Starting phenix.real_space_refine on Wed Mar 4 01:10:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nf7_12297/03_2026/7nf7_12297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nf7_12297/03_2026/7nf7_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 { model { file = "/net/cci-nas-00/data/ceres_data/7nf7_12297/03_2026/7nf7_12297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nf7_12297/03_2026/7nf7_12297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nf7_12297/03_2026/7nf7_12297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nf7_12297/03_2026/7nf7_12297.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.16, per 1000 atoms: 0.22 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: 0.75 Conformation dependent library (CDL) restraints added in 470.2 milliseconds 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: 0.30 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: 1.34 Time building geometry restraints manager: 0.97 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: 0.02 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: 1.870 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.001 ARG A 574 TYR 0.019 0.002 TYR A 259 PHE 0.019 0.002 PHE A 278 TRP 0.011 0.002 TRP A 443 HIS 0.006 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9898) covalent geometry : angle 0.71103 (13434) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.55753 ( 12) hydrogen bonds : bond 0.28784 ( 298) hydrogen bonds : angle 8.26668 ( 756) link_BETA1-4 : bond 0.02711 ( 4) link_BETA1-4 : angle 11.34866 ( 12) link_NAG-ASN : bond 0.05611 ( 12) link_NAG-ASN : angle 6.44873 ( 36) *********************** 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 : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.8098 (mmm) cc_final: 0.7795 (mmt) REVERT: A 294 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6936 (mm-30) 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: 0.6222 (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: 0.7700 (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 294 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6938 (mm-30) 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: 0.6235 (t0) REVERT: D 619 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7210 (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: 42 residues processed: 225 average time/residue: 0.5526 time to fit residues: 132.8341 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 : 0.254 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0060 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 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 561 ASN D 606 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.094764 restraints weight = 10687.362| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.28 r_work: 0.2743 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9920 Z= 0.148 Angle : 0.795 15.520 13494 Z= 0.371 Chirality : 0.052 0.492 1462 Planarity : 0.005 0.048 1714 Dihedral : 11.044 81.978 1688 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 3.65 % Allowed : 20.83 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1146 helix: -0.80 (0.28), residues: 292 sheet: -1.17 (0.37), residues: 176 loop : -1.06 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.014 0.001 TYR D 259 PHE 0.015 0.001 PHE D 278 TRP 0.008 0.001 TRP A 443 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9898) covalent geometry : angle 0.67624 (13434) SS BOND : bond 0.01372 ( 6) SS BOND : angle 1.48815 ( 12) hydrogen bonds : bond 0.05416 ( 298) hydrogen bonds : angle 5.10703 ( 756) link_BETA1-4 : bond 0.01305 ( 4) link_BETA1-4 : angle 6.09431 ( 12) link_NAG-ASN : bond 0.00829 ( 12) link_NAG-ASN : angle 7.28499 ( 36) *********************** 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 205 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.8089 (t70) cc_final: 0.7608 (m90) REVERT: A 279 MET cc_start: 0.8767 (mmm) cc_final: 0.8564 (mmt) REVERT: A 377 ARG cc_start: 0.8227 (mtp180) cc_final: 0.8010 (mtp180) REVERT: A 546 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7085 (ptp90) REVERT: A 590 ASN cc_start: 0.6750 (t0) cc_final: 0.6403 (p0) REVERT: A 613 ASN cc_start: 0.6677 (t0) cc_final: 0.6100 (t0) REVERT: A 621 ARG cc_start: 0.8394 (tpt90) cc_final: 