Starting phenix.real_space_refine on Fri Aug 22 22:55:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqg_29387/08_2025/8fqg_29387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqg_29387/08_2025/8fqg_29387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqg_29387/08_2025/8fqg_29387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqg_29387/08_2025/8fqg_29387.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqg_29387/08_2025/8fqg_29387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqg_29387/08_2025/8fqg_29387.cif" } resolution = 3.01 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 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s 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: 8392 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 1.90, per 1000 atoms: 0.23 Number of scatterers: 8392 At special positions: 0 Unit cell: (118.9, 86.1, 83.64, 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 1608 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=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 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: 0.53 Conformation dependent library (CDL) restraints added in 399.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 17 sheets defined 43.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.670A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (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: 4.065A 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 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 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 removed outlier: 3.569A pdb=" N MET C 414 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.584A 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 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 654 through 662 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 Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.034A 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: 3.754A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 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 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.386A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.386A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.414A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.622A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.622A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) 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 646 through 648 removed outlier: 6.615A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 439 through 444 removed outlier: 6.564A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB2, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.903A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.498A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.530A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.933A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.615A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1014 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: 0.95 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2630 1.35 - 1.47: 2035 1.47 - 1.60: 3729 1.60 - 1.72: 40 1.72 - 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 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=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+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 1.24e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 11336 2.18 - 4.35: 115 4.35 - 6.53: 42 6.53 - 8.71: 18 8.71 - 10.88: 9 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C LYS A 409 " pdb=" CA LYS A 409 " pdb=" CB LYS A 409 " ideal model delta sigma weight residual 115.79 109.83 5.96 1.19e+00 7.06e-01 2.51e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CA GLU B 416 " pdb=" CB GLU B 416 " pdb=" CG GLU B 416 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.13 -9.38 3.00e+00 1.11e-01 9.78e+00 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.05 -9.30 3.00e+00 1.11e-01 9.61e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 4733 23.08 - 46.16: 437 46.16 - 69.25: 53 69.25 - 92.33: 13 92.33 - 115.41: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: 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 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 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 93.00 169.77 -76.77 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 151.45 -58.45 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1179 0.085 - 0.170: 86 0.170 - 0.255: 3 0.255 - 0.340: 0 0.340 - 0.425: 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 0.42 2.00e-01 2.50e+01 4.51e+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 2.89 0.42 2.00e-01 2.50e+01 4.49e+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 4.48e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 737 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 625 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C THR B 625 " 0.027 2.00e-02 2.50e+03 pdb=" O THR B 625 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 626 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 454 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" CG ASP B 454 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP B 454 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP B 454 " 0.007 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1450 