Starting phenix.real_space_refine on Tue Jul 29 17:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aua_11926/07_2025/7aua_11926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aua_11926/07_2025/7aua_11926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2025/7aua_11926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2025/7aua_11926.map" model { file = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2025/7aua_11926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aua_11926/07_2025/7aua_11926.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 56 5.16 5 C 7276 2.51 5 N 1896 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11300 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5546 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 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: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: E, F, B Time building chain proxies: 12.18, per 1000 atoms: 1.08 Number of scatterers: 11300 At special positions: 0 Unit cell: (94.785, 99.045, 104.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 56 16.00 P 4 15.00 O 2066 8.00 N 1896 7.00 C 7276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 182 " distance=2.04 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 793 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 879 " distance=2.03 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 182 " distance=2.04 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 879 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN A 790 " " NAG E 1 " - " ASN B 592 " " NAG F 1 " - " ASN B 790 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 38.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 210 removed outlier: 4.568A pdb=" N TYR A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 252 through 262 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 327 through 331 removed outlier: 4.137A pdb=" N GLU A 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.520A pdb=" N LYS A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 4.206A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.547A pdb=" N VAL A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 486 through 491 removed outlier: 4.209A pdb=" N THR A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.552A pdb=" N LEU A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 522 through 538 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.692A pdb=" N THR A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 624 through 631 removed outlier: 3.521A pdb=" N ALA A 627 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 629 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.710A pdb=" N GLY A 641 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.657A pdb=" N ALA A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.558A pdb=" N LEU A 730 " --> pdb=" O ASN A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 818 through 828 removed outlier: 3.931A pdb=" N ARG A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 removed outlier: 3.925A pdb=" N ALA A 835 " --> pdb=" O CYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 888 removed outlier: 3.917A pdb=" N ARG A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 210 removed outlier: 4.569A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 327 through 331 removed outlier: 4.137A pdb=" N GLU B 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.519A pdb=" N LYS B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 4.206A pdb=" N LEU B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.546A pdb=" N VAL B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 486 through 491 removed outlier: 4.208A pdb=" N THR B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.552A pdb=" N LEU B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'B' and resid 522 through 538 Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.692A pdb=" N THR B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 624 through 631 removed outlier: 3.521A pdb=" N ALA B 627 " --> pdb=" O PRO B 624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 628 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 629 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.710A pdb=" N GLY B 641 " --> pdb=" O PRO B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.657A pdb=" N ALA B 652 " --> pdb=" O LYS B 648 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.558A pdb=" N LEU B 730 " --> pdb=" O ASN B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 Processing helix chain 'B' and resid 807 through 816 Processing helix chain 'B' and resid 818 through 828 removed outlier: 3.931A pdb=" N ARG B 822 " --> pdb=" O PRO B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 removed outlier: 3.926A pdb=" N ALA B 835 " --> pdb=" O CYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 888 removed outlier: 3.917A pdb=" N ARG B 876 " --> pdb=" O HIS B 