0.7813 (tpt-90) REVERT: A 634 ASP cc_start: 0.7348 (p0) cc_final: 0.6858 (t0) REVERT: A 658 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.6741 (mmp-170) REVERT: D 279 MET cc_start: 0.8773 (mmm) cc_final: 0.8570 (mmt) REVERT: D 377 ARG cc_start: 0.8231 (mtp180) cc_final: 0.8014 (mtp180) REVERT: D 546 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7083 (ptp90) REVERT: D 590 ASN cc_start: 0.6693 (t0) cc_final: 0.6344 (p0) REVERT: D 613 ASN cc_start: 0.6684 (t0) cc_final: 0.6108 (t0) REVERT: D 621 ARG cc_start: 0.8407 (tpt90) cc_final: 0.7822 (tpt-90) REVERT: D 634 ASP cc_start: 0.7338 (p0) cc_final: 0.6843 (t0) REVERT: D 658 ARG cc_start: 0.7162 (mmm-85) cc_final: 0.6746 (mmp-170) outliers start: 38 outliers final: 19 residues processed: 195 average time/residue: 0.5402 time to fit residues: 112.9276 Evaluate side-chains 176 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 601 GLU 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 257 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 563 LEU 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 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.095038 restraints weight = 10693.667| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.17 r_work: 0.2803 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9920 Z= 0.123 Angle : 0.707 14.203 13494 Z= 0.333 Chirality : 0.048 0.388 1462 Planarity : 0.004 0.042 1714 Dihedral : 9.412 79.583 1644 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 4.41 % Allowed : 21.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1146 helix: 0.02 (0.31), residues: 294 sheet: -0.83 (0.37), residues: 174 loop : -0.84 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.014 0.001 TYR A 259 PHE 0.013 0.001 PHE D 278 TRP 0.007 0.001 TRP A 303 HIS 0.005 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9898) covalent geometry : angle 0.60393 (13434) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.85626 ( 12) hydrogen bonds : bond 0.04687 ( 298) hydrogen bonds : angle 4.62140 ( 756) link_BETA1-4 : bond 0.01312 ( 4) link_BETA1-4 : angle 6.04474 ( 12) link_NAG-ASN : bond 0.00685 ( 12) link_NAG-ASN : angle 6.23640 ( 36) *********************** 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 210 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7980 (t70) cc_final: 0.7583 (m90) REVERT: A 298 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: A 336 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7760 (mt) REVERT: A 423 SER cc_start: 0.8229 (t) cc_final: 0.7917 (m) REVERT: A 433 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7766 (pt0) REVERT: A 546 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7053 (ptp90) REVERT: A 589 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7516 (mp) REVERT: A 590 ASN cc_start: 0.6601 (t0) cc_final: 0.6336 (p0) REVERT: A 613 ASN cc_start: 0.6632 (t0) cc_final: 0.6080 (t0) REVERT: A 621 ARG cc_start: 0.8328 (tpt90) cc_final: 0.7811 (tpt-90) REVERT: A 634 ASP cc_start: 0.7215 (p0) cc_final: 0.6788 (t0) REVERT: A 658 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.6733 (mmp-170) REVERT: D 298 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: D 336 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7752 (mt) REVERT: D 423 SER cc_start: 0.8220 (t) cc_final: 0.7908 (m) REVERT: D 433 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7764 (pt0) REVERT: D 546 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7052 (ptp90) REVERT: D 589 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7510 (mp) REVERT: D 590 ASN cc_start: 0.6578 (t0) cc_final: 0.6314 (p0) REVERT: D 613 ASN cc_start: 0.6625 (t0) cc_final: 0.6069 (t0) REVERT: D 621 ARG cc_start: 0.8338 (tpt90) cc_final: 0.7819 (tpt-90) REVERT: D 634 ASP cc_start: 0.7197 (p0) cc_final: 0.6771 (t0) REVERT: D 658 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.6733 (mmp-170) outliers start: 46 outliers final: 20 residues processed: 194 average time/residue: 0.5713 time to fit residues: 118.3982 Evaluate side-chains 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 294 GLU Chi-restraints excluded: chain A residue 298 GLU 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 546 ARG Chi-restraints excluded: chain A residue 589 ILE 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 