2.77 - 3.30: 7851 3.30 - 3.83: 14300 3.83 - 4.37: 17137 4.37 - 4.90: 29425 Nonbonded interactions: 70163 Sorted by model distance: nonbonded pdb=" OD1 ASP B 454 " pdb=" N ALA B 455 " model vdw 2.233 3.120 nonbonded pdb=" OE2 GLU A 402 " pdb=" OH TYR A 450 " model vdw 2.243 3.040 nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.258 3.040 nonbonded pdb=" NH1 ARG B 715 " pdb=" O TRP B 767 " model vdw 2.273 3.120 nonbonded pdb=" O VAL D 681 " pdb=" OH TYR D 700 " model vdw 2.286 3.040 ... (remaining 70158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 4.250 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.580 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.730 10.883 11528 Z= 0.324 Chirality : 0.062 0.425 1284 Planarity : 0.003 0.044 1422 Dihedral : 17.672 115.409 3288 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.22 % Allowed : 21.25 % Favored : 78.52 % 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: 0.88 (0.25), residues: 424 sheet: -1.24 (0.37), residues: 160 loop : -1.08 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 675 TYR 0.011 0.001 TYR D 673 PHE 0.009 0.001 PHE B 495 TRP 0.007 0.001 TRP B 671 HIS 0.004 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.01461 ( 8538) covalent geometry : angle 0.72975 (11520) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.81046 ( 8) hydrogen bonds : bond 0.17677 ( 344) hydrogen bonds : angle 6.79775 ( 1014) *********************** 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 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.345 Fit side-chains REVERT: A 669 LYS cc_start: 0.6943 (tttp) cc_final: 0.6713 (tttp) REVERT: B 416 GLU cc_start: 0.6002 (tp30) cc_final: 0.5296 (tt0) REVERT: C 651 ASP cc_start: 0.7570 (t70) cc_final: 0.7359 (p0) REVERT: D 453 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7769 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 124 average time/residue: 0.1214 time to fit residues: 18.9252 Evaluate side-chains 121 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 414 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 714 GLN D 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113264 restraints weight = 10382.101| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.10 r_work: 0.3155 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8542 Z= 0.213 Angle : 0.579 7.560 11528 Z= 0.298 Chirality : 0.047 0.237 1284 Planarity : 0.004 0.044 1422 Dihedral : 11.708 106.308 1270 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.02 % Allowed : 19.35 % Favored : 77.63 % 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: -0.60 (0.25), residues: 1044 helix: 0.69 (0.25), residues: 438 sheet: -1.30 (0.39), residues: 146 loop : -1.09 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 628 TYR 0.017 0.002 TYR D 673 PHE 0.015 0.002 PHE D 659 TRP 0.010 0.001 TRP B 671 HIS 0.005 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8538) covalent geometry : angle 0.57812 (11520) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.98561 ( 8) hydrogen bonds : bond 0.04373 ( 344) hydrogen bonds : angle 5.09540 ( 1014) *********************** 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 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.234 Fit side-chains REVERT: A 669 LYS cc_start: 0.7115 (tttp) cc_final: 0.6872 (tttp) REVERT: B 399 THR cc_start: 0.8660 (m) cc_final: 0.8455 (m) REVERT: B 414 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6053 (pmm) REVERT: B 628 ARG cc_start: 0.7021 (mtt-85) cc_final: 0.6389 (mtm110) REVERT: C 660 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7760 (ttm170) REVERT: C 695 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7511 (mtmt) outliers start: 27 outliers final: 19 residues processed: 143 average time/residue: 0.1011 time to fit residues: 18.3962 Evaluate side-chains 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LYS 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 B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN D 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116433 restraints weight = 10298.158| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.08 r_work: 0.3194 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8542 Z= 0.107 Angle : 0.475 6.102 11528 Z= 0.243 Chirality : 0.043 0.172 1284 Planarity : 0.003 0.047 1422 Dihedral : 10.534 96.023 1266 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.01 % Allowed : 21.81 % Favored : 76.17 % 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: -0.39 (0.25), residues: 1044 helix: 0.90 (0.25), residues: 440 sheet: -1.17 (0.40), residues: 138 loop : -1.05 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 628 TYR 0.011 0.001 TYR D 673 PHE 0.010 0.001 PHE B 438 TRP 0.007 0.001 TRP B 671 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8538) covalent geometry : angle 0.47446 (11520) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.92141 ( 8) hydrogen bonds : bond 0.03049 ( 344) hydrogen bonds : angle 4.68859 ( 1014) *********************** 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 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.284 Fit side-chains REVERT: A 634 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6378 (tp30) REVERT: A 669 LYS cc_start: 0.7084 (tttp) cc_final: 0.6738 (tttp) REVERT: B 399 THR cc_start: 0.8513 (m) cc_final: 0.8300 (m) REVERT: B 628 ARG cc_start: 0.6870 (mtt-85) cc_final: 0.6282 (mtm110) REVERT: C 695 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7473 (mtmt) REVERT: D 466 GLU cc_start: 0.8108 (pp20) cc_final: 0.7642 (pt0) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.0892 time to fit residues: 16.2555 Evaluate side-chains 131 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 718 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN D 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109468 restraints weight = 10622.513| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.11 r_work: 0.3104 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.007 0.095 8542 Z= 0.307 Angle : 0.659 8.345 11528 Z= 0.336 Chirality : 0.052 0.301 1284 Planarity : 0.004 0.045 1422 Dihedral : 12.034 109.972 1266 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.91 % Allowed : 21.59 % Favored : 74.50 % 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: -0.82 (0.25), residues: 1044 helix: 0.48 (0.25), residues: 436 sheet: -1.51 (0.37), residues: 156 loop : -1.11 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 715 TYR 0.020 0.002 TYR D 673 PHE 0.022 0.003 PHE D 659 TRP 0.009 0.002 TRP D 671 HIS 0.007 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00745 ( 8538) covalent geometry : angle 0.65798 (11520) SS BOND : bond 0.00527 ( 4) SS BOND : angle 1.41317 ( 8) hydrogen bonds : bond 0.04554 ( 344) hydrogen bonds : angle 5.02192 ( 1014) *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.246 Fit side-chains REVERT: A 634 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6426 (tp30) REVERT: B 399 THR cc_start: 0.8670 (m) cc_final: 0.8417 (m) REVERT: B 414 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6212 (pmm) REVERT: B 628 ARG cc_start: 0.7025 (mtt-85) cc_final: 0.6397 (mtm110) REVERT: B 765 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7667 (pttp) REVERT: C 441 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8250 (ttmt) REVERT: C 643 THR cc_start: 0.7117 (p) cc_final: 0.6887 (t) REVERT: C 660 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8135 (ttm170) REVERT: C 695 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7521 (mtmt) REVERT: D 466 GLU cc_start: 0.8204 (pp20) cc_final: 0.7771 (pt0) REVERT: D 661 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7769 (mtm-85) outliers start: 35 outliers final: 23 residues processed: 155 average time/residue: 0.1086 time to fit residues: 21.1541 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 681 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN B 747 ASN C 642 GLN D 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113998 restraints weight = 10507.196| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.08 r_work: 0.3170 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8542 Z= 0.123 Angle : 0.499 7.488 11528 Z= 0.256 Chirality : 0.043 0.148 1284 Planarity : 0.004 0.044 1422 Dihedral : 10.845 98.654 1266 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.02 % Allowed : 22.48 % Favored : 74.50 % 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: -0.50 (0.25), residues: 1044 helix: 0.81 (0.25), residues: 436 sheet: -1.34 (0.38), residues: 156 loop : -1.02 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 628 TYR 0.013 0.001 TYR B 673 PHE 0.010 0.001 PHE B 438 TRP 0.008 0.001 TRP B 671 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8538) covalent geometry : angle 0.49861 (11520) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.85098 ( 8) hydrogen bonds : bond 0.03117 ( 344) hydrogen bonds : angle 4.66516 ( 1014) *********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.266 Fit side-chains REVERT: A 393 LYS cc_start: 0.6420 (tptt) cc_final: 0.6135 (mppt) REVERT: A 407 MET cc_start: 0.8003 (mpp) cc_final: 0.7582 (mtt) REVERT: A 634 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6389 (tp30) REVERT: B 414 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6185 (pmm) REVERT: B 628 ARG cc_start: 0.6976 (mtt-85) cc_final: 0.6367 (mtm110) REVERT: C 695 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7544 (mtmt) REVERT: D 466 GLU cc_start: 0.8108 (pp20) cc_final: 0.7725 (pt0) outliers start: 27 outliers final: 23 residues processed: 151 average time/residue: 0.0940 time to fit residues: 18.4715 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL 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 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN C 714 GLN D 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110973 restraints weight = 10485.557| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.10 r_work: 0.3132 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8542 Z= 0.200 Angle : 0.564 7.964 11528 Z= 0.287 Chirality : 0.047 0.218 1284 Planarity : 0.004 0.041 1422 Dihedral : 11.319 107.024 1266 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.36 % Allowed : 21.48 % 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 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: -0.63 (0.25), residues: 1044 helix: 0.68 (0.25), residues: 436 sheet: -1.38 (0.37), residues: 156 loop : -1.07 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 628 TYR 0.016 0.002 TYR D 673 PHE 0.015 0.002 PHE B 438 TRP 0.009 0.001 TRP D 671 HIS 0.005 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8538) covalent geometry : angle 0.56365 (11520) SS BOND : bond 0.00313 ( 4) SS BOND : angle 1.14806 ( 8) hydrogen