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.388A pdb=" N TYR A 238 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE A 276 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 240 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 298 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.936A pdb=" N ILE A 443 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 8.553A pdb=" N TYR A 341 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA A 431 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE A 343 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE A 433 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N PHE A 345 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR A 429 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A 462 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA A 431 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU A 464 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 433 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 553 removed outlier: 4.504A pdb=" N VAL A 717 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 663 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL A 693 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 665 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 695 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 667 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 664 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A 743 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A 666 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 788 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 198 removed outlier: 6.387A pdb=" N TYR B 238 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE B 276 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 240 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 298 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.936A pdb=" N ILE B 443 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 395 through 397 removed outlier: 8.553A pdb=" N TYR B 341 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA B 431 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 343 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE B 433 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N PHE B 345 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 429 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 462 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA B 431 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 464 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE B 433 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 552 through 553 removed outlier: 4.504A pdb=" N VAL B 717 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE B 663 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL B 693 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 665 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 695 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET B 667 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 664 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE B 743 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL B 666 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 784 through 788 374 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3586 1.34 - 1.46: 2953 1.46 - 1.59: 4991 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 11618 Sorted by residual: bond pdb=" C HIS B 555 " pdb=" N ARG B 556 " ideal model delta sigma weight residual 1.330 1.533 -0.204 1.32e-02 5.74e+03 2.38e+02 bond pdb=" C HIS A 555 " pdb=" N ARG A 556 " ideal model delta sigma weight residual 1.330 1.533 -0.204 1.32e-02 5.74e+03 2.38e+02 bond pdb=" O1B UDP A1002 " pdb=" PB UDP A1002 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" O1B UDP B1002 " pdb=" PB UDP B1002 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" N PHE B 918 " pdb=" CA PHE B 918 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.14e-02 7.69e+03 6.76e+00 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 15498 1.84 - 3.67: 266 3.67 - 5.51: 43 5.51 - 7.34: 9 7.34 - 9.18: 4 Bond angle restraints: 15820 Sorted by residual: angle pdb=" O1B UDP B1002 " pdb=" PB UDP B1002 " pdb=" O3A UDP B1002 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O1B UDP A1002 " pdb=" PB UDP A1002 " pdb=" O3A UDP A1002 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O3A UDP A1002 " pdb=" PB UDP A1002 " pdb=" O3B UDP A1002 " ideal model delta sigma weight residual 112.01 102.98 9.03 1.00e+00 1.00e+00 8.16e+01 angle pdb=" O3A UDP B1002 " pdb=" PB UDP B1002 " pdb=" O3B UDP B1002 " ideal model delta sigma weight residual 112.01 103.00 9.01 1.00e+00 1.00e+00 8.11e+01 angle pdb=" CA TYR A 808 " pdb=" CB TYR A 808 " pdb=" CG TYR A 808 " ideal model delta sigma weight residual 113.90 117.96 -4.06 1.80e+00 3.09e-01 5.08e+00 ... (remaining 15815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.70: 