294 GLU Chi-restraints excluded: chain D residue 298 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 546 ARG Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 601 GLU 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 83 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN A 497 ASN A 516 ASN A 561 ASN D 301 GLN D 516 ASN D 561 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.091801 restraints weight = 10646.006| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.17 r_work: 0.2715 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9920 Z= 0.218 Angle : 0.788 14.474 13494 Z= 0.378 Chirality : 0.053 0.363 1462 Planarity : 0.005 0.044 1714 Dihedral : 9.222 80.381 1634 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.46 % Rotamer: Outliers : 4.61 % Allowed : 19.48 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1146 helix: 0.09 (0.31), residues: 290 sheet: -1.08 (0.36), residues: 186 loop : -0.76 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 229 TYR 0.019 0.002 TYR A 259 PHE 0.019 0.002 PHE A 407 TRP 0.009 0.002 TRP A 443 HIS 0.008 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 9898) covalent geometry : angle 0.69923 (13434) SS BOND : bond 0.00517 ( 6) SS BOND : angle 1.66113 ( 12) hydrogen bonds : bond 0.05843 ( 298) hydrogen bonds : angle 4.78671 ( 756) link_BETA1-4 : bond 0.01395 ( 4) link_BETA1-4 : angle 5.96554 ( 12) link_NAG-ASN : bond 0.00647 ( 12) link_NAG-ASN : angle 6.14027 ( 36) *********************** 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 202 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7784 (t70) cc_final: 0.7574 (m90) REVERT: A 336 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 433 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8009 (pt0) REVERT: A 453 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 546 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7015 (ptp90) REVERT: A 589 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7566 (mp) REVERT: A 590 ASN cc_start: 0.6627 (t0) cc_final: 0.6336 (p0) REVERT: A 613 ASN cc_start: 0.6724 (t0) cc_final: 0.6156 (t0) REVERT: A 621 ARG cc_start: 0.8333 (tpt90) cc_final: 0.7755 (tpt-90) REVERT: A 634 ASP cc_start: 0.7183 (p0) cc_final: 0.6804 (t70) REVERT: A 658 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6731 (mmp-170) REVERT: D 336 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7710 (mt) REVERT: D 433 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8010 (pt0) REVERT: D 437 GLU cc_start: 0.6835 (tt0) cc_final: 0.6261 (mp0) REVERT: D 453 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8565 (tt) REVERT: D 546 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7001 (ptp90) REVERT: D 589 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7558 (mp) REVERT: D 590 ASN cc_start: 0.6598 (t0) cc_final: 0.6320 (p0) REVERT: D 613 ASN cc_start: 0.6714 (t0) cc_final: 0.6143 (t0) REVERT: D 621 ARG cc_start: 0.8344 (tpt90) cc_final: 0.7765 (tpt-90) REVERT: D 634 ASP cc_start: 0.7171 (p0) cc_final: 0.6791 (t70) REVERT: D 658 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.6740 (mmp-170) outliers start: 48 outliers final: 26 residues processed: 194 average time/residue: 0.5474 time to fit residues: 113.7406 Evaluate side-chains 187 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 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 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 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 113 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 D 670 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.092009 restraints weight = 10719.655| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.26 r_work: 0.2744 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9920 Z= 0.205 Angle : 0.766 15.487 13494 Z= 0.370 Chirality : 0.052 0.355 1462 Planarity : 0.005 0.046 1714 Dihedral : 9.148 82.030 1634 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.41 % Allowed : 20.83 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1146 helix: 0.03 (0.30), residues: 290 sheet: -1.06 (0.36), residues: 186 loop : -0.74 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.018 0.002 TYR D 259 PHE 0.018 0.002 PHE D 278 TRP 0.009 0.001 TRP A 443 HIS 0.006 