225 time to fit residues: 41.3647 Evaluate side-chains 123 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 375 ASN A 500 HIS B 553 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN D 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122343 restraints weight = 13086.741| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.02 r_work: 0.3163 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11352 Z= 0.228 Angle : 0.623 21.860 15473 Z= 0.312 Chirality : 0.048 0.517 1705 Planarity : 0.004 0.051 2021 Dihedral : 5.967 59.548 1681 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.12 % Allowed : 20.68 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1409 helix: 0.70 (0.29), residues: 359 sheet: -0.11 (0.31), residues: 309 loop : -1.19 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 122 HIS 0.005 0.001 HIS B 458 PHE 0.020 0.002 PHE B 262 TYR 0.013 0.002 TYR B 481 ARG 0.004 0.000 ARG B 441 Details of bonding type rmsd link_NAG-ASN : bond 0.00875 ( 6) link_NAG-ASN : angle 6.03811 ( 18) hydrogen bonds : bond 0.03789 ( 369) hydrogen bonds : angle 5.41222 ( 1059) SS BOND : bond 0.00475 ( 4) SS BOND : angle 1.18579 ( 8) covalent geometry : bond 0.00561 (11342) covalent geometry : angle 0.58827 (15447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7564 (mt) REVERT: A 454 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 503 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: B 82 ARG cc_start: 0.7455 (mtm110) cc_final: 0.7208 (mtm180) REVERT: B 276 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 336 GLU cc_start: 0.7222 (mp0) cc_final: 0.6492 (mp0) REVERT: D 232 ARG cc_start: 0.5997 (OUTLIER) cc_final: 0.4171 (mtt-85) outliers start: 47 outliers final: 23 residues processed: 175 average time/residue: 0.2345 time to fit residues: 59.0084 Evaluate side-chains 150 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN D 103 ASN D 153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.176202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126411 restraints weight = 13236.422| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.97 r_work: 0.3199 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11352 Z= 0.101 Angle : 0.527 18.945 15473 Z= 0.262 Chirality : 0.046 0.761 1705 Planarity : 0.004 0.048 2021 Dihedral : 5.367 56.503 1681 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.07 % Allowed : 22.44 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1409 helix: 0.98 (0.30), residues: 362 sheet: -0.07 (0.31), residues: 309 loop : -1.07 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 122 HIS 0.003 0.001 HIS B 582 PHE 0.014 0.001 PHE A 413 TYR 0.012 0.001 TYR A 481 ARG 0.006 0.000 ARG B 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00799 ( 6) link_NAG-ASN : angle 5.26907 ( 18) hydrogen bonds : bond 0.03119 ( 369) hydrogen bonds : angle 5.04279 ( 1059) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.81999 ( 8) covalent geometry : bond 0.00235 (11342) covalent geometry : angle 0.49556 (15447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8360 (mtmm) REVERT: B 82 ARG cc_start: 0.7464 (mtm110) cc_final: 0.7222 (mtm180) REVERT: B 336 GLU cc_start: 0.7318 (mp0) cc_final: 0.6571 (mp0) REVERT: B 386 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8410 (mt-10) REVERT: D 232 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.4227 (mtt-85) outliers start: 35 outliers final: 22 residues processed: 155 average time/residue: 0.2425 time to fit residues: 55.2433 Evaluate side-chains 145 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 37 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN D 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123682 restraints weight = 13090.908| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.15 r_work: 0.3183 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11352 Z= 0.167 Angle : 0.547 8.222 15473 Z= 0.277 Chirality : 0.044 0.175 1705 Planarity : 0.004 0.049 2021 Dihedral : 5.251 57.183 1681 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.21 % Allowed : 21.30 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1409 helix: 0.94 (0.29), residues: 362 sheet: -0.14 (0.31), residues: 309 loop : -1.06 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.004 0.001 HIS B 458 PHE 0.017 0.002 PHE A 413 TYR 0.014 0.001 TYR A 481 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 6) link_NAG-ASN : angle 3.08309 ( 18) hydrogen bonds : bond 0.03292 ( 369) hydrogen bonds : angle 4.96847 ( 1059) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.99656 ( 8) covalent geometry : bond 0.00415 (11342) covalent geometry : angle 0.53718 (15447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8445 (mtmm) REVERT: B 82 ARG cc_start: 0.7476 (mtm110) cc_final: 0.7273 (mtm180) REVERT: B 336 GLU cc_start: 0.7442 (mp0) cc_final: 0.6711 (mp0) REVERT: B 386 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8615 (mt-10) REVERT: B 470 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8313 (mp) REVERT: D 232 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.4279 (mtt-85) outliers start: 48 outliers final: 34 residues processed: 163 average time/residue: 0.2213 time to fit residues: 52.7343 Evaluate side-chains 157 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 84 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125906 restraints weight = 13100.066| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.91 r_work: 0.3221 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11352 Z= 0.114 Angle : 0.512 7.004 15473 Z= 0.259 Chirality : 0.043 0.164 1705 Planarity : 0.004 0.048 2021 Dihedral : 5.038 58.222 1677 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.94 % Allowed : 21.