Starting phenix.real_space_refine on Sun May 11 20:59:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fph_29364/05_2025/8fph_29364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fph_29364/05_2025/8fph_29364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fph_29364/05_2025/8fph_29364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fph_29364/05_2025/8fph_29364.map" model { file = "/net/cci-nas-00/data/ceres_data/8fph_29364/05_2025/8fph_29364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fph_29364/05_2025/8fph_29364.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.05, per 1000 atoms: 0.72 Number of scatterers: 8388 At special positions: 0 Unit cell: (117.189, 88.506, 84.4085, 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) Cl 4 17.00 S 64 16.00 O 1604 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 43.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.570A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.005A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.590A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.733A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.929A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.994A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.595A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.592A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.653A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.548A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.573A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.814A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.633A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.507A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.603A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.834A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.628A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.006A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.624A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.386A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.498A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.498A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.522A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.487A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.004A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.661A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.506A pdb=" N LYS D 441 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.296A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.576A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 933 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: 2.34 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2043 1.48 - 1.60: 3721 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11293 1.95 - 3.89: 152 3.89 - 5.84: 37 5.84 - 7.79: 24 7.79 - 9.74: 14 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.49 -9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.43 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 110.98 -9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 110.98 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.32 9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 4736 22.71 - 45.42: 415 45.42 - 68.12: 72 68.12 - 90.83: 13 90.83 - 113.54: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual -86.00 -149.05 63.05 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual -86.00 -28.29 -57.71 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" N2 CYZ B1302 " pdb=" C8 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" S1 CYZ B1302 " ideal model delta sinusoidal sigma weight residual 55.73 -57.81 113.54 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1175 0.086 - 0.172: 93 0.172 - 0.258: 0 0.258 - 0.344: 0 0.344 - 0.429: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 737 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 494 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 494 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.023 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1349 2.76 - 3.30: 7681 3.30 - 3.83: 13772 3.83 - 4.37: 16252 4.37 - 4.90: 28491 Nonbonded interactions: 67545 Sorted by model distance: nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 654 " pdb=" O HOH B1401 " model vdw 2.245 3.040 nonbonded pdb=" O LEU D 639 " pdb=" NE2 GLN D 642 " model vdw 2.270 3.120 nonbonded pdb=" NH1 ARG D 715 " pdb=" O TRP D 767 " model vdw 2.318 3.120 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.323 3.040 ... (remaining 67540 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' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } 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: 2.290 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.130 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.015 0.243 8542 Z= 0.727 Angle : 0.723 9.736 11528 Z= 0.314 Chirality : 0.062 0.429 1284 Planarity : 0.004 0.048 1422 Dihedral : 17.886 113.541 3288 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.11 % Allowed : 24.38 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.80 (0.25), residues: 1044 helix: 0.52 (0.26), residues: 416 sheet: -1.04 (0.38), residues: 172 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.005 0.001 HIS D 412 PHE 0.010 0.001 PHE D 495 TYR 0.010 0.001 TYR D 405 ARG 0.007 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.16395 ( 322) hydrogen bonds : angle 6.57010 ( 933) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.91750 ( 8) covalent geometry : bond 0.01459 ( 8538) covalent geometry : angle 0.72238 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.024 Fit side-chains REVERT: A 684 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7516 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2749 time to fit residues: 49.0908 Evaluate side-chains 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.164830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140842 restraints weight = 10241.151| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.07 r_work: 0.3481 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8542 Z= 0.109 Angle : 0.500 6.975 11528 Z= 0.248 Chirality : 0.043 0.138 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.095 93.638 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.46 % Allowed : 21.81 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.74 (0.25), residues: 1044 helix: 0.63 (0.25), residues: 436 sheet: -0.98 (0.39), residues: 156 loop : -1.38 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.017 0.001 PHE D 438 TYR 0.009 0.001 TYR D 405 ARG 0.004 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 322) hydrogen bonds : angle 4.94688 ( 933) SS BOND : bond 0.00320 ( 4) SS BOND : angle 0.84398 ( 8) covalent geometry : bond 0.00259 ( 8538) covalent geometry : angle 0.49935 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.922 Fit side-chains REVERT: A 408 MET cc_start: 0.7750 (mtp) cc_final: 0.7534 (mtp) REVERT: D 402 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7417 (mm-30) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.2626 time to fit residues: 55.0454 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140704 restraints weight = 10327.025| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.07 r_work: 0.3480 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.106 Angle : 0.500 7.054 11528 Z= 0.244 Chirality : 0.043 0.180 1284 Planarity : 0.003 0.036 1422 Dihedral : 9.247 88.569 1266 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.24 % Allowed : 22.60 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1044 helix: 0.86 (0.25), residues: 432 sheet: -0.83 (0.41), residues: 146 loop : -1.36 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE D 495 TYR 0.016 0.001 TYR C 450 ARG 0.003 0.000 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.02799 ( 322) hydrogen bonds : angle 4.73273 ( 933) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.78341 ( 8) covalent geometry : bond 0.00253 ( 8538) covalent geometry : angle 0.49944 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.035 Fit side-chains REVERT: A 760 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: A 773 CYS cc_start: 0.4667 (t) cc_final: 0.4343 (t) REVERT: C 408 MET cc_start: 0.8180 (tpp) cc_final: 0.7894 (tpp) REVERT: D 402 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7455 (mm-30) outliers start: 29 outliers final: 19 residues processed: 150 average time/residue: 0.2714 time to fit residues: 53.1583 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 0.0060 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132621 restraints weight = 10496.464| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.07 r_work: 0.3376 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 8542 Z= 0.287 Angle : 0.682 9.428 11528 Z= 0.343 Chirality : 0.052 0.244 1284 Planarity : 0.004 0.038 1422 Dihedral : 9.581 106.350 1266 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.82 % Allowed : 21.70 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -1.22 (0.24), residues: 1044 helix: 0.39 (0.25), residues: 424 sheet: -1.43 (0.38), residues: 162 loop : -1.68 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 460 HIS 0.005 0.002 HIS D 412 PHE 0.018 0.003 PHE A 495 TYR 0.015 0.002 TYR D 405 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 322) hydrogen bonds : angle 5.02038 ( 933) SS BOND : bond 0.00604 ( 4) SS BOND : angle 1.29035 ( 8) covalent geometry : bond 0.00713 ( 8538) covalent geometry : angle 0.68150 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 1.046 Fit side-chains REVERT: B 466 GLU cc_start: 0.8130 (pp20) cc_final: 0.7753 (pt0) REVERT: C 497 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8633 (p) REVERT: D 402 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7713 (mm-30) REVERT: D 453 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7619 (ttm-80) REVERT: D 466 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7775 (pp20) REVERT: D 695 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7132 (tptt) outliers start: 52 outliers final: 32 residues processed: 179 average time/residue: 0.2851 time to fit residues: 65.4501 Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 678 GLU Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.0570 chunk 78 optimal weight: 0.4980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.162878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139259 restraints weight = 10222.962| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.03 r_work: 0.3459 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8542 Z= 0.096 Angle : 0.486 7.181 11528 Z= 0.242 Chirality : 0.043 0.175 1284 Planarity : 0.003 0.038 1422 Dihedral : 8.403 93.629 1266 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.02 % Allowed : 25.06 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.76 (0.25), residues: 1044 helix: 0.92 (0.25), residues: 426 sheet: -1.20 (0.35), residues: 182 loop : -1.60 