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9898) covalent geometry : angle 0.67817 (13434) SS BOND : bond 0.00438 ( 6) SS BOND : angle 1.18100 ( 12) hydrogen bonds : bond 0.05502 ( 298) hydrogen bonds : angle 4.70047 ( 756) link_BETA1-4 : bond 0.01332 ( 4) link_BETA1-4 : angle 5.87308 ( 12) link_NAG-ASN : bond 0.00647 ( 12) link_NAG-ASN : angle 6.05099 ( 36) *********************** 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 201 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7799 (t70) cc_final: 0.7593 (m90) REVERT: A 280 LYS cc_start: 0.9093 (pttm) cc_final: 0.8857 (pttp) REVERT: A 336 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 453 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8542 (tt) REVERT: A 512 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (p0) REVERT: A 546 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7133 (ptp90) REVERT: A 589 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 590 ASN cc_start: 0.6609 (t0) cc_final: 0.6350 (p0) REVERT: A 613 ASN cc_start: 0.6709 (t0) cc_final: 0.6159 (t0) REVERT: A 621 ARG cc_start: 0.8349 (tpt90) cc_final: 0.7769 (tpt-90) REVERT: A 634 ASP cc_start: 0.7228 (p0) cc_final: 0.6836 (t70) REVERT: A 658 ARG cc_start: 0.7180 (mmm-85) cc_final: 0.6803 (mmp-170) REVERT: D 280 LYS cc_start: 0.9095 (pttm) cc_final: 0.8856 (pttp) REVERT: D 336 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7710 (mt) REVERT: D 437 GLU cc_start: 0.7035 (tt0) cc_final: 0.6362 (mp0) REVERT: D 453 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8548 (tt) REVERT: D 546 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7115 (ptp90) REVERT: D 589 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7593 (mp) REVERT: D 590 ASN cc_start: 0.6586 (t0) cc_final: 0.6336 (p0) REVERT: D 613 ASN cc_start: 0.6694 (t0) cc_final: 0.6141 (t0) REVERT: D 621 ARG cc_start: 0.8366 (tpt90) cc_final: 0.7783 (tpt-90) REVERT: D 634 ASP cc_start: 0.7213 (p0) cc_final: 0.6821 (t70) REVERT: D 658 ARG cc_start: 0.7186 (mmm-85) cc_final: 0.6809 (mmp-170) outliers start: 46 outliers final: 27 residues processed: 190 average time/residue: 0.5557 time to fit residues: 112.7800 Evaluate side-chains 187 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 325 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 57 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 561 ASN A 670 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 = 0.3499 r_free = 0.3499 target = 0.133381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.095294 restraints weight = 10686.270| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.28 r_work: 0.2710 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9920 Z= 0.149 Angle : 0.725 14.532 13494 Z= 0.350 Chirality : 0.050 0.351 1462 Planarity : 0.004 0.045 1714 Dihedral : 8.883 80.146 1634 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.41 % Allowed : 20.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1146 helix: 0.13 (0.30), residues: 294 sheet: -1.36 (0.34), residues: 214 loop : -0.68 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 671 TYR 0.016 0.001 TYR D 259 PHE 0.016 0.002 PHE D 278 TRP 0.007 0.001 TRP A 443 HIS 0.005 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9898) covalent geometry : angle 0.63900 (13434) SS BOND : bond 0.00320 ( 6) SS BOND : angle 0.91540 ( 12) hydrogen bonds : bond 0.04870 ( 298) hydrogen bonds : angle 4.57256 ( 756) link_BETA1-4 : bond 0.01349 ( 4) link_BETA1-4 : angle 5.75317 ( 12) link_NAG-ASN : bond 0.00899 ( 12) link_NAG-ASN : angle 5.75417 ( 36) *********************** 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 198 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.7827 (t70) cc_final: 0.7621 (m90) REVERT: A 280 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8856 (pttp) REVERT: A 336 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (mt) REVERT: A 453 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 546 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7136 (ptp90) REVERT: A 589 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7614 (mp) REVERT: A 590 ASN cc_start: 0.6610 (t0) cc_final: 0.6378 (p0) REVERT: A 613 ASN cc_start: 0.6685 (t0) cc_final: 0.6139 (t0) REVERT: A 621 ARG cc_start: 0.8341 (tpt90) cc_final: 0.7811 (tpt-90) REVERT: A 634 ASP cc_start: 0.7222 (p0) cc_final: 0.6829 (t70) REVERT: A 658 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6784 (mmp-170) REVERT: D 245 GLU cc_start: 0.7067 (pm20) cc_final: 0.6858 (pt0) REVERT: D 280 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8846 (pttp) REVERT: D 336 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (mt) REVERT: D 453 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8490 (tt) REVERT: D 546 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7110 (ptp90) REVERT: D 589 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7579 (mp) REVERT: D 590 ASN cc_start: 0.6703 (t0) cc_final: 0.6411 (p0) REVERT: D 613 ASN cc_start: 0.6682 (t0) cc_final: 0.6129 (t0) REVERT: D 621 ARG cc_start: 0.8350 (tpt90) cc_final: 0.7819 (tpt-90) REVERT: D 634 ASP cc_start: 0.7212 (p0) cc_final: 0.6819 (t70) REVERT: D 658 ARG cc_start: 0.7191 (mmm-85) cc_final: 0.6792 (mmp-170) outliers start: 46 outliers final: 25 residues processed: 185 average time/residue: 0.5741 time to fit residues: 113.3519 Evaluate side-chains 184 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 280 LYS Chi-restraints excluded: chain A residue 294 GLU 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 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 210 ASP Chi-restraints excluded: chain D residue 212 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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 D 670 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.094967 restraints weight = 10619.902| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.29 r_work: 0.2710 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9920 Z= 0.145 Angle : 0.721 14.104 13494 Z= 0.349 Chirality : 0.050 0.346 1462 Planarity : 0.004 0.042 1714 Dihedral : 8.720 79.823 1634 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.61 % Allowed : 20.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1146 helix: 0.21 (0.30), residues: 294 sheet: -1.33 (0.34), residues: 214 loop : -0.68 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.016 0.001 TYR D 259 PHE 0.015 0.002 PHE D 278 TRP 0.007 0.001 TRP A 443 HIS 0.005 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9898) covalent geometry : angle 0.63468 (13434) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.78239 ( 12) hydrogen bonds : bond 0.04742 ( 298) hydrogen bonds : angle 4.51075 ( 756) link_BETA1-4 : bond 0.01357 ( 4) link_BETA1-4 : angle 5.65204 ( 12) link_NAG-ASN : bond 0.00725 ( 12) link_NAG-ASN : angle 5.73215 ( 36) *********************** 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 199 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6534 (mpp80) REVERT: A 240 HIS cc_start: 0.7824 (t70) cc_final: 0.7616 (m90) REVERT: A 280 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8864 (pttp) REVERT: A 336 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7667 (mt) REVERT: A 423 SER cc_start: 0.8195 (t) cc_final: 0.7924 (m) REVERT: A 453 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 509 MET cc_start: 0.9314 (tpt) cc_final: 0.9089 (tpt) REVERT: A 546 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7126 (ptp90) REVERT: A 589 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7609 (mp) REVERT: A 590 ASN cc_start: 0.6551 (t0) cc_final: 0.6324 (p0) REVERT: A 613 ASN cc_start: 0.6693 (t0) cc_final: 0.6123 (t0) REVERT: A 621 ARG cc_start: 0.8338 (tpt90) cc_final: 0.7818 (tpt-90) REVERT: A 634 ASP cc_start: 0.7217 (p0) cc_final: 0.6825 (t70) REVERT: A 658 ARG cc_start: 0.7125 (mmm-85) cc_final: 0.6686 (mmp-170) REVERT: D 174 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6527 (mpp80) REVERT: D 280 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8843 (pttp) REVERT: D 336 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7667 (mt) REVERT: D 423 SER cc_start: 0.8187 (t) cc_final: 0.7913 (m) REVERT: D 453 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8483 (tt) REVERT: D 509 MET cc_start: 0.9303 (tpt) cc_final: 0.9097 (tpt) REVERT: D 546 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7108 (ptp90) REVERT: D 589 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7560 (mp) REVERT: D 590 ASN cc_start: 0.6673 (t0) cc_final: 0.6387 (p0) REVERT: D 613 ASN cc_start: 0.6693 (t0) cc_final: 