bonds : bond 0.03787 ( 344) hydrogen bonds : angle 4.76315 ( 1014) *********************** 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 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.230 Fit side-chains REVERT: A 634 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6397 (tp30) REVERT: B 399 THR cc_start: 0.8583 (m) cc_final: 0.8306 (m) REVERT: B 414 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6176 (pmm) REVERT: B 628 ARG cc_start: 0.6903 (mtt-85) cc_final: 0.6334 (mtm110) REVERT: B 765 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7627 (pttp) REVERT: C 441 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8237 (ttmt) REVERT: C 638 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: C 660 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8101 (ttm170) REVERT: C 695 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7438 (mtmt) REVERT: D 399 THR cc_start: 0.8606 (m) cc_final: 0.8357 (m) REVERT: D 466 GLU cc_start: 0.8154 (pp20) cc_final: 0.7831 (pt0) outliers start: 39 outliers final: 29 residues processed: 158 average time/residue: 0.1012 time to fit residues: 20.4381 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL 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 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.0070 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN D 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113323 restraints weight = 10482.327| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.11 r_work: 0.3159 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8542 Z= 0.133 Angle : 0.510 7.729 11528 Z= 0.261 Chirality : 0.044 0.206 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.532 101.333 1266 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.91 % Allowed : 22.15 % Favored : 73.94 % 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: -0.48 (0.25), residues: 1044 helix: 0.83 (0.25), residues: 436 sheet: -1.30 (0.38), residues: 156 loop : -1.02 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.015 0.001 TYR C 673 PHE 0.013 0.002 PHE B 438 TRP 0.008 0.001 TRP D 671 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8538) covalent geometry : angle 0.51002 (11520) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.92142 ( 8) hydrogen bonds : bond 0.03224 ( 344) hydrogen bonds : angle 4.62484 ( 1014) *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.201 Fit side-chains REVERT: A 407 MET cc_start: 0.8010 (mpp) cc_final: 0.7695 (mtt) REVERT: A 634 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6383 (tp30) REVERT: B 414 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6204 (pmm) REVERT: B 765 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7582 (pttp) REVERT: C 441 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8251 (ttmt) REVERT: C 638 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6445 (m-30) REVERT: C 695 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7439 (mtmt) REVERT: D 399 THR cc_start: 0.8585 (m) cc_final: 0.8312 (m) REVERT: D 466 GLU cc_start: 0.8118 (pp20) cc_final: 0.7846 (pt0) outliers start: 35 outliers final: 29 residues processed: 158 average time/residue: 0.0891 time to fit residues: 18.1186 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN C 714 GLN D 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115333 restraints weight = 10344.314| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.10 r_work: 0.3188 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8542 Z= 0.110 Angle : 0.481 7.100 11528 Z= 0.246 Chirality : 0.043 0.162 1284 Planarity : 0.003 0.039 1422 Dihedral : 9.697 96.564 1266 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.91 % Allowed : 22.48 % Favored : 73.60 % 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: -0.26 (0.26), residues: 1044 helix: 1.07 (0.26), residues: 428 sheet: -1.28 (0.38), residues: 158 loop : -0.90 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.017 0.001 TYR C 673 PHE 0.012 0.001 PHE B 438 TRP 0.007 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8538) covalent geometry : angle 0.48057 (11520) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.75702 ( 8) hydrogen bonds : bond 0.02822 ( 344) hydrogen bonds : angle 4.49512 ( 1014) *********************** 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: 35 poor density : 127 time to evaluate : 0.330 Fit side-chains REVERT: A 407 MET cc_start: 0.7934 (mpp) cc_final: 0.7601 (mtt) REVERT: A 634 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6323 (tp30) REVERT: A 642 GLN cc_start: 0.6504 (mp10) cc_final: 0.6109 (mp10) REVERT: B 414 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6157 (pmm) REVERT: B 416 GLU cc_start: 0.5614 (tp30) cc_final: 0.5354 (tt0) REVERT: B 765 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7811 (pttp) REVERT: C 651 ASP cc_start: 0.7611 (t70) cc_final: 0.7341 (p0) REVERT: C 695 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7457 (mtmt) REVERT: D 399 THR cc_start: 0.8543 (m) cc_final: 0.8248 (m) REVERT: D 416 GLU cc_start: 0.5729 (tp30) cc_final: 0.5381 (tp30) REVERT: D 466 GLU cc_start: 0.8077 (pp20) cc_final: 0.7778 (pt0) REVERT: D 661 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7515 (mtm-85) outliers start: 35 outliers final: 28 residues processed: 150 average time/residue: 0.0990 time to fit residues: 19.2860 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL 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 721 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116701 restraints weight = 10423.909| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.09 r_work: 0.3194 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1884 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= 0.103 Angle : 0.479 7.196 11528 Z= 0.243 Chirality : 0.042 0.140 1284 Planarity : 0.003 0.038 1422 Dihedral : 9.310 96.307 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.58 % Allowed : 22.60 % Favored : 73.83 % 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: -0.14 (0.26), residues: 1044 helix: 1.14 (0.26), residues: 428 sheet: -1.05 (0.39), residues: 154 loop : -0.86 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.016 0.001 TYR C 673 PHE 0.012 0.001 PHE B 438 TRP 0.009 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8538) covalent geometry : angle 0.47898 (11520) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.70446 ( 8) hydrogen bonds : bond 0.02731 ( 344) hydrogen bonds : angle 4.45683 ( 1014) *********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.271 Fit side-chains REVERT: A 407 MET cc_start: 0.7863 (mpp) cc_final: 0.7591 (mtt) REVERT: A 634 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6328 (tp30) REVERT: B 414 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.6147 (pmm) REVERT: B 416 GLU cc_start: 0.5677 (tp30) cc_final: 0.5439 (tt0) REVERT: B 765 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7818 (pttp) REVERT: C 441 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8223 (ttmt) REVERT: C 695 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7458 (mtmt) REVERT: D 399 THR cc_start: 0.8581 (m) cc_final: 0.8286 (m) REVERT: D 416 GLU cc_start: 0.5767 (tp30) cc_final: 0.5421 (tp30) REVERT: D 466 GLU cc_start: 0.8028 (pp20) cc_final: 0.7786 (pt0) outliers start: 32 outliers final: 23 residues processed: 149 average time/residue: 0.0982 time to fit residues: 18.8293 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115040 restraints weight = 10456.535| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.10 r_work: 0.3173 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8542 Z= 0.125 Angle : 0.509 8.138 11528 Z= 0.256 Chirality : 0.044 0.211 1284 Planarity : 0.003 0.037 1422 Dihedral : 9.189 99.483 1266 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.36 % Allowed : 23.49 % 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: -0.20 (0.26), residues: 1044 helix: 1.10 (0.26), residues: 428 sheet: -1.19 (0.38), residues: 158 loop : -0.86 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.015 0.001 TYR C 673 PHE 0.013 0.001 PHE B 438 TRP 0.008 0.001 TRP A 460 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8538) covalent geometry : angle 0.50830 (11520) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.84816 ( 8) hydrogen bonds : bond 0.02979 ( 344) hydrogen bonds : angle 4.48919 ( 1014) ********************** 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 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.322 Fit side-chains REVERT: A 407 MET cc_start: 0.7875 (mpp) cc_final: 0.7648 (mtt) REVERT: A 634 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6324 (tp30) REVERT: A 642 GLN cc_start: 0.6482 (mp10) cc_final: 0.6134 (mp10) REVERT: B 414 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.6180 (pmm) REVERT: B 416 GLU cc_start: 0.5633 (tp30) cc_final: 0.5416 (tt0) REVERT: B 765 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7835 (pttp) REVERT: C 441 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8231 (ttmt) REVERT: C 651 ASP cc_start: 0.7604 (t70) cc_final: 0.7303 (p0) REVERT: C 657 GLU cc_start: 0.8325 (mp0) cc_final: 0.7820 (mp0) REVERT: C 695 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7452 (mtmt) REVERT: D 399 THR cc_start: 0.8585 (m) cc_final: 0.8322 (m) REVERT: D 416 GLU cc_start: 0.5758 (tp30) cc_final: 0.5422 (tp30) REVERT: D 466 GLU cc_start: 0.8042 (pp20) cc_final: 0.7809 (pt0) outliers start: 30 outliers final: 24 residues processed: 150 average time/residue: 0.0890 time to fit residues: 17.3761 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 VAL 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 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 75 optimal weight: 0.0040 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117434 restraints weight = 10360.307| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.06 r_work: 0.3212 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.096 Angle : 0.467 7.169 11528 Z= 0.239 Chirality : 0.042 0.163 1284 Planarity : 0.003 0.037 1422 Dihedral : 8.356 93.914 1266 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.58 % Allowed : 23.04 % Favored : 73.38 % 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: -0.04 (0.26), residues: 1044 helix: 1.18 (0.26), residues: 428 sheet: -0.91 (0.40), residues: 154 loop : -0.80 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 661 TYR 0.016 0.001 TYR C 673 PHE 0.011 0.001 PHE B 438 TRP 0.007 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8538) covalent geometry : angle 0.46729 (11520) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.60681 ( 8) hydrogen bonds : bond 0.02598 ( 344) hydrogen bonds : angle 4.40378 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.09 seconds wall clock time: 29 minutes 13.11 seconds (1753.11 seconds total)