6682 20.70 - 41.40: 364 41.40 - 62.09: 38 62.09 - 82.79: 34 82.79 - 103.49: 12 Dihedral angle restraints: 7130 sinusoidal: 3092 harmonic: 4038 Sorted by residual: dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS A 188 " pdb=" SG CYS A 188 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CA ARG A 267 " pdb=" C ARG A 267 " pdb=" N THR A 268 " pdb=" CA THR A 268 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 7127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1752 0.147 - 0.293: 6 0.293 - 0.440: 0 0.440 - 0.586: 0 0.586 - 0.733: 2 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CG LEU A 251 " pdb=" CB LEU A 251 " pdb=" CD1 LEU A 251 " pdb=" CD2 LEU A 251 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU B 251 " pdb=" CB LEU B 251 " pdb=" CD1 LEU B 251 " pdb=" CD2 LEU B 251 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1757 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 817 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 818 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 818 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 818 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 817 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 818 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 818 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 818 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 609 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 610 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.021 5.00e-02 4.00e+02 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 30 2.43 - 3.05: 7252 3.05 - 3.66: 15879 3.66 - 4.28: 25356 4.28 - 4.90: 43190 Nonbonded interactions: 91707 Sorted by model distance: nonbonded pdb="MN MN A1001 " pdb=" O2A UDP A1002 " model vdw 1.809 2.320 nonbonded pdb="MN MN B1001 " pdb=" O2A UDP B1002 " model vdw 1.809 2.320 nonbonded pdb="MN MN B1001 " pdb=" O2B UDP B1002 " model vdw 1.970 2.320 nonbonded pdb="MN MN A1001 " pdb=" O2B UDP A1002 " model vdw 1.970 2.320 nonbonded pdb=" OG1 THR B 617 " pdb=" OD1 ASP B 620 " model vdw 2.143 3.040 ... (remaining 91702 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: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.270 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.950 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.008 0.204 11640 Z= 0.350 Angle : 0.651 9.176 15876 Z= 0.359 Chirality : 0.052 0.733 1760 Planarity : 0.004 0.047 2008 Dihedral : 13.954 103.488 4488 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1356 helix: 0.73 (0.26), residues: 432 sheet: -1.32 (0.40), residues: 160 loop : -0.28 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 266 HIS 0.005 0.001 HIS B 872 PHE 0.019 0.002 PHE A 600 TYR 0.018 0.002 TYR A 808 ARG 0.004 0.001 ARG B 822 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 4) link_NAG-ASN : angle 2.76400 ( 12) link_BETA1-4 : bond 0.00738 ( 6) link_BETA1-4 : angle 1.43132 ( 18) link_ALPHA1-3 : bond 0.01091 ( 2) link_ALPHA1-3 : angle 2.21317 ( 6) hydrogen bonds : bond 0.18700 ( 374) hydrogen bonds : angle 6.85160 ( 996) SS BOND : bond 0.00286 ( 10) SS BOND : angle 2.35719 ( 20) covalent geometry : bond 0.00756 (11618) covalent geometry : angle 0.63894 (15820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.6670 time to fit residues: 212.9412 Evaluate side-chains 76 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089925 restraints weight = 15557.275| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.22 r_work: 0.2873 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11640 Z= 0.131 Angle : 0.568 5.627 15876 Z= 0.293 Chirality : 0.045 0.149 1760 Planarity : 0.005 0.043 2008 Dihedral : 8.642 64.648 1820 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.99 % Allowed : 6.19 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1356 helix: 1.22 (0.26), residues: 424 sheet: -0.91 (0.39), residues: 172 loop : 0.01 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 266 HIS 0.006 0.001 HIS A 872 PHE 0.013 0.001 PHE B 873 TYR 0.014 0.001 TYR B 808 ARG 0.007 0.001 ARG B 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 4) link_NAG-ASN : angle 2.54791 ( 12) link_BETA1-4 : bond 0.00572 ( 6) link_BETA1-4 : angle 1.48766 ( 18) link_ALPHA1-3 : bond 0.01511 ( 2) link_ALPHA1-3 : angle 2.19396 ( 6) hydrogen bonds : bond 0.04534 ( 374) hydrogen bonds : angle 5.31198 ( 996) SS BOND : bond 0.00365 ( 10) SS BOND : angle 1.16978 ( 20) covalent geometry : bond 0.00299 (11618) covalent geometry : angle 0.55904 (15820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.236 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 97 average time/residue: 1.4868 time to fit residues: 155.1702 Evaluate side-chains 81 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 115 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088435 restraints weight = 15815.893| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.26 r_work: 0.2862 