Starting phenix.real_space_refine on Fri Aug 22 22:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fph_29364/08_2025/8fph_29364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fph_29364/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fph_29364/08_2025/8fph_29364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fph_29364/08_2025/8fph_29364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fph_29364/08_2025/8fph_29364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fph_29364/08_2025/8fph_29364.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.83, per 1000 atoms: 0.34 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: 0.92 Conformation dependent library (CDL) restraints added in 578.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.34 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: 1.34 Time building geometry restraints manager: 1.16 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 through 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 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 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 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG C 675 TYR 0.010 0.001 TYR D 405 PHE 0.010 0.001 PHE D 495 TRP 0.006 0.001 TRP D 460 HIS 0.005 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.01459 ( 8538) covalent geometry : angle 0.72238 (11520) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.91750 ( 8) hydrogen bonds : bond 0.16395 ( 322) hydrogen bonds : angle 6.57010 ( 933) *********************** 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 : 0.342 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: 0.1412 time to fit residues: 25.1569 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.161792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137656 restraints weight = 10358.613| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.08 r_work: 0.3435 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8542 Z= 0.172 Angle : 0.563 8.212 11528 Z= 0.282 Chirality : 0.046 0.152 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.439 98.349 1266 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.13 % Allowed : 22.15 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.25), residues: 1044 helix: 0.48 (0.25), residues: 432 sheet: -1.16 (0.38), residues: 156 loop : -1.47 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 684 TYR 0.013 0.001 TYR D 405 PHE 0.017 0.002 PHE D 438 TRP 0.010 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8538) covalent geometry : angle 0.56274 (11520) SS BOND : bond 0.00419 ( 4) SS BOND : angle 1.08505 ( 8) hydrogen bonds : bond 0.03468 ( 322) hydrogen bonds : angle 5.01611 ( 933) *********************** 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 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.282 Fit side-chains REVERT: D 402 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7494 (mm-30) outliers start: 28 outliers final: 20 residues processed: 159 average time/residue: 0.1314 time to fit residues: 27.1070 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 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 B residue 403 SER Chi-restraints excluded: chain B residue 630 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 666 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 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 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.162084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138244 restraints weight = 10333.552| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.06 r_work: 0.3442 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8542 Z= 0.133 Angle : 0.528 7.786 11528 Z= 0.259 Chirality : 0.044 0.167 1284 Planarity : 0.004 0.038 1422 Dihedral : 9.503 90.750 1266 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.47 % Allowed : 22.37 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.25), residues: 1044 helix: 0.67 (0.25), residues: 430 sheet: -1.00 (0.37), residues: 172 loop : -1.54 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 715 TYR 0.017 0.001 TYR C 450 PHE 0.010 0.001 PHE D 495 TRP 0.009 0.001 TRP D 460 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8538) covalent geometry : angle 0.52732 (11520) SS BOND : bond 0.00477 ( 4) SS BOND : angle 0.95223 ( 8) hydrogen bonds : bond 0.03095 ( 322) hydrogen bonds : angle 4.80960 ( 933) *********************** 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 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 760 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: C 408 MET cc_start: 0.8243 (tpp) cc_final: 0.7942 (tpp) REVERT: D 402 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 40 outliers final: 26 residues processed: 171 average time/residue: 0.1281 time to fit residues: 28.5366 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 445 VAL Chi-restraints excluded: chain B residue 498 LEU 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 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 662 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.161850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137872 restraints weight = 10415.029| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.07 r_work: 0.3436 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8542 Z= 0.130 Angle : 0.523 7.687 11528 Z= 0.257 Chirality : 0.045 0.220 1284 Planarity : 0.004 0.038 1422 Dihedral : 8.464 87.309 1266 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.70 % Allowed : 23.04 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1044 helix: 0.86 (0.25), residues: 428 sheet: -1.16 (0.35), residues: 182 loop : -1.61 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 684 TYR 0.009 0.001 TYR A 450 PHE 0.010 0.001 PHE D 495 TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8538) covalent geometry : angle 0.52298 (11520) SS BOND : bond 0.00378 ( 4) SS BOND : angle 0.78535 ( 8) hydrogen bonds : bond 0.02966 ( 322) hydrogen bonds : angle 4.69703 ( 933) *********************** 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 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.367 Fit side-chains REVERT: A 684 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7893 (mtm180) REVERT: A 760 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: C 408 MET cc_start: 0.8256 (tpp) cc_final: 0.8039 (tpp) REVERT: D 402 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7506 (mm-30) outliers start: 42 outliers final: 29 residues processed: 169 average time/residue: 0.1300 time to fit residues: 28.5538 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 