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1409 helix: 1.05 (0.29), residues: 362 sheet: -0.11 (0.31), residues: 309 loop : -0.99 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 122 HIS 0.005 0.001 HIS B 582 PHE 0.016 0.001 PHE B 565 TYR 0.019 0.001 TYR B 484 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 6) link_NAG-ASN : angle 2.65925 ( 18) hydrogen bonds : bond 0.03032 ( 369) hydrogen bonds : angle 4.83838 ( 1059) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.89297 ( 8) covalent geometry : bond 0.00277 (11342) covalent geometry : angle 0.50368 (15447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8415 (mtmm) REVERT: A 503 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: B 336 GLU cc_start: 0.7411 (mp0) cc_final: 0.6702 (mp0) REVERT: B 386 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8400 (mt-10) REVERT: D 232 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.4237 (mtt-85) outliers start: 45 outliers final: 35 residues processed: 152 average time/residue: 0.2203 time to fit residues: 49.3900 Evaluate side-chains 155 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.173114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122928 restraints weight = 13212.789| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.21 r_work: 0.3174 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11352 Z= 0.199 Angle : 0.560 6.798 15473 Z= 0.284 Chirality : 0.045 0.163 1705 Planarity : 0.004 0.048 2021 Dihedral : 5.121 58.315 1677 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.65 % Allowed : 21.03 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1409 helix: 0.90 (0.29), residues: 362 sheet: -0.23 (0.31), residues: 309 loop : -1.05 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 538 HIS 0.005 0.001 HIS B 458 PHE 0.019 0.002 PHE A 262 TYR 0.016 0.002 TYR B 484 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 6) link_NAG-ASN : angle 2.61884 ( 18) hydrogen bonds : bond 0.03399 ( 369) hydrogen bonds : angle 4.90037 ( 1059) SS BOND : bond 0.00386 ( 4) SS BOND : angle 1.12106 ( 8) covalent geometry : bond 0.00494 (11342) covalent geometry : angle 0.55237 (15447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7559 (tttp) REVERT: A 389 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8402 (mtmm) REVERT: A 503 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: B 386 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8490 (mt-10) REVERT: B 470 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8210 (mp) REVERT: D 232 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.4338 (mtt-85) outliers start: 53 outliers final: 36 residues processed: 167 average time/residue: 0.2147 time to fit residues: 52.5672 Evaluate side-chains 162 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 389 LYS 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 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.0270 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124671 restraints weight = 13311.324| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.00 r_work: 0.3209 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11352 Z= 0.126 Angle : 0.520 6.858 15473 Z= 0.263 Chirality : 0.043 0.154 1705 Planarity : 0.004 0.047 2021 Dihedral : 4.910 59.903 1677 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.21 % Allowed : 21.47 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1409 helix: 1.02 (0.29), residues: 363 sheet: -0.19 (0.31), residues: 309 loop : -0.98 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.004 0.001 HIS B 582 PHE 0.016 0.001 PHE B 565 TYR 0.013 0.001 TYR B 484 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 6) link_NAG-ASN : angle 2.60621 ( 18) hydrogen bonds : bond 0.03045 ( 369) hydrogen bonds : angle 4.75145 ( 1059) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.91959 ( 8) covalent geometry : bond 0.00308 (11342) covalent geometry : angle 0.51184 (15447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: A 503 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: B 470 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 232 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.4262 (mtt-85) outliers start: 48 outliers final: 38 residues processed: 160 average time/residue: 0.2169 time to fit residues: 50.8056 Evaluate side-chains 158 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 72 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 389 LYS 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 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124955 restraints weight = 13095.292| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.95 r_work: 0.3180 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11352 Z= 0.134 Angle : 0.524 6.804 15473 Z= 0.265 Chirality : 0.043 0.155 1705 Planarity : 0.004 0.047 2021 Dihedral : 4.841 59.000 1677 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.38 % Allowed : 21.30 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1409 helix: 1.04 (0.29), residues: 363 sheet: -0.22 (0.31), residues: 309 loop : -0.96 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 122 HIS 0.005 0.001 HIS B 582 PHE 0.016 0.001 PHE A 413 TYR 0.012 0.001 TYR B 484 ARG 0.007 0.000 ARG B 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 