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11640 Z= 0.123 Angle : 0.528 7.365 15876 Z= 0.271 Chirality : 0.043 0.156 1760 Planarity : 0.004 0.041 2008 Dihedral : 7.402 55.353 1820 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.99 % Allowed : 8.17 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1356 helix: 1.44 (0.25), residues: 422 sheet: -1.02 (0.40), residues: 160 loop : 0.11 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 266 HIS 0.005 0.001 HIS A 872 PHE 0.011 0.001 PHE A 873 TYR 0.010 0.001 TYR A 811 ARG 0.003 0.000 ARG B 719 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 2.49401 ( 12) link_BETA1-4 : bond 0.00545 ( 6) link_BETA1-4 : angle 1.33190 ( 18) link_ALPHA1-3 : bond 0.01315 ( 2) link_ALPHA1-3 : angle 1.50985 ( 6) hydrogen bonds : bond 0.04367 ( 374) hydrogen bonds : angle 5.08139 ( 996) SS BOND : bond 0.00200 ( 10) SS BOND : angle 2.63446 ( 20) covalent geometry : bond 0.00290 (11618) covalent geometry : angle 0.51334 (15820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.255 Fit side-chains REVERT: A 391 LEU cc_start: 0.8741 (mp) cc_final: 0.8470 (mt) REVERT: A 661 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: B 391 LEU cc_start: 0.8739 (mp) cc_final: 0.8452 (mt) REVERT: B 661 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8002 (tt0) outliers start: 12 outliers final: 2 residues processed: 91 average time/residue: 1.4408 time to fit residues: 141.6406 Evaluate side-chains 82 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 661 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.085430 restraints weight = 15772.029| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.25 r_work: 0.2815 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11640 Z= 0.192 Angle : 0.567 5.392 15876 Z= 0.291 Chirality : 0.045 0.154 1760 Planarity : 0.004 0.039 2008 Dihedral : 6.783 55.724 1820 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.40 % Allowed : 8.58 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1356 helix: 1.30 (0.25), residues: 424 sheet: -1.15 (0.38), residues: 164 loop : 0.04 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 266 HIS 0.005 0.001 HIS B 616 PHE 0.015 0.002 PHE A 452 TYR 0.012 0.001 TYR B 811 ARG 0.002 0.000 ARG B 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 4) link_NAG-ASN : angle 2.71167 ( 12) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 1.41061 ( 18) link_ALPHA1-3 : bond 0.01260 ( 2) link_ALPHA1-3 : angle 1.67972 ( 6) hydrogen bonds : bond 0.04877 ( 374) hydrogen bonds : angle 5.08107 ( 996) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.56012 ( 20) covalent geometry : bond 0.00478 (11618) covalent geometry : angle 0.55776 (15820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.214 Fit side-chains REVERT: A 391 LEU cc_start: 0.8785 (mp) cc_final: 0.8487 (mt) REVERT: A 505 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8897 (tt) REVERT: B 391 LEU cc_start: 0.8798 (mp) cc_final: 0.8498 (mt) REVERT: B 505 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8899 (tt) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 1.3488 time to fit residues: 140.3313 Evaluate side-chains 88 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 96 optimal weight: 0.0470 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088113 restraints weight = 15673.742| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.25 r_work: 0.2854 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11640 Z= 0.114 Angle : 0.522 7.240 15876 Z= 0.268 Chirality : 0.042 0.140 1760 Planarity : 0.004 0.039 2008 Dihedral : 6.196 55.077 1820 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.07 % Allowed : 9.32 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1356 helix: 1.46 (0.25), residues: 422 sheet: -0.93 (0.39), residues: 160 loop : 0.03 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 761 HIS 0.004 0.001 HIS A 872 PHE 0.009 0.001 PHE B 452 TYR 0.011 0.001 TYR A 787 ARG 0.004 0.000 ARG B 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 2.48597 ( 12) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 1.31332 ( 18) link_ALPHA1-3 : bond 0.01064 ( 2) link_ALPHA1-3 : angle 1.54992 ( 6) hydrogen bonds : bond 0.04037 ( 374) hydrogen bonds : angle 4.89666 ( 996) SS BOND : bond 0.00274 ( 10) SS BOND : angle 2.63071 ( 20) covalent geometry : bond 0.00268 (11618) covalent geometry : angle 0.50723 (15820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.093 Fit side-chains REVERT: A 391 LEU cc_start: 0.8806 (mp) cc_final: 0.8473 (tm) REVERT: A 505 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8891 (tt) REVERT: B 391 LEU cc_start: 0.8814 (mp) cc_final: 0.8474 (tm) REVERT: B 505 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8898 (tt) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 1.7944 time to fit residues: 184.0942 Evaluate side-chains 90 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.2980 chunk 117 