Starting phenix.real_space_refine on Sun Jul 27 22:17:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nf7_12297/07_2025/7nf7_12297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nf7_12297/07_2025/7nf7_12297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nf7_12297/07_2025/7nf7_12297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nf7_12297/07_2025/7nf7_12297.map" model { file = "/net/cci-nas-00/data/ceres_data/7nf7_12297/07_2025/7nf7_12297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nf7_12297/07_2025/7nf7_12297.cif" } resolution = 2.68 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= 0.000 sd= 0.003 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 46 5.16 5 C 6114 2.51 5 N 1624 2.21 5 O 1856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 9642 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4708 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 551} 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: 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: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 4708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4708 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 551} Chain: "E" 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: "F" 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: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.29, per 1000 atoms: 0.76 Number of scatterers: 9642 At special positions: 0 Unit cell: (130.729, 121.94, 90.0819, 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 46 16.00 O 1856 8.00 N 1624 7.00 C 6114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.04 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 666 " distance=2.04 Simple disulfide: pdb=" SG CYS D 673 " - pdb=" SG CYS D 685 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 702 " - " ASN A 513 " " NAG A 703 " - " ASN A 246 " " NAG A 704 " - " ASN A 228 " " NAG A 705 " - " ASN A 523 " " NAG B 1 " - " ASN A 332 " " NAG C 1 " - " ASN A 261 " " NAG D 702 " - " ASN D 513 " " NAG D 703 " - " ASN D 246 " " NAG D 704 " - " ASN D 228 " " NAG D 705 " - " ASN D 523 " " NAG E 1 " - " ASN D 332 " " NAG F 1 " - " ASN D 261 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 35.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.909A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.759A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.573A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.501A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.610A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.838A pdb=" N GLN A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.684A pdb=" N TYR A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.779A pdb=" N VAL A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.785A pdb=" N ILE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.521A pdb=" N VAL A 395 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.501A pdb=" N VAL A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.984A pdb=" N SER A 505 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 530 through 535 removed outlier: 4.389A pdb=" N HIS A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 561 Processing helix chain 'A' and resid 587 through 590 removed outlier: 4.050A pdb=" N ASN A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.892A pdb=" N MET A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.909A pdb=" N GLY D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.759A pdb=" N PHE D 131 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 removed outlier: 3.573A pdb=" N LYS D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.501A pdb=" N ILE D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 188 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.610A pdb=" N THR D 234 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP D 235 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 306 removed outlier: 3.838A pdb=" N GLN D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.684A pdb=" N TYR D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.779A pdb=" N VAL D 340 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.785A pdb=" N ILE D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.521A pdb=" N VAL D 395 " --> pdb=" O GLU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 435 removed outlier: 3.501A pdb=" N VAL D 427 " --> pdb=" O SER D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 458 through 460 No H-bonds generated for 'chain 'D' and resid 458 through 460' Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.984A pdb=" N SER D 505 " --> pdb=" O THR D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 519 Processing helix chain 'D' and resid 530 through 535 removed outlier: 4.389A pdb=" N HIS D 534 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 547 through 561 Processing helix chain 'D' and resid 587 through 590 removed outlier: 4.050A pdb=" N ASN D 590 " --> pdb=" O ASP D 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 587 through 590' Processing helix chain 'D' and resid 606 through 