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 PHE 0.008 0.001 PHE D 495 TYR 0.009 0.001 TYR B 673 ARG 0.005 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02616 ( 322) hydrogen bonds : angle 4.66166 ( 933) SS BOND : bond 0.00516 ( 4) SS BOND : angle 0.70421 ( 8) covalent geometry : bond 0.00219 ( 8538) covalent geometry : angle 0.48625 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.040 Fit side-chains REVERT: A 684 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7946 (mtm180) REVERT: A 695 LYS cc_start: 0.7632 (tppt) cc_final: 0.7212 (tptt) REVERT: A 760 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: D 402 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7454 (mm-30) REVERT: D 405 TYR cc_start: 0.8455 (m-80) cc_final: 0.8074 (m-80) REVERT: D 422 GLU cc_start: 0.7960 (pt0) cc_final: 0.7758 (pt0) REVERT: D 675 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7872 (ttm-80) REVERT: D 761 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7960 (tmmt) outliers start: 27 outliers final: 15 residues processed: 151 average time/residue: 0.2596 time to fit residues: 50.7973 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135862 restraints weight = 10327.318| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.05 r_work: 0.3419 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8542 Z= 0.169 Angle : 0.549 7.937 11528 Z= 0.274 Chirality : 0.046 0.167 1284 Planarity : 0.004 0.038 1422 Dihedral : 8.326 96.955 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.70 % Allowed : 23.60 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.90 (0.24), residues: 1044 helix: 0.81 (0.25), residues: 426 sheet: -1.50 (0.35), residues: 176 loop : -1.58 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.012 0.002 PHE A 495 TYR 0.017 0.001 TYR C 450 ARG 0.004 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 322) hydrogen bonds : angle 4.72618 ( 933) SS BOND : bond 0.00433 ( 4) SS BOND : angle 0.80097 ( 8) covalent geometry : bond 0.00416 ( 8538) covalent geometry : angle 0.54830 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.934 Fit side-chains REVERT: A 760 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: B 466 GLU cc_start: 0.8195 (pp20) cc_final: 0.7799 (pt0) REVERT: B 634 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 634 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 402 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 675 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7797 (ttm-80) REVERT: D 684 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6546 (tpm170) REVERT: D 695 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7096 (tptt) REVERT: D 761 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7974 (tmmt) outliers start: 42 outliers final: 28 residues processed: 161 average time/residue: 0.2760 time to fit residues: 56.6352 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.162263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138490 restraints weight = 10372.144| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.05 r_work: 0.3454 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8542 Z= 0.103 Angle : 0.488 6.744 11528 Z= 0.242 Chirality : 0.043 0.213 1284 Planarity : 0.003 0.037 1422 Dihedral : 7.544 91.761 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.58 % Allowed : 24.50 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.65 (0.25), residues: 1044 helix: 0.98 (0.25), residues: 428 sheet: -1.08 (0.36), residues: 172 loop : -1.56 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.010 0.001 TYR B 673 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 322) hydrogen bonds : angle 4.59535 ( 933) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.67183 ( 8) covalent geometry : bond 0.00243 ( 8538) covalent geometry : angle 0.48825 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 684 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7943 (mtm180) REVERT: A 695 LYS cc_start: 0.7628 (tppt) cc_final: 0.7241 (tptt) REVERT: A 760 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 705 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C 497 SER cc_start: 0.8838 (t) cc_final: 0.8578 (p) REVERT: D 402 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7525 (mm-30) REVERT: D 405 TYR cc_start: 0.8519 (m-80) cc_final: 0.8140 (m-80) REVERT: D 408 MET cc_start: 0.7293 (mmt) cc_final: 0.6938 (mmt) REVERT: D 675 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: D 684 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6555 (tpm170) REVERT: D 761 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7986 (tmmt) outliers start: 32 outliers final: 24 residues processed: 158 average time/residue: 0.2684 time to fit residues: 54.6067 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 0.0770 chunk 49 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140816 restraints weight = 10287.742| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.04 r_work: 0.3480 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8542 Z= 0.089 Angle : 0.464 6.393 11528 Z= 0.232 Chirality : 0.042 0.167 1284 Planarity : 0.003 0.036 1422 Dihedral : 6.573 79.959 1266 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 24.83 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 (0.25), residues: 1044 helix: 1.23 (0.26), residues: 426 sheet: -0.95 (0.36), residues: 172 loop : -1.37 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.008 0.001 TYR B 673 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02514 ( 322) hydrogen bonds : angle 4.49944 ( 933) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.58001 ( 8) covalent geometry : bond 0.00206 ( 8538) covalent geometry : angle 0.46346 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 684 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7907 (mtm180) REVERT: A 695 LYS cc_start: 0.7640 (tppt) cc_final: 0.7220 (tptt) REVERT: A 760 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: C 486 GLU cc_start: 0.7332 (tp30) cc_final: 0.7058 (tp30) REVERT: C 497 SER cc_start: 0.8808 (t) cc_final: 0.8560 (p) REVERT: D 405 TYR cc_start: 0.8451 (m-80) cc_final: 0.8127 (m-80) REVERT: D 414 MET cc_start: 0.5542 (ppp) cc_final: 0.4922 (ppp) REVERT: D 684 ARG cc_start: 0.7276 (ptp-110) cc_final: 0.6524 (tpm170) REVERT: D 761 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7967 (tmmt) outliers start: 27 outliers final: 22 residues processed: 152 average time/residue: 0.2556 time to fit residues: 50.1764 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.0050 chunk 65 optimal weight: 6.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140174 restraints weight = 10409.516| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.07 r_work: 0.3479 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8542 Z= 0.094 Angle : 0.474 7.000 11528 Z= 0.236 Chirality : 0.043 0.203 1284 Planarity : 0.003 0.035 1422 Dihedral : 5.939 61.502 1266 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.91 % Allowed : 24.72 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.29 (0.25), residues: 1044 helix: 1.24 (0.25), residues: 428 sheet: -0.94 (0.36), residues: 172 loop : -1.28 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.004 0.001 HIS D 412 PHE 0.008 0.001 PHE D 438 TYR 0.008 0.001 TYR B 673 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02537 ( 322) hydrogen bonds : angle 4.51012 ( 933) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.56050 ( 8) covalent geometry : bond 0.00223 ( 8538) covalent geometry : angle 0.47421 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 684 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7913 (mtm180) REVERT: A 695 LYS cc_start: 0.7616 (tppt) cc_final: 0.7214 (tptt) REVERT: A 760 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: C 486 GLU cc_start: 0.7346 (tp30) cc_final: 0.7079 (tp30) REVERT: C 497 SER cc_start: 0.8792 (t) cc_final: 0.8570 (p) REVERT: D 402 GLU cc_start: 0.7935 (tp30) cc_final: 0.7735 (tp30) REVERT: D 414 MET cc_start: 0.5418 (ppp) cc_final: 0.4885 (ppp) REVERT: D 466 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: D 684 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6566 (tpm170) REVERT: D 761 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7951 (tmmt) outliers start: 26 outliers final: 21 residues processed: 156 average time/residue: 0.2607 time to fit residues: 52.8352 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140678 restraints weight = 10340.313| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.04 r_work: 0.3488 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8542 Z= 0.094 Angle : 0.470 6.358 11528 Z= 0.238 Chirality : 0.042 0.176 1284 Planarity : 0.003 0.034 1422 Dihedral : 5.324 49.691 1266 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.13 % Allowed : 24.83 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.21 (0.25), residues: 1044 helix: 1.29 (0.25), residues: 428 sheet: -0.85 (0.37), residues: 170 loop : -1.25 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS D 412 PHE 0.008 0.001 PHE D 495 TYR 0.008 0.001 TYR B 673 ARG 0.005 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02515 ( 322) hydrogen bonds : angle 4.48402 ( 933) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.57613 ( 8) covalent geometry : bond 0.00219 ( 8538) covalent geometry : angle 0.47035 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.037 Fit side-chains REVERT: A 695 LYS cc_start: 0.7631 (tppt) cc_final: 0.7223 (tptt) REVERT: A 760 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: D 414 MET cc_start: 0.5345 (ppp) cc_final: 0.4831 (ppp) REVERT: D 466 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: D 684 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6573 (tpm170) REVERT: D 761 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7943 (tmmt) outliers start: 28 outliers final: 22 residues processed: 153 average time/residue: 0.2425 time to fit residues: 48.6989 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138105 restraints weight = 10451.901| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.05 r_work: 0.3454 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8542 Z= 0.125 Angle : 0.510 7.714 11528 Z= 0.257 Chirality : 0.044 0.148 1284 Planarity : 0.003 0.035 1422 Dihedral : 5.465 45.464 1266 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.91 % Allowed : 25.06 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1044 helix: 1.18 (0.25), residues: 426 sheet: -0.99 (0.39), residues: 144 loop : -1.32 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS D 412 PHE 0.010 0.001 PHE D 495 TYR 0.010 0.001 TYR B 673 ARG 0.002 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 322) hydrogen bonds : angle 4.55293 ( 933) SS BOND : bond 0.00240 ( 4) SS BOND : angle 1.09687 ( 8) covalent geometry : bond 0.00302 ( 8538) covalent geometry : angle 0.50945 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4604.83 seconds wall clock time: 80 minutes 27.55 seconds (4827.55 seconds total)