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS B 321 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.087411 restraints weight = 16098.834| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.34 r_work: 0.2840 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11640 Z= 0.100 Angle : 0.508 5.604 15876 Z= 0.259 Chirality : 0.042 0.138 1760 Planarity : 0.004 0.038 2008 Dihedral : 5.777 54.836 1820 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.07 % Allowed : 10.56 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1356 helix: 1.52 (0.25), residues: 422 sheet: -0.89 (0.39), residues: 160 loop : 0.10 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 761 HIS 0.004 0.001 HIS A 872 PHE 0.009 0.001 PHE A 452 TYR 0.011 0.001 TYR B 787 ARG 0.008 0.000 ARG A 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 4) link_NAG-ASN : angle 2.42847 ( 12) link_BETA1-4 : bond 0.00536 ( 6) link_BETA1-4 : angle 1.27301 ( 18) link_ALPHA1-3 : bond 0.01061 ( 2) link_ALPHA1-3 : angle 1.50409 ( 6) hydrogen bonds : bond 0.03701 ( 374) hydrogen bonds : angle 4.80107 ( 996) SS BOND : bond 0.00203 ( 10) SS BOND : angle 1.79878 ( 20) covalent geometry : bond 0.00231 (11618) covalent geometry : angle 0.49738 (15820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 2.041 Fit side-chains REVERT: A 391 LEU cc_start: 0.8745 (mp) cc_final: 0.8477 (tm) REVERT: A 397 GLU cc_start: 0.8327 (pt0) cc_final: 0.8106 (pm20) REVERT: A 505 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8879 (tt) REVERT: B 391 LEU cc_start: 0.8765 (mp) cc_final: 0.8488 (tm) REVERT: B 397 GLU cc_start: 0.8265 (pt0) cc_final: 0.8062 (pm20) REVERT: B 505 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8883 (tt) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 2.2085 time to fit residues: 237.7311 Evaluate side-chains 96 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 116 optimal weight: 0.0020 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 HIS B 872 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085410 restraints weight = 16206.820| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.27 r_work: 0.2805 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11640 Z= 0.160 Angle : 0.541 6.505 15876 Z= 0.277 Chirality : 0.044 0.165 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.788 55.198 1820 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.57 % Allowed : 10.81 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1356 helix: 1.48 (0.25), residues: 422 sheet: -1.08 (0.39), residues: 164 loop : 0.07 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 266 HIS 0.005 0.001 HIS B 872 PHE 0.014 0.002 PHE A 452 TYR 0.011 0.001 TYR B 787 ARG 0.008 0.000 ARG A 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 2.58369 ( 12) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.36894 ( 18) link_ALPHA1-3 : bond 0.00949 ( 2) link_ALPHA1-3 : angle 1.47696 ( 6) hydrogen bonds : bond 0.04368 ( 374) hydrogen bonds : angle 4.89350 ( 996) SS BOND : bond 0.00235 ( 10) SS BOND : angle 1.52746 ( 20) covalent geometry : bond 0.00397 (11618) covalent geometry : angle 0.53197 (15820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 2.475 Fit side-chains REVERT: A 391 LEU cc_start: 0.8758 (mp) cc_final: 0.8484 (tm) REVERT: A 505 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8902 (tt) REVERT: B 391 LEU cc_start: 0.8769 (mp) cc_final: 0.8474 (mt) REVERT: B 505 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8911 (tt) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 2.2451 time to fit residues: 236.1526 Evaluate side-chains 95 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086527 restraints weight = 16072.522| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.32 r_work: 0.2825 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11640 Z= 0.115 Angle : 0.516 6.501 15876 Z= 0.263 Chirality : 0.042 0.164 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.614 54.930 1820 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.40 % Allowed : 11.30 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1356 helix: 1.55 (0.26), residues: 420 sheet: -0.94 (0.39), residues: 160 loop : 0.11 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 266 HIS 0.004 0.001 HIS B 872 PHE 0.010 0.001 PHE B 452 TYR 0.011 0.001 TYR A 787 ARG 0.008 0.000 ARG A 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 2.45025 ( 12) link_BETA1-4 : bond 0.00516 ( 6) link_BETA1-4 : angle 1.30431 ( 18) link_ALPHA1-3 : bond 0.00826 ( 2) link_ALPHA1-3 : angle 1.39227 ( 6) hydrogen bonds : bond 0.03873 ( 374) hydrogen bonds : angle 4.81508 ( 996) SS BOND : bond 0.00209 ( 10) SS BOND : angle 1.38222 ( 20) covalent geometry : bond 0.00277 (11618) covalent geometry : angle 0.50711 (15820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.344 Fit side-chains REVERT: A 391 LEU cc_start: 0.8711 (mp) cc_final: 0.8449 (tm) REVERT: A 505 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8897 (tt) REVERT: B 391 LEU cc_start: 0.8726 (mp) cc_final: 0.8457 (tm) REVERT: B 505 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8887 (tt) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 1.5152 time to fit residues: 164.9065 Evaluate side-chains 91 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086268 restraints weight = 16086.236| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.34 r_work: 0.2824 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11640 Z= 0.124 Angle : 0.529 6.963 15876 Z= 0.270 Chirality : 0.043 0.190 1760 Planarity : 0.004 0.054 2008 Dihedral : 5.577 55.167 1820 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.49 % Allowed : 11.47 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1356 helix: 1.54 (0.25), residues: 420 sheet: -0.89 (0.40), residues: 160 loop : 0.11 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 266 HIS 0.004 0.001 HIS B 872 PHE 0.011 0.001 PHE B 452 TYR 0.011 0.001 TYR A 787 ARG 0.013 0.000 ARG B 719 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 4) link_NAG-ASN : angle 2.46830 ( 12) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 1.33806 ( 18) link_ALPHA1-3 : bond 0.00766 ( 2) link_ALPHA1-3 : angle 1.36603 ( 6) hydrogen bonds : bond 0.03965 ( 374) hydrogen bonds : angle 4.80846 ( 996) SS BOND : bond 0.00210 ( 10) SS BOND : angle 1.32570 ( 20) covalent geometry : bond 0.00301 (11618) covalent geometry : angle 0.52073 (15820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.177 Fit side-chains REVERT: A 391 LEU cc_start: 0.8690 (mp) cc_final: 0.8415 (mt) REVERT: A 505 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8914 (tt) REVERT: B 216 GLN cc_start: 0.8146 (tp40) cc_final: 0.7943 (tp40) REVERT: B 391 LEU cc_start: 0.8707 (mp) cc_final: 0.8432 (mt) REVERT: B 505 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (tt) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 1.4241 time to fit residues: 140.0094 Evaluate side-chains 91 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.087170 restraints weight = 16014.189| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.28 r_work: 0.2832 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11640 Z= 0.116 Angle : 0.524 6.866 15876 Z= 0.267 Chirality : 0.042 0.198 1760 Planarity : 0.004 0.056 2008 Dihedral : 5.488 55.010 1820 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.16 % Allowed : 11.88 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1356 helix: 1.58 (0.26), residues: 420 sheet: -0.86 (0.40), residues: 160 loop : 0.12 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 761 HIS 0.004 0.001 HIS A 872 PHE 0.010 0.001 PHE A 452 TYR 0.011 0.001 TYR A 787 ARG 0.014 0.000 ARG B 719 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 2.41886 ( 12) link_BETA1-4 : bond 0.00506 ( 6) link_BETA1-4 : angle 1.33018 ( 18) link_ALPHA1-3 : bond 0.00729 ( 2) link_ALPHA1-3 : angle 1.37631 ( 6) hydrogen bonds : bond 0.03790 ( 374) hydrogen bonds : angle 4.78254 ( 996) SS BOND : bond 0.00212 ( 10) SS BOND : angle 1.29612 ( 20) covalent geometry : bond 0.00281 (11618) covalent geometry : angle 0.51647 (15820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.326 Fit side-chains REVERT: A 391 LEU cc_start: 0.8666 (mp) cc_final: 0.8414 (OUTLIER) REVERT: A 505 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8899 (tt) REVERT: B 391 LEU cc_start: 0.8679 (mp) cc_final: 0.8427 (OUTLIER) REVERT: B 505 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8900 (tt) outliers start: 14 outliers final: 13 residues processed: 91 average time/residue: 1.3394 time to fit residues: 132.7556 Evaluate side-chains 92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.085534 restraints weight = 16049.440| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.32 r_work: 0.2808 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11640 Z= 0.144 Angle : 0.543 6.810 15876 Z= 0.277 Chirality : 0.043 0.201 1760 Planarity : 0.004 0.037 2008 Dihedral : 5.551 55.586 1820 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.07 % Allowed : 12.05 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1356 helix: 1.50 (0.25), residues: 420 sheet: -1.04 (0.40), residues: 164 loop : 0.11 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.005 0.001 HIS B 872 PHE 0.013 0.001 PHE A 452 TYR 0.011 0.001 TYR B 787 ARG 0.008 0.000 ARG B 854 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 4) link_NAG-ASN : angle 2.49569 ( 12) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 1.39871 ( 18) link_ALPHA1-3 : bond 0.00753 ( 2) link_ALPHA1-3 : angle 1.41623 ( 6) hydrogen bonds : bond 0.04171 ( 374) hydrogen bonds : angle 4.84139 ( 996) SS BOND : bond 0.00220 ( 10) SS BOND : angle 1.39448 ( 20) covalent geometry : bond 0.00355 (11618) covalent geometry : angle 0.53414 (15820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7430.67 seconds wall clock time: 135 minutes 3.59 seconds (8103.59 seconds total)