612 removed outlier: 3.892A pdb=" N MET D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing sheet with id=1, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.697A pdb=" N MET A 381 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 409 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 383 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 310 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.038A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.606A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.912A pdb=" N ASN A 243 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.165A pdb=" N ALA A 329 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 632 through 634 removed outlier: 3.506A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=8, first strand: chain 'A' and resid 673 through 674 Processing sheet with id=9, first strand: chain 'D' and resid 407 through 409 removed outlier: 6.697A pdb=" N MET D 381 " --> pdb=" O PHE D 407 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE D 409 " --> pdb=" O MET D 381 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR D 383 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY D 310 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP D 443 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR D 479 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.038A pdb=" N LYS D 167 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA D 176 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 239 through 240 removed outlier: 3.606A pdb=" N GLN D 272 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 243 through 245 removed outlier: 3.912A pdb=" N ASN D 243 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 329 through 330 removed outlier: 4.165A pdb=" N ALA D 329 " --> pdb=" O HIS D 347 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'D' and resid 632 through 634 removed outlier: 3.506A pdb=" N ARG D 619 " --> pdb=" O GLU D 649 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 647 " --> pdb=" O ARG D 621 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 623 " --> pdb=" O GLY D 645 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY D 645 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 603 through 605 Processing sheet with id=16, first strand: chain 'D' and resid 673 through 674 298 hydrogen bonds defined for protein. 756 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: 3.05 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2996 1.33 - 1.45: 1804 1.45 - 1.57: 5020 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 9898 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG D 703 " pdb=" O5 NAG D 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG D 704 " pdb=" O5 NAG D 704 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 9893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 13228 2.24 - 4.49: 182 4.49 - 6.73: 18 6.73 - 8.97: 4 8.97 - 11.22: 2 Bond angle restraints: 13434 Sorted by residual: angle pdb=" C PHE A 173 " pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C PHE D 173 " pdb=" N ARG D 174 " pdb=" CA ARG D 174 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 angle pdb=" CA PHE D 173 " pdb=" C PHE D 173 " pdb=" N ARG D 174 " ideal model delta sigma weight residual 116.21 111.96 4.25 1.29e+00 6.01e-01 1.08e+01 angle pdb=" CA PHE A 173 " pdb=" C PHE A 173 " pdb=" N ARG A 174 " ideal model delta sigma weight residual 116.21 111.96 4.25 1.29e+00 6.01e-01 1.08e+01 angle pdb=" C GLU D 562 " pdb=" N LEU D 563 " pdb=" CA LEU D 563 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 ... (remaining 13429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5224 17.99 - 35.97: 580 35.97 - 53.96: 176 53.96 - 71.95: 44 71.95 - 89.94: 16 Dihedral angle restraints: 6040 sinusoidal: 2670 harmonic: 3370 Sorted by residual: dihedral pdb=" CA ARG D 174 " pdb=" C ARG D 174 " pdb=" N HIS D 175 " pdb=" CA HIS D 175 " ideal model delta harmonic sigma weight residual 180.00 135.39 44.61 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N HIS A 175 " pdb=" CA HIS A 175 " ideal model delta harmonic sigma weight residual 180.00 135.39 44.61 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA ASN A 575 " pdb=" C ASN A 575 " pdb=" N ASP A 576 " pdb=" CA ASP A 576 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1172 0.057 - 0.114: 266 0.114 - 0.171: 18 0.171 - 0.228: 4 0.228 - 0.285: 2 Chirality restraints: 1462 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 1.03e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 1.03e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1459 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 513 " 0.036 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 513 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 513 " -0.285 2.00e-02 2.50e+03 pdb=" ND2 ASN A 513 " 0.553 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 513 " -0.036 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN D 513 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN D 513 " 0.285 2.00e-02 2.50e+03 pdb=" ND2 ASN D 513 " -0.553 