0.6115 (t0) REVERT: D 621 ARG cc_start: 0.8347 (tpt90) cc_final: 0.7824 (tpt-90) REVERT: D 634 ASP cc_start: 0.7204 (p0) cc_final: 0.6811 (t70) REVERT: D 658 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6790 (mmp-170) outliers start: 48 outliers final: 29 residues processed: 188 average time/residue: 0.5553 time to fit residues: 111.7290 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 : 0.356 ------------------------------------------------------------------------------- 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 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 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 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 6 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 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 D 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094729 restraints weight = 10617.104| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.25 r_work: 0.2721 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1880 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= 0.171 Angle : 0.739 16.043 13494 Z= 0.359 Chirality : 0.050 0.346 1462 Planarity : 0.004 0.042 1714 Dihedral : 8.711 79.769 1634 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.81 % Rotamer: Outliers : 4.51 % Allowed : 21.21 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1146 helix: 0.18 (0.30), residues: 294 sheet: -1.33 (0.34), residues: 214 loop : -0.67 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 671 TYR 0.017 0.001 TYR D 259 PHE 0.016 0.002 PHE D 278 TRP 0.008 0.001 TRP D 443 HIS 0.005 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9898) covalent geometry : angle 0.65119 (13434) SS BOND : bond 0.00557 ( 6) SS BOND : angle 2.28896 ( 12) hydrogen bonds : bond 0.05030 ( 298) hydrogen bonds : angle 4.55018 ( 756) link_BETA1-4 : bond 0.01311 ( 4) link_BETA1-4 : angle 5.61545 ( 12) link_NAG-ASN : bond 0.00686 ( 12) link_NAG-ASN : angle 5.85487 ( 36) *********************** 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: 47 poor density : 151 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6618 (mpp80) REVERT: A 280 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8807 (pttp) REVERT: A 294 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 336 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7689 (mt) REVERT: A 423 SER cc_start: 0.8246 (t) cc_final: 0.7965 (m) REVERT: A 453 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8564 (tt) REVERT: A 546 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7173 (ptp90) REVERT: A 589 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7629 (mp) REVERT: A 590 ASN cc_start: 0.6551 (t0) cc_final: 0.6348 (p0) REVERT: A 613 ASN cc_start: 0.6736 (t0) cc_final: 0.6166 (t0) REVERT: A 621 ARG cc_start: 0.8329 (tpt90) cc_final: 0.7813 (tpt-90) REVERT: A 634 ASP cc_start: 0.7229 (p0) cc_final: 0.6845 (t70) REVERT: A 658 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.6727 (mmp-170) REVERT: D 174 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6624 (mpp80) REVERT: D 245 GLU cc_start: 0.6922 (pt0) cc_final: 0.6491 (pm20) REVERT: D 280 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8798 (pttp) REVERT: D 294 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: D 336 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7703 (mt) REVERT: D 423 SER cc_start: 0.8218 (t) cc_final: 0.7937 (m) REVERT: D 453 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8566 (tt) REVERT: D 546 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7163 (ptp90) REVERT: D 589 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7632 (mp) REVERT: D 590 ASN cc_start: 0.6673 (t0) cc_final: 0.6407 (p0) REVERT: D 613 ASN cc_start: 0.6758 (t0) cc_final: 0.6242 (t0) REVERT: D 621 ARG cc_start: 0.8340 (tpt90) cc_final: 0.7823 (tpt-90) REVERT: D 634 ASP cc_start: 0.7218 (p0) cc_final: 0.6832 (t70) REVERT: D 658 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6721 (mmp-170) outliers start: 47 outliers final: 28 residues processed: 190 average time/residue: 0.5610 time to fit residues: 113.7230 Evaluate side-chains 192 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 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 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 