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 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 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 466 GLU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 662 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 4.9990 chunk 69 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139609 restraints weight = 10335.945| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.06 r_work: 0.3464 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1454 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 : 0.481 6.967 11528 Z= 0.237 Chirality : 0.043 0.179 1284 Planarity : 0.003 0.036 1422 Dihedral : 7.494 77.784 1266 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.69 % Allowed : 24.05 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.25), residues: 1044 helix: 1.00 (0.25), residues: 430 sheet: -1.09 (0.35), residues: 182 loop : -1.44 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 675 TYR 0.009 0.001 TYR B 673 PHE 0.008 0.001 PHE D 495 TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8538) covalent geometry : angle 0.48125 (11520) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.59956 ( 8) hydrogen bonds : bond 0.02611 ( 322) hydrogen bonds : angle 4.59647 ( 933) *********************** 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 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.356 Fit side-chains REVERT: A 695 LYS cc_start: 0.7510 (tppt) cc_final: 0.7198 (tptt) REVERT: A 760 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 466 GLU cc_start: 0.8119 (pp20) cc_final: 0.7794 (pt0) REVERT: D 402 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7511 (mm-30) REVERT: D 642 GLN cc_start: 0.7250 (pp30) cc_final: 0.7038 (pp30) REVERT: D 761 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7989 (tmmt) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 0.1222 time to fit residues: 26.5555 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 666 VAL 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 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.163177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139509 restraints weight = 10331.377| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.04 r_work: 0.3471 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8542 Z= 0.102 Angle : 0.479 6.584 11528 Z= 0.237 Chirality : 0.044 0.223 1284 Planarity : 0.003 0.036 1422 Dihedral : 6.265 56.793 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.25 % Allowed : 23.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.25), residues: 1044 helix: 1.06 (0.25), residues: 430 sheet: -1.19 (0.37), residues: 156 loop : -1.42 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 675 TYR 0.009 0.001 TYR B 673 PHE 0.009 0.001 PHE D 495 TRP 0.009 0.001 TRP D 460 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8538) covalent geometry : angle 0.47845 (11520) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.67184 ( 8) hydrogen bonds : bond 0.02632 ( 322) hydrogen bonds : angle 4.52673 ( 933) *********************** 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 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.364 Fit side-chains REVERT: A 695 LYS cc_start: 0.7656 (tppt) cc_final: 0.7256 (tptt) REVERT: A 760 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: B 466 GLU cc_start: 0.8149 (pp20) cc_final: 0.7818 (pt0) REVERT: D 402 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 408 MET cc_start: 0.7313 (mmt) cc_final: 0.6965 (mmt) REVERT: D 761 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7976 (tmmt) outliers start: 38 outliers final: 28 residues processed: 166 average time/residue: 0.1150 time to fit residues: 25.1136 Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 497 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 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 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 630 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.164535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140950 restraints weight = 10360.384| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.05 r_work: 0.3465 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8542 Z= 0.104 Angle : 0.477 6.634 11528 Z= 0.239 Chirality : 0.043 0.183 1284 Planarity : 0.003 0.035 1422 Dihedral : 5.637 49.915 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.47 % Allowed : 23.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.25), residues: 1044 helix: 1.10 (0.25), residues: 430 sheet: -1.20 (0.37), residues: 156 loop : -1.39 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 675 TYR 0.009 0.001 TYR B 673 PHE 0.009 0.001 PHE D 495 TRP 0.008 0.001 TRP D 460 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8538) covalent geometry : angle 0.47694 (11520) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.58655 ( 8) hydrogen bonds : bond 0.02698 ( 322) hydrogen bonds : angle 4.52767 ( 933) *********************** 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 176 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.384 Fit side-chains REVERT: A 695 LYS cc_start: 0.7691 (tppt) cc_final: 0.7283 (tptt) REVERT: A 705 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: A 760 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: B 466 GLU cc_start: 0.8138 (pp20) cc_final: 0.7824 (pt0) REVERT: D 408 MET cc_start: 0.7249 (mmt) cc_final: 0.6904 (mmt) REVERT: D 684 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6540 (tpm170) REVERT: D 761 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7949 (tmmt) outliers start: 40 outliers final: 29 residues processed: 164 average time/residue: 0.1169 time to fit residues: 24.9613 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 705 GLU 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 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 442 LEU 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 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 630 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.0050 chunk 39 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.165182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141585 restraints weight = 10267.426| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.05 r_work: 0.3502 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8542 Z= 0.085 Angle : 0.450 6.328 11528 Z= 0.226 Chirality : 0.042 0.136 1284 Planarity : 0.003 0.035 1422 Dihedral : 5.178 43.606 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.68 % Allowed : 24.61 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.25), residues: 