2.00e-02 2.50e+03 pdb=" C1 NAG D 702 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 246 " 0.090 2.00e-02 2.50e+03 3.22e-01 1.30e+03 pdb=" CG ASN D 246 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN D 246 " 0.195 2.00e-02 2.50e+03 pdb=" ND2 ASN D 246 " -0.571 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " 0.374 2.00e-02 2.50e+03 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3358 2.85 - 3.36: 8349 3.36 - 3.87: 16324 3.87 - 4.39: 20480 4.39 - 4.90: 33221 Nonbonded interactions: 81732 Sorted by model distance: nonbonded pdb=" OG SER A 226 " pdb=" O TYR A 233 " model vdw 2.336 3.040 nonbonded pdb=" OG SER D 226 " pdb=" O TYR D 233 " model vdw 2.336 3.040 nonbonded pdb=" NH1 ARG A 574 " pdb=" OD1 ASP A 576 " model vdw 2.349 3.120 nonbonded pdb=" NH1 ARG D 574 " pdb=" OD1 ASP D 576 " model vdw 2.349 3.120 nonbonded pdb=" OH TYR D 151 " pdb=" OE2 GLU D 483 " model vdw 2.365 3.040 ... (remaining 81727 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 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.400 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 9920 Z= 0.276 Angle : 0.855 22.049 13494 Z= 0.430 Chirality : 0.048 0.285 1462 Planarity : 0.005 0.055 1714 Dihedral : 17.227 89.937 3858 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.11 % Rotamer: Outliers : 6.53 % Allowed : 18.43 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.11 (0.21), residues: 1146 helix: -3.42 (0.18), residues: 272 sheet: -1.83 (0.34), residues: 186 loop : -1.53 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 443 HIS 0.006 0.001 HIS D 348 PHE 0.019 0.002 PHE A 278 TYR 0.019 0.002 TYR A 259 ARG 0.004 0.001 ARG A 574 Details of bonding type rmsd link_NAG-ASN : bond 0.05611 ( 12) link_NAG-ASN : angle 6.44873 ( 36) link_BETA1-4 : bond 0.02711 ( 4) link_BETA1-4 : angle 11.34866 ( 12) hydrogen bonds : bond 0.28784 ( 298) hydrogen bonds : angle 8.26668 ( 756) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.55753 ( 12) covalent geometry : bond 0.00579 ( 9898) covalent geometry : angle 0.71103 (13434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.8098 (mmm) cc_final: 0.7795 (mmt) REVERT: A 546 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6311 (ptp-110) REVERT: A 589 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 590 ASN cc_start: 0.6512 (t0) cc_final: 0.6274 (p0) REVERT: A 613 ASN cc_start: 0.6707 (t0) cc_final: 0.6223 (t0) REVERT: A 619 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7210 (ttm110) REVERT: A 621 ARG cc_start: 0.8216 (tpt90) cc_final: 0.7701 (tpt-90) REVERT: A 634 ASP cc_start: 0.7425 (p0) cc_final: 0.7202 (t0) REVERT: D 279 MET cc_start: 0.8099 (mmm) cc_final: 0.7795 (mmt) REVERT: D 546 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6312 (ptp-110) REVERT: D 589 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7320 (mp) REVERT: D 590 ASN cc_start: 0.6513 (t0) cc_final: 0.6277 (p0) REVERT: D 613 ASN cc_start: 0.6715 (t0) cc_final: 0.6236 (t0) REVERT: D 619 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7211 (ttm110) REVERT: D 621 ARG cc_start: 0.8220 (tpt90) cc_final: 0.7702 (tpt-90) REVERT: D 634 ASP cc_start: 0.7427 (p0) cc_final: 0.7200 (t0) outliers start: 68 outliers final: 44 residues processed: 225 average time/residue: 1.2080 time to fit residues: 291.0001 Evaluate side-chains 203 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 181 GLN A 201 HIS A 220 HIS A 243 ASN A 282 GLN A 301 GLN A 335 GLN A 345 GLN A 366 GLN A 370 GLN A 422 ASN A 434 ASN A 442 ASN A 463 ASN A 466 ASN A 497 ASN A 510 GLN A 561 ASN A 590 ASN A 606 ASN D 146 GLN D 181 GLN D 201 HIS D 220 HIS D 243 ASN D 282 GLN D 301 GLN D 335 GLN D 345 GLN D 366 GLN D 370 GLN D 422 ASN D 434 ASN D 442 ASN D 463 ASN D 466 ASN D 497 ASN D 510 GLN D 561 ASN D 606 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.093367 restraints weight = 10579.837| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.28 r_work: 0.2718 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9920 Z= 0.169 Angle : 0.816 15.268 13494 Z= 0.381 Chirality : 0.053 0.511 1462 Planarity : 0.005 0.049 1714 Dihedral : 11.157 83.312 1688 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 3.84 % Allowed : 20.35 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.24), residues: 1146 helix: -1.03 (0.27), residues: 304 sheet: -1.37 (0.36), residues: 186 loop : -1.02 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 443 HIS 0.005 0.001 HIS D 175 PHE 0.016 0.002 PHE D 278 TYR 0.016 0.002 TYR A 259 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00939 ( 12) link_NAG-ASN : angle 7.47486 ( 36) link_BETA1-4 : bond 0.01328 ( 4) link_BETA1-4 : angle 6.30693 ( 12) hydrogen bonds : bond 0.05883 ( 298) hydrogen bonds : angle 5.17116 ( 756) SS BOND : bond 0.00333 ( 6) SS BOND : angle 1.49436 ( 12) covalent geometry : bond 0.00377 ( 9898) covalent geometry : angle 0.69428 (13434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7884 (t70) cc_final: 0.7407 (t70) REVERT: A 377 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7959 (mtp180) REVERT: A 546 