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 677 VAL 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 10 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.0670 chunk 96 optimal weight: 0.8980 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.134680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.096292 restraints weight = 10489.353| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.24 r_work: 0.2748 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9920 Z= 0.135 Angle : 0.690 14.479 13494 Z= 0.336 Chirality : 0.048 0.336 1462 Planarity : 0.004 0.042 1714 Dihedral : 8.518 80.056 1634 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 4.13 % Allowed : 21.98 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.25), residues: 1146 helix: 0.34 (0.31), residues: 294 sheet: -1.23 (0.35), residues: 212 loop : -0.69 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 671 TYR 0.014 0.001 TYR D 259 PHE 0.014 0.001 PHE A 278 TRP 0.006 0.001 TRP D 443 HIS 0.005 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9898) covalent geometry : angle 0.61292 (13434) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.81412 ( 12) hydrogen bonds : bond 0.04445 ( 298) hydrogen bonds : angle 4.44573 ( 756) link_BETA1-4 : bond 0.01393 ( 4) link_BETA1-4 : angle 5.44859 ( 12) link_NAG-ASN : bond 0.00669 ( 12) link_NAG-ASN : angle 5.23705 ( 36) *********************** 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 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6485 (mpp80) REVERT: A 280 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8796 (pttp) REVERT: A 294 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 336 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 423 SER cc_start: 0.8277 (t) cc_final: 0.8040 (m) REVERT: A 546 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7118 (ptp90) REVERT: A 589 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 590 ASN cc_start: 0.6536 (t0) cc_final: 0.6289 (p0) REVERT: A 613 ASN cc_start: 0.6827 (t0) cc_final: 0.6353 (t0) REVERT: A 621 ARG cc_start: 0.8268 (tpt90) cc_final: 0.7828 (tpt-90) REVERT: A 634 ASP cc_start: 0.7223 (p0) cc_final: 0.6847 (t70) REVERT: A 658 ARG cc_start: 0.7114 (mmm-85) cc_final: 0.6690 (mmp-170) REVERT: D 174 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6475 (mpp80) REVERT: D 245 GLU cc_start: 0.6962 (pt0) cc_final: 0.6534 (pm20) REVERT: D 280 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8787 (pttp) REVERT: D 294 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: D 336 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (mt) REVERT: D 423 SER cc_start: 0.8269 (t) cc_final: 0.8030 (m) REVERT: D 546 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7111 (ptp90) REVERT: D 589 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7581 (mp) REVERT: D 590 ASN cc_start: 0.6644 (t0) cc_final: 0.6414 (p0) REVERT: D 613 ASN cc_start: 0.6822 (t0) cc_final: 0.6340 (t0) REVERT: D 621 ARG cc_start: 0.8274 (tpt90) cc_final: 0.7833 (tpt-90) REVERT: D 634 ASP cc_start: 0.7218 (p0) cc_final: 0.6843 (t70) REVERT: D 658 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6671 (mmp-170) outliers start: 43 outliers final: 24 residues processed: 183 average time/residue: 0.5970 time to fit residues: 116.3909 Evaluate side-chains 188 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 280 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 ILE 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 670 ASN 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 174 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 212 ILE 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 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 680 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3490 r_free = 0.3490 target = 0.132557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.094224 restraints weight = 10626.625| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.26 r_work: 0.2711 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9920 Z= 0.183 Angle : 0.740 15.266 13494 Z= 0.361 Chirality : 0.050 0.338 1462 Planarity : 0.004 0.044 1714 Dihedral : 8.629 79.753 1632 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 4.41 % Allowed : 21.69 