6) link_NAG-ASN : angle 2.64803 ( 18) hydrogen bonds : bond 0.03042 ( 369) hydrogen bonds : angle 4.71796 ( 1059) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.90502 ( 8) covalent geometry : bond 0.00331 (11342) covalent geometry : angle 0.51608 (15447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7537 (mt) REVERT: A 389 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8432 (mtmm) REVERT: A 503 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: B 470 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 232 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4315 (mtt-85) outliers start: 50 outliers final: 42 residues processed: 159 average time/residue: 0.1990 time to fit residues: 47.1794 Evaluate side-chains 159 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 389 LYS 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 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 100 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126791 restraints weight = 13151.236| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.91 r_work: 0.3235 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11352 Z= 0.098 Angle : 0.506 6.831 15473 Z= 0.255 Chirality : 0.043 0.149 1705 Planarity : 0.004 0.046 2021 Dihedral : 4.689 57.952 1677 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.59 % Allowed : 22.17 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1409 helix: 1.17 (0.29), residues: 361 sheet: -0.09 (0.32), residues: 303 loop : -0.95 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 122 HIS 0.004 0.000 HIS B 582 PHE 0.015 0.001 PHE D 178 TYR 0.013 0.001 TYR B 484 ARG 0.007 0.000 ARG B 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 6) link_NAG-ASN : angle 2.51596 ( 18) hydrogen bonds : bond 0.02855 ( 369) hydrogen bonds : angle 4.62643 ( 1059) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.80937 ( 8) covalent geometry : bond 0.00236 (11342) covalent geometry : angle 0.49839 (15447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8438 (mtmm) REVERT: A 425 ASP cc_start: 0.7481 (p0) cc_final: 0.7276 (p0) REVERT: A 503 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: B 189 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7952 (mtt) REVERT: B 470 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8249 (mp) outliers start: 41 outliers final: 36 residues processed: 150 average time/residue: 0.2107 time to fit residues: 47.1387 Evaluate side-chains 156 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 LYS 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 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN D 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127058 restraints weight = 13113.353| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.90 r_work: 0.3243 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11352 Z= 0.103 Angle : 0.507 6.714 15473 Z= 0.256 Chirality : 0.043 0.147 1705 Planarity : 0.004 0.047 2021 Dihedral : 4.348 38.882 1673 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.94 % Allowed : 22.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1409 helix: 1.12 (0.29), residues: 367 sheet: -0.02 (0.32), residues: 303 loop : -0.92 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.004 0.000 HIS B 582 PHE 0.016 0.001 PHE D 178 TYR 0.015 0.001 TYR B 376 ARG 0.006 0.000 ARG B 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 6) link_NAG-ASN : angle 2.64252 ( 18) hydrogen bonds : bond 0.02821 ( 369) hydrogen bonds : angle 4.58713 ( 1059) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.83651 ( 8) covalent geometry : bond 0.00249 (11342) covalent geometry : angle 0.49934 (15447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6722 (mp) REVERT: A 389 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8452 (mtmm) REVERT: A 503 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: B 189 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: B 470 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8278 (mp) outliers start: 45 outliers final: 36 residues processed: 153 average time/residue: 0.2042 time to fit residues: 47.1007 Evaluate side-chains 152 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 LYS 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 470 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 373 PHE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125132 restraints weight = 13167.949| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.96 r_work: 0.3190 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11352 Z= 0.154 Angle : 0.531 6.514 15473 Z= 0.269 Chirality : 0.044 0.152 1705 Planarity : 0.004 0.047 2021 Dihedral : 4.424 41.308 1673 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.03 % Allowed : 21.47 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1409 helix: 1.10 (0.29), residues: 361 sheet: -0.13 (0.32), residues: 303 loop : -0.96 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 538 HIS 0.004 0.001 HIS B 458 PHE 0.017 0.002 PHE A 413 TYR 0.013 0.001 TYR A 481 ARG 0.006 0.000 ARG A 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 2.56308 ( 18) hydrogen bonds : bond 0.03082 ( 369) hydrogen bonds : angle 4.64996 ( 1059) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.98778 ( 8) covalent geometry : bond 0.00381 (11342) covalent geometry : angle 0.52338 (15447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5557.98 seconds wall clock time: 95 minutes 53.26 seconds (5753.26 seconds total)