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7091 (ptp90) REVERT: A 589 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7469 (mp) REVERT: A 590 ASN cc_start: 0.6778 (t0) cc_final: 0.6422 (p0) REVERT: A 613 ASN cc_start: 0.6658 (t0) cc_final: 0.6098 (t0) REVERT: A 621 ARG cc_start: 0.8373 (tpt90) cc_final: 0.7757 (tpt-90) REVERT: A 634 ASP cc_start: 0.7350 (p0) cc_final: 0.6838 (t0) REVERT: A 658 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6713 (mmp-170) REVERT: D 377 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7968 (mtp180) REVERT: D 546 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7086 (ptp90) REVERT: D 589 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7462 (mp) REVERT: D 590 ASN cc_start: 0.6723 (t0) cc_final: 0.6362 (p0) REVERT: D 613 ASN cc_start: 0.6655 (t0) cc_final: 0.6099 (t0) REVERT: D 621 ARG cc_start: 0.8386 (tpt90) cc_final: 0.7768 (tpt-90) REVERT: D 634 ASP cc_start: 0.7339 (p0) cc_final: 0.6826 (t0) REVERT: D 658 ARG cc_start: 0.7129 (mmm-85) cc_final: 0.6715 (mmp-170) outliers start: 40 outliers final: 22 residues processed: 200 average time/residue: 1.4336 time to fit residues: 307.4164 Evaluate side-chains 183 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN A 561 ASN D 301 GLN D 516 ASN D 561 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.095017 restraints weight = 10631.242| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.28 r_work: 0.2744 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9920 Z= 0.148 Angle : 0.738 14.900 13494 Z= 0.349 Chirality : 0.049 0.385 1462 Planarity : 0.004 0.044 1714 Dihedral : 9.774 80.553 1654 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 5.18 % Allowed : 20.35 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1146 helix: -0.03 (0.30), residues: 294 sheet: -0.95 (0.37), residues: 176 loop : -0.91 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 303 HIS 0.005 0.001 HIS A 175 PHE 0.015 0.002 PHE A 278 TYR 0.015 0.002 TYR A 259 ARG 0.002 0.000 ARG D 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 12) link_NAG-ASN : angle 6.52778 ( 36) link_BETA1-4 : bond 0.01402 ( 4) link_BETA1-4 : angle 6.06738 ( 12) hydrogen bonds : bond 0.05170 ( 298) hydrogen bonds : angle 4.70533 ( 756) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.91449 ( 12) covalent geometry : bond 0.00331 ( 9898) covalent geometry : angle 0.63199 (13434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.8016 (t70) cc_final: 0.7608 (m90) REVERT: A 298 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: A 336 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7744 (mt) REVERT: A 423 SER cc_start: 0.8226 (t) cc_final: 0.7899 (m) REVERT: A 433 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7883 (pt0) REVERT: A 546 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7085 (ptp90) REVERT: A 590 ASN cc_start: 0.6588 (t0) cc_final: 0.6292 (p0) REVERT: A 613 ASN cc_start: 0.6669 (t0) cc_final: 0.6110 (t0) REVERT: A 621 ARG cc_start: 0.8364 (tpt90) cc_final: 0.7817 (tpt-90) REVERT: A 634 ASP cc_start: 0.7162 (p0) cc_final: 0.6758 (t0) REVERT: A 658 ARG cc_start: 0.7139 (mmm-85) cc_final: 0.6736 (mmp-170) REVERT: D 298 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: D 336 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7737 (mt) REVERT: D 423 SER cc_start: 0.8222 (t) cc_final: 0.7894 (m) REVERT: D 433 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7882 (pt0) REVERT: D 546 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7074 (ptp90) REVERT: D 590 ASN cc_start: 0.6601 (t0) cc_final: 0.6307 (p0) REVERT: D 613 ASN cc_start: 0.6664 (t0) cc_final: 0.6098 (t0) REVERT: D 621 ARG cc_start: 0.8380 (tpt90) cc_final: 0.7830 (tpt-90) REVERT: D 634 ASP cc_start: 0.7141 (p0) cc_final: 0.6734 (t0) REVERT: D 658 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6742 (mmp-170) outliers start: 54 outliers final: 27 residues processed: 201 average time/residue: 1.1613 time to fit residues: 250.8277 Evaluate side-chains 194 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 561 ASN D 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.093529 restraints weight = 10565.986| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.27 r_work: 0.2718 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9920 Z= 0.186 Angle : 0.757 14.023 13494 Z= 0.363 Chirality : 0.051 0.356 1462 Planarity : 0.005 0.045 1714 Dihedral : 9.554 81.504 1640 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.46 % Rotamer: Outliers : 5.09 % Allowed : 20.15 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.93 (0.24), residues: 1146 helix: 0.02 (0.30), residues: 290 sheet: -0.88 (0.37), residues: 176 loop : -0.78 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 443 HIS 0.006 0.001 HIS A 348 PHE 0.016 0.002 PHE D 278 TYR 0.017 0.002 TYR A 259 ARG 0.003 0.000 ARG D 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 12) link_NAG-ASN : angle 5.93634 ( 36) link_BETA1-4 : bond 0.01343 ( 4) link_BETA1-4 : angle 5.88988 ( 12) hydrogen bonds : bond 0.05398 ( 298) hydrogen bonds : angle 4.73518 ( 756) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.74824 ( 12) covalent geometry : bond 0.00434 ( 9898) covalent geometry : angle 0.66891 (13434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.9088 (pttm) cc_final: 0.8858 (pttp) REVERT: A 336 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7707 (mt) REVERT: A 546 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7057 (ptp90) REVERT: A 589 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7597 (mp) REVERT: A 590 ASN cc_start: 0.6587 (t0) cc_final: 0.6327 (p0) REVERT: A 613 ASN cc_start: 0.6692 (t0) cc_final: 0.6124 (t0) REVERT: A 621 ARG cc_start: 0.8341 (tpt90) cc_final: 0.7771 (tpt-90) REVERT: A 634 ASP cc_start: 0.7189 (p0) cc_final: 0.6807 (t70) REVERT: A 658 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6736 (mmp-170) REVERT: D 280 LYS cc_start: 0.9091 (pttm) cc_final: 0.8862 (pttp) REVERT: D 336 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7699 (mt) REVERT: D 546 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7037 (ptp90) REVERT: D 589 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7596 (mp) REVERT: D 590 ASN cc_start: 0.6568 (t0) cc_final: 0.6313 (p0) REVERT: D 613 ASN cc_start: 0.6686 (t0) cc_final: 0.6114 (t0) REVERT: D 621 ARG cc_start: 0.8352 (tpt90) cc_final: 0.7781 (tpt-90) REVERT: D 634 ASP cc_start: 0.7175 (p0) cc_final: 0.6794 (t70) REVERT: D 658 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6742 (mmp-170) outliers start: 53 outliers final: 32 residues processed: 199 average time/residue: 1.1833 time to fit residues: 252.4239 Evaluate side-chains 192 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.0270 chunk 90 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN D 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.096169 restraints weight = 10460.332| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.26 r_work: 0.2754 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9920 Z= 0.122 Angle : 0.685 13.874 13494 Z= 0.331 Chirality : 0.049 0.342 1462 Planarity : 0.004 0.043 1714 Dihedral : 9.110 79.955 1640 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.46 % Rotamer: Outliers : 3.93 % Allowed : 21.69 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.94 (0.25), residues: 1146 helix: 0.20 (0.31), residues: 294 sheet: -1.28 (0.34), residues: 212 loop : -0.71 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 303 HIS 0.006 0.001 HIS A 175 PHE 0.013 0.001 PHE A 278 TYR 0.015 0.001 TYR D 259 ARG 0.001 0.000 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 12) link_NAG-ASN : angle 5.35001 ( 36) link_BETA1-4 : bond 0.01283 ( 4) link_BETA1-4 : angle 5.70044 ( 12) hydrogen bonds : bond 0.04340 ( 298) hydrogen bonds : angle 4.49959 ( 756) SS BOND : bond 0.00412 ( 6) SS BOND : angle 1.87097 ( 12) covalent geometry : bond 0.00270 ( 9898) covalent geometry : angle 0.60165 (13434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8827 (pttp) REVERT: A 336 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7667 (mt) REVERT: A 423 SER cc_start: 0.8265 (t) cc_final: 0.8028 (m) REVERT: A 512 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8331 (p0) REVERT: A 546 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6974 (ptp90) REVERT: A 590 ASN cc_start: 0.6540 (t0) cc_final: 0.6314 (p0) REVERT: A 613 ASN cc_start: 0.6834 (t0) cc_final: 0.6181 (t0) REVERT: A 621 ARG cc_start: 0.8290 (tpt90) cc_final: 0.7835 (tpt-90) REVERT: A 634 ASP cc_start: 0.7208 (p0) cc_final: 0.6848 (t70) REVERT: A 658 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6707 (mmp-170) REVERT: D 280 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8828 (pttp) REVERT: D 336 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7661 (mt) REVERT: D 423 SER cc_start: 0.8273 (t) cc_final: 0.8038 (m) REVERT: D 512 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (p0) REVERT: D 546 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6969 (ptp90) REVERT: D 590 ASN cc_start: 0.6677 (t0) cc_final: 0.6399 (p0) REVERT: D 613 ASN cc_start: 0.6822 (t0) cc_final: 0.6165 (t0) REVERT: D 621 ARG cc_start: 0.8302 (tpt90) cc_final: 0.7841 (tpt-90) REVERT: D 634 ASP cc_start: 0.7203 (p0) cc_final: 0.6841 (t70) REVERT: D 658 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6705 (mmp-170) outliers start: 41 outliers final: 25 residues processed: 179 average time/residue: 1.2950 time to fit residues: 248.2384 Evaluate side-chains 181 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 512 ASP Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.0000 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN D 510 GLN D 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.094813 restraints weight = 10512.486| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.23 r_work: 0.2729 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9920 Z= 0.154 Angle : 0.707 12.874 13494 Z= 0.343 Chirality : 0.050 0.341 1462 Planarity : 0.004 0.041 1714 Dihedral : 8.834 79.528 1634 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.32 % Allowed : 21.11 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.92 (0.25), residues: 1146 helix: 0.23 (0.30), residues: 294 sheet: -1.40 (0.34), residues: 214 loop : -0.65 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 443 HIS 0.005 0.001 HIS A 348 PHE 0.015 0.002 PHE D 407 TYR 0.017 0.002 TYR A 259 ARG 0.002 0.000 ARG D 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 12) link_NAG-ASN : angle 5.39393 ( 36) link_BETA1-4 : bond 0.01345 ( 4) link_BETA1-4 : angle 5.60396 ( 12) hydrogen bonds : bond 0.04835 ( 298) hydrogen bonds : angle 4.49104 ( 756) SS BOND : bond 0.00398 ( 6) SS BOND : angle 1.36398 ( 12) covalent geometry : bond 0.00353 ( 9898) covalent geometry : angle 0.62812 (13434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.9112 (pttm) cc_final: 0.8800 (pttp) REVERT: A 336 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7681 (mt) REVERT: A 423 SER cc_start: 0.8241 (t) cc_final: 0.7978 (m) REVERT: A 546 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7134 (ptp90) REVERT: A 590 ASN cc_start: 0.6537 (t0) cc_final: 0.6308 (p0) REVERT: A 613 ASN cc_start: 0.6700 (t0) cc_final: 0.6133 (t0) REVERT: A 621 ARG cc_start: 0.8318 (tpt90) cc_final: 0.7808 (tpt-90) REVERT: A 634 ASP cc_start: 0.7214 (p0) cc_final: 0.6841 (t70) REVERT: A 658 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6706 (mmp-170) REVERT: D 280 LYS cc_start: 0.9115 (pttm) cc_final: 0.8800 (pttp) REVERT: D 336 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7694 (mt) REVERT: D 423 SER cc_start: 0.8228 (t) cc_final: 0.7963 (m) REVERT: D 546 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7130 (ptp90) REVERT: D 590 ASN cc_start: 0.6660 (t0) cc_final: 0.6370 (p0) REVERT: D 613 ASN cc_start: 0.6689 (t0) cc_final: 0.6119 (t0) REVERT: D 621 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7809 (tpt-90) REVERT: D 634 ASP cc_start: 0.7209 (p0) cc_final: 0.6834 (t70) REVERT: D 658 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6714 (mmp-170) outliers start: 45 outliers final: 30 residues processed: 191 average time/residue: 1.2586 time to fit residues: 257.9563 Evaluate side-chains 184 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 670 ASN D 561 ASN D 670 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095980 restraints weight = 10605.155| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.26 r_work: 0.2741 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9920 Z= 0.142 Angle : 0.683 12.163 13494 Z= 0.334 Chirality : 0.049 0.335 1462 Planarity : 0.004 0.042 1714 Dihedral : 8.701 79.690 1634 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.89 % Allowed : 20.63 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.88 (0.25), residues: 1146 helix: 0.28 (0.31), residues: 294 sheet: -1.31 (0.34), residues: 212 loop : -0.66 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 443 HIS 0.005 0.001 HIS A 175 PHE 0.014 0.002 PHE A 278 TYR 0.015 0.001 TYR D 259 ARG 0.002 0.000 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 12) link_NAG-ASN : angle 5.00284 ( 36) link_BETA1-4 : bond 0.01344 ( 4) link_BETA1-4 : angle 5.49940 ( 12) hydrogen bonds : bond 0.04553 ( 298) hydrogen bonds : angle 4.43118 ( 756) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.09879 ( 12) covalent geometry : bond 0.00321 ( 9898) covalent geometry : angle 0.61098 (13434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6572 (mpp80) REVERT: A 280 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8800 (pttp) REVERT: A 294 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: A 336 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (mt) REVERT: A 423 SER cc_start: 0.8295 (t) cc_final: 0.8065 (m) REVERT: A 546 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7161 (ptp90) REVERT: A 589 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7596 (mp) REVERT: A 590 ASN cc_start: 0.6559 (t0) cc_final: 0.6287 (p0) REVERT: A 613 ASN cc_start: 0.6812 (t0) cc_final: 0.6326 (t0) REVERT: A 621 ARG cc_start: 0.8287 (tpt90) cc_final: 0.7835 (tpt-90) REVERT: A 634 ASP cc_start: 0.7226 (p0) cc_final: 0.6853 (t70) REVERT: A 658 ARG cc_start: 0.7164 (mmm-85) cc_final: 0.6712 (mmp-170) REVERT: D 174 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6552 (mpp80) REVERT: D 280 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8796 (pttp) REVERT: D 294 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: D 336 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7658 (mt) REVERT: D 423 SER cc_start: 0.8285 (t) cc_final: 0.8053 (m) REVERT: D 546 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7153 (ptp90) REVERT: D 589 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7579 (mp) REVERT: D 590 ASN cc_start: 0.6685 (t0) cc_final: 0.6444 (p0) REVERT: D 613 ASN cc_start: 0.6797 (t0) cc_final: 0.6305 (t0) REVERT: D 621 ARG cc_start: 0.8289 (tpt90) cc_final: 0.7835 (tpt-90) REVERT: D 634 ASP cc_start: 0.7218 (p0) cc_final: 0.6845 (t70) REVERT: D 658 ARG cc_start: 0.7170 (mmm-85) cc_final: 0.6722 (mmp-170) outliers start: 51 outliers final: 29 residues processed: 190 average time/residue: 1.3563 time to fit residues: 277.9197 Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 