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1146 helix: 0.46 (0.31), residues: 280 sheet: -0.83 (0.37), residues: 176 loop : -0.70 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 229 TYR 0.018 0.002 TYR A 259 PHE 0.017 0.002 PHE D 407 TRP 0.008 0.001 TRP A 443 HIS 0.006 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9898) covalent geometry : angle 0.66383 (13434) SS BOND : bond 0.00483 ( 6) SS BOND : angle 1.80860 ( 12) hydrogen bonds : bond 0.05126 ( 298) hydrogen bonds : angle 4.52165 ( 756) link_BETA1-4 : bond 0.01419 ( 4) link_BETA1-4 : angle 5.47327 ( 12) link_NAG-ASN : bond 0.00639 ( 12) link_NAG-ASN : angle 5.44676 ( 36) ********************** 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 199 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6665 (mpp80) REVERT: A 280 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8806 (pttp) REVERT: A 294 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: A 336 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7673 (mt) REVERT: A 423 SER cc_start: 0.8302 (t) cc_final: 0.8037 (m) REVERT: A 546 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7130 (ptp90) REVERT: A 589 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7553 (mp) REVERT: A 590 ASN cc_start: 0.6572 (t0) cc_final: 0.6305 (p0) REVERT: A 613 ASN cc_start: 0.6860 (t0) cc_final: 0.6381 (t0) REVERT: A 621 ARG cc_start: 0.8319 (tpt90) cc_final: 0.7808 (tpt-90) REVERT: A 634 ASP cc_start: 0.7222 (p0) cc_final: 0.6836 (t70) REVERT: A 658 ARG cc_start: 0.7160 (mmm-85) cc_final: 0.6765 (mmp-170) REVERT: D 174 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6651 (mpp80) REVERT: D 245 GLU cc_start: 0.6951 (pt0) cc_final: 0.6518 (pm20) REVERT: D 280 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8807 (pttp) REVERT: D 294 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: D 336 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7679 (mt) REVERT: D 423 SER cc_start: 0.8282 (t) cc_final: 0.8014 (m) REVERT: D 437 GLU cc_start: 0.7603 (tt0) cc_final: 0.6633 (mp0) REVERT: D 546 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7121 (ptp90) REVERT: D 589 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7619 (mp) REVERT: D 590 ASN cc_start: 0.6682 (t0) cc_final: 0.6443 (p0) REVERT: D 613 ASN cc_start: 0.6867 (t0) cc_final: 0.6377 (t0) REVERT: D 621 ARG cc_start: 0.8312 (tpt90) cc_final: 0.7803 (tpt-90) REVERT: D 634 ASP cc_start: 0.7217 (p0) cc_final: 0.6832 (t70) REVERT: D 658 ARG cc_start: 0.7121 (mmm-85) cc_final: 0.6700 (mmp-170) outliers start: 46 outliers final: 30 residues processed: 183 average time/residue: 0.5747 time to fit residues: 112.2443 Evaluate side-chains 191 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 589 ILE Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 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 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 609 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 45 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.133510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.094816 restraints weight = 10497.493| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.26 r_work: 0.2727 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9920 Z= 0.140 Angle : 0.713 14.598 13494 Z= 0.347 Chirality : 0.048 0.336 1462 Planarity : 0.004 0.043 1714 Dihedral : 8.577 79.877 1632 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.10 % Favored : 95.72 % Rotamer: Outliers : 4.51 % Allowed : 21.59 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.25), residues: 1146 helix: 0.30 (0.31), residues: 294 sheet: -1.06 (0.36), residues: 194 loop : -0.66 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.016 0.001 TYR D 259 PHE 0.016 0.002 PHE D 278 TRP 0.008 0.001 TRP A 303 HIS 0.005 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9898) covalent geometry : angle 0.63776 (13434) SS BOND : bond 0.00430 ( 6) SS BOND : angle 1.66522 ( 12) hydrogen bonds : bond 0.04776 ( 298) hydrogen bonds : angle 4.48209 ( 756) link_BETA1-4 : bond 0.01327 ( 4) link_BETA1-4 : angle 5.43857 ( 12) link_NAG-ASN : bond 0.00653 ( 12) link_NAG-ASN : angle 5.26876 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.93 seconds wall clock time: 65 minutes 0.86 seconds (3900.86 seconds total)