1044 helix: 1.24 (0.25), residues: 430 sheet: -1.07 (0.35), residues: 182 loop : -1.28 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 675 TYR 0.009 0.001 TYR B 673 PHE 0.008 0.001 PHE B 438 TRP 0.009 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8538) covalent geometry : angle 0.44983 (11520) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.51430 ( 8) hydrogen bonds : bond 0.02394 ( 322) hydrogen bonds : angle 4.47053 ( 933) *********************** 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 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.288 Fit side-chains REVERT: A 695 LYS cc_start: 0.7644 (tppt) cc_final: 0.7231 (tptt) REVERT: A 705 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: A 760 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: A 773 CYS cc_start: 0.4790 (t) cc_final: 0.4546 (t) REVERT: B 466 GLU cc_start: 0.8135 (pp20) cc_final: 0.7849 (pt0) REVERT: D 408 MET cc_start: 0.7252 (mmt) cc_final: 0.6944 (mmt) REVERT: D 761 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7875 (tmmt) outliers start: 24 outliers final: 20 residues processed: 150 average time/residue: 0.1179 time to fit residues: 23.0699 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU 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 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 662 SER 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 104 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.159422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135518 restraints weight = 10461.511| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.06 r_work: 0.3415 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8542 Z= 0.184 Angle : 0.572 8.127 11528 Z= 0.286 Chirality : 0.047 0.166 1284 Planarity : 0.004 0.036 1422 Dihedral : 5.826 46.522 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.59 % Allowed : 22.71 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.25), residues: 1044 helix: 0.89 (0.25), residues: 428 sheet: -1.48 (0.35), residues: 176 loop : -1.40 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 675 TYR 0.020 0.002 TYR C 450 PHE 0.013 0.002 PHE A 495 TRP 0.005 0.001 TRP B 460 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8538) covalent geometry : angle 0.57131 (11520) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.20224 ( 8) hydrogen bonds : bond 0.03467 ( 322) hydrogen bonds : angle 4.69082 ( 933) *********************** 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 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.375 Fit side-chains REVERT: A 705 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: A 760 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: B 634 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7050 (mt-10) REVERT: D 408 MET cc_start: 0.7468 (mmt) cc_final: 0.7147 (mmt) REVERT: D 675 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: D 684 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6631 (tpm170) REVERT: D 761 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7989 (tmmt) outliers start: 41 outliers final: 30 residues processed: 165 average time/residue: 0.1288 time to fit residues: 27.5948 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 705 GLU 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 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 748 LEU 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 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 630 VAL 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 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138865 restraints weight = 10252.454| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.04 r_work: 0.3458 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8542 Z= 0.106 Angle : 0.497 7.013 11528 Z= 0.249 Chirality : 0.043 0.130 1284 Planarity : 0.003 0.036 1422 Dihedral : 5.509 43.570 1266 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.02 % Allowed : 24.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.25), residues: 1044 helix: 1.09 (0.25), residues: 428 sheet: -1.27 (0.36), residues: 154 loop : -1.41 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 661 TYR 0.009 0.001 TYR A 450 PHE 0.009 0.001 PHE D 495 TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8538) covalent geometry : angle 0.49688 (11520) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.92551 ( 8) hydrogen bonds : bond 0.02706 ( 322) hydrogen bonds : angle 4.55997 ( 933) ********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.404 Fit side-chains REVERT: A 695 LYS cc_start: 0.7659 (tppt) cc_final: 0.7237 (tptt) REVERT: A 705 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: A 760 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 422 GLU cc_start: 0.8031 (pt0) cc_final: 0.7794 (pt0) REVERT: B 705 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8362 (mm-30) REVERT: D 761 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7933 (tmmt) outliers start: 27 outliers final: 22 residues processed: 151 average time/residue: 0.1215 time to fit residues: 23.6629 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU 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 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 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 D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL 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 10 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.162890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139088 restraints weight = 10368.357| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.06 r_work: 0.3461 rms_B_bonded: 2.62 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: 0.8076 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.109 Angle : 0.498 7.020 11528 Z= 0.250 Chirality : 0.043 0.129 1284 Planarity : 0.003 0.036 1422 Dihedral : 5.385 42.450 1266 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.36 % Allowed : 23.83 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.25), residues: 1044 helix: 1.16 (0.25), residues: 426 sheet: -1.26 (0.36), residues: 154 loop : -1.33 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 675 TYR 0.014 0.001 TYR C 450 PHE 0.009 0.001 PHE D 495 TRP 0.006 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8538) covalent geometry : angle 0.49803 (11520) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.79439 ( 8) hydrogen bonds : bond 0.02743 ( 322) hydrogen bonds : angle 4.53858 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.86 seconds wall clock time: 40 minutes 31.50 seconds (2431.50 seconds total)