561 ASN D 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094740 restraints weight = 10737.424| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.29 r_work: 0.2786 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9920 Z= 0.114 Angle : 0.661 13.839 13494 Z= 0.321 Chirality : 0.046 0.330 1462 Planarity : 0.004 0.040 1714 Dihedral : 8.497 80.133 1634 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 3.84 % Allowed : 21.59 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.81 (0.25), residues: 1146 helix: 0.39 (0.31), residues: 294 sheet: -1.27 (0.34), residues: 212 loop : -0.64 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 303 HIS 0.006 0.001 HIS A 175 PHE 0.013 0.001 PHE A 278 TYR 0.014 0.001 TYR D 259 ARG 0.008 0.000 ARG D 671 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 12) link_NAG-ASN : angle 5.13185 ( 36) link_BETA1-4 : bond 0.01310 ( 4) link_BETA1-4 : angle 5.37145 ( 12) hydrogen bonds : bond 0.04133 ( 298) hydrogen bonds : angle 4.35058 ( 756) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.88434 ( 12) covalent geometry : bond 0.00251 ( 9898) covalent geometry : angle 0.58424 (13434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.9100 (pttm) cc_final: 0.8771 (pttp) REVERT: A 294 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: A 336 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7616 (mt) REVERT: A 423 SER cc_start: 0.8258 (t) cc_final: 0.8038 (m) REVERT: A 546 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7142 (ptp90) REVERT: A 590 ASN cc_start: 0.6579 (t0) cc_final: 0.6319 (p0) REVERT: A 613 ASN cc_start: 0.6965 (t0) cc_final: 0.6381 (t0) REVERT: A 621 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7814 (tpt-90) REVERT: A 634 ASP cc_start: 0.7196 (p0) cc_final: 0.6847 (t70) REVERT: A 658 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6690 (mmp-170) REVERT: D 174 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6371 (mpp80) REVERT: D 280 LYS cc_start: 0.9095 (pttm) cc_final: 0.8765 (pttp) REVERT: D 294 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: D 336 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7613 (mt) REVERT: D 423 SER cc_start: 0.8248 (t) cc_final: 0.8030 (m) REVERT: D 546 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7139 (ptp90) REVERT: D 589 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7545 (mp) REVERT: D 590 ASN cc_start: 0.6722 (t0) cc_final: 0.6410 (p0) REVERT: D 613 ASN cc_start: 0.6792 (t0) cc_final: 0.6310 (t0) REVERT: D 621 ARG cc_start: 0.8237 (tpt90) cc_final: 0.7818 (tpt-90) REVERT: D 634 ASP cc_start: 0.7190 (p0) cc_final: 0.6838 (t70) REVERT: D 658 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6697 (mmp-170) outliers start: 40 outliers final: 25 residues processed: 190 average time/residue: 1.3447 time to fit residues: 272.9300 Evaluate side-chains 185 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 670 ASN A 679 ASN D 561 ASN D 670 ASN D 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094436 restraints weight = 10564.211| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.26 r_work: 0.2715 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9920 Z= 0.195 Angle : 0.742 14.668 13494 Z= 0.364 Chirality : 0.051 0.333 1462 Planarity : 0.004 0.039 1714 Dihedral : 8.676 79.765 1634 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.70 % Allowed : 21.31 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.78 (0.24), residues: 1146 helix: 0.21 (0.30), residues: 294 sheet: -0.88 (0.37), residues: 176 loop : -0.70 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 161 HIS 0.007 0.001 HIS A 348 PHE 0.019 0.002 PHE A 407 TYR 0.018 0.002 TYR D 259 ARG 0.003 0.000 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 12) link_NAG-ASN : angle 5.31458 ( 36) link_BETA1-4 : bond 0.01366 ( 4) link_BETA1-4 : angle 5.46360 ( 12) hydrogen bonds : bond 0.05307 ( 298) hydrogen bonds : angle 4.56766 ( 756) SS BOND : bond 0.00409 ( 6) SS BOND : angle 2.56864 ( 12) covalent geometry : bond 0.00462 ( 9898) covalent geometry : angle 0.66676 (13434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6531 (mpp80) REVERT: A 280 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8813 (pttp) REVERT: A 294 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 423 SER cc_start: 0.8346 (t) cc_final: 0.8069 (m) REVERT: A 546 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7103 (ptp90) REVERT: A 589 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7647 (mp) REVERT: A 590 ASN cc_start: 0.6585 (t0) cc_final: 0.6317 (p0) REVERT: A 613 ASN cc_start: 0.6898 (t0) cc_final: 0.6399 (t0) REVERT: A 621 ARG cc_start: 0.8309 (tpt90) cc_final: 0.7806 (tpt-90) REVERT: A 634 ASP cc_start: 0.7231 (p0) cc_final: 0.6851 (t70) REVERT: A 658 ARG cc_start: 0.7137 (mmm-85) cc_final: 0.6712 (mmp-170) REVERT: D 174 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6575 (mpp80) REVERT: D 280 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8810 (pttp) REVERT: D 294 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: D 423 SER cc_start: 0.8335 (t) cc_final: 0.8053 (m) REVERT: D 546 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7095 (ptp90) REVERT: D 589 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7628 (mp) REVERT: D 590 ASN cc_start: 0.6771 (t0) cc_final: 0.6432 (p0) REVERT: D 613 ASN cc_start: 0.6893 (t0) cc_final: 0.6389 (t0) REVERT: D 621 ARG cc_start: 0.8317 (tpt90) cc_final: 0.7806 (tpt-90) REVERT: D 634 ASP cc_start: 0.7228 (p0) cc_final: 0.6847 (t70) REVERT: D 658 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6719 (mmp-170) outliers start: 49 outliers final: 33 residues processed: 187 average time/residue: 1.2878 time to fit residues: 256.9668 Evaluate side-chains 199 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 677 VAL Chi-restraints excluded: chain D residue 679 ASN Chi-restraints excluded: chain D residue 680 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 670 ASN A 679 ASN D 561 ASN D 670 ASN D 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.095139 restraints weight = 10671.939| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.25 r_work: 0.2723 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9920 Z= 0.171 Angle : 0.720 14.045 13494 Z= 0.353 Chirality : 0.049 0.334 1462 Planarity : 0.004 0.040 1714 Dihedral : 8.594 79.624 1634 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 4.22 % Allowed : 21.79 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.92 (0.25), residues: 1146 helix: 0.23 (0.30), residues: 294 sheet: -1.38 (0.34), residues: 214 loop : -0.66 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 443 HIS 0.005 0.001 HIS A 348 PHE 0.016 0.002 PHE D 407 TYR 0.016 0.002 TYR A 259 ARG 0.004 0.000 ARG A 671 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 12) link_NAG-ASN : angle 5.12487 ( 36) link_BETA1-4 : bond 0.01348 ( 4) link_BETA1-4 : angle 5.46444 ( 12) hydrogen bonds : bond 0.05057 ( 298) hydrogen bonds : angle 4.53729 ( 756) SS BOND : bond 0.00557 ( 6) SS BOND : angle 2.49585 ( 12) covalent geometry : bond 0.00401 ( 9898) covalent geometry : angle 0.64639 (13434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6578 (mpp80) REVERT: A 280 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8808 (pttp) REVERT: A 294 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 423 SER cc_start: 0.8317 (t) cc_final: 0.8052 (m) REVERT: A 546 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7075 (ptp90) REVERT: A 589 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 590 ASN cc_start: 0.6576 (t0) cc_final: 0.6323 (p0) REVERT: A 613 ASN cc_start: 0.6811 (t0) cc_final: 0.6296 (t0) REVERT: A 621 ARG cc_start: 0.8300 (tpt90) cc_final: 0.7796 (tpt-90) REVERT: A 634 ASP cc_start: 0.7229 (p0) cc_final: 0.6849 (t70) REVERT: A 658 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6693 (mmp-170) REVERT: D 174 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6517 (mpp80) REVERT: D 280 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8803 (pttp) REVERT: D 294 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: D 423 SER cc_start: 0.8301 (t) cc_final: 0.8036 (m) REVERT: D 546 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7073 (ptp90) REVERT: D 589 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7624 (mp) REVERT: D 590 ASN cc_start: 0.6768 (t0) cc_final: 0.6436 (p0) REVERT: D 613 ASN cc_start: 0.6889 (t0) cc_final: 0.6387 (t0) REVERT: D 621 ARG cc_start: 0.8308 (tpt90) cc_final: 0.7799 (tpt-90) REVERT: D 634 ASP cc_start: 0.7222 (p0) cc_final: 0.6841 (t70) REVERT: D 658 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6703 (mmp-170) outliers start: 44 outliers final: 28 residues processed: 186 average time/residue: 1.5306 time to fit residues: 302.0395 Evaluate side-chains 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 677 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN D 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.094822 restraints weight = 10555.215| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.26 r_work: 0.2716 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 9920 Z= 0.230 Angle : 1.163 59.199 13494 Z= 0.672 Chirality : 0.052 0.336 1462 Planarity : 0.005 0.073 1714 Dihedral : 8.527 79.635 1632 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.13 % Allowed : 21.88 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.93 (0.25), residues: 1146 helix: 0.23 (0.30), residues: 294 sheet: -1.37 (0.34), residues: 214 loop : -0.67 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 443 HIS 0.005 0.001 HIS D 348 PHE 0.015 0.002 PHE A 278 TYR 0.017 0.002 TYR A 259 ARG 0.003 0.000 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00995 ( 12) link_NAG-ASN : angle 5.07842 ( 36) link_BETA1-4 : bond 0.01220 ( 4) link_BETA1-4 : angle 5.62084 ( 12) hydrogen bonds : bond 0.05118 ( 298) hydrogen bonds : angle 4.53995 ( 756) SS BOND : bond 0.00530 ( 6) SS BOND : angle 2.27086 ( 12) covalent geometry : bond 0.00498 ( 9898) covalent geometry : angle 1.12152 (13434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9093.72 seconds wall clock time: 161 minutes 34.93 seconds (9694.93 seconds total)