Starting phenix.real_space_refine on Sat Jun 7 03:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqg_29387/06_2025/8fqg_29387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqg_29387/06_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_29387/06_2025/8fqg_29387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqg_29387/06_2025/8fqg_29387.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqg_29387/06_2025/8fqg_29387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqg_29387/06_2025/8fqg_29387.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.86, per 1000 atoms: 0.70 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: 1.96 Conformation dependent library (CDL) restraints added in 927.4 milliseconds 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: 0.99 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: 2.24 Time building geometry restraints manager: 2.34 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.070 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), 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 TRP 0.007 0.001 TRP B 671 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE B 495 TYR 0.011 0.001 TYR D 673 ARG 0.008 0.001 ARG B 675 Details of bonding type rmsd hydrogen bonds : bond 0.17677 ( 344) hydrogen bonds : angle 6.79775 ( 1014) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.81046 ( 8) covalent geometry : bond 0.01461 ( 8538) covalent geometry : angle 0.72975 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.992 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: 0.3054 time to fit residues: 47.8099 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 : 1.011 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.143045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117046 restraints weight = 10271.416| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.08 r_work: 0.3205 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8542 Z= 0.134 Angle : 0.508 7.359 11528 Z= 0.262 Chirality : 0.044 0.160 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.980 99.981 1270 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.13 % Allowed : 19.91 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1044 helix: 0.83 (0.25), residues: 442 sheet: -1.12 (0.41), residues: 138 loop : -1.09 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 671 HIS 0.004 0.001 HIS D 412 PHE 0.012 0.002 PHE B 438 TYR 0.012 0.001 TYR D 673 ARG 0.005 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 344) hydrogen bonds : angle 4.95637 ( 1014) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.76749 ( 8) covalent geometry : bond 0.00321 ( 8538) covalent geometry : angle 0.50742 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.898 Fit side-chains REVERT: A 669 LYS cc_start: 0.7056 (tttp) cc_final: 0.6854 (tttp) REVERT: B 496 MET cc_start: 0.9055 (ttm) cc_final: 0.8846 (ttp) REVERT: B 628 ARG cc_start: 0.6879 (mtt-85) cc_final: 0.6319 (mtm110) REVERT: D 453 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7907 (ttp-170) REVERT: D 466 GLU cc_start: 0.8150 (pp20) cc_final: 0.7687 (pp20) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.2624 time to fit residues: 47.3517 Evaluate side-chains 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 395 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 498 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 443 THR 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 773 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.141519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115325 restraints weight = 10411.968| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8542 Z= 0.138 Angle : 0.503 6.522 11528 Z= 0.256 Chirality : 0.044 0.154 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.780 101.004 1266 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.69 % Allowed : 20.02 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1044 helix: 0.84 (0.25), residues: 442 sheet: -1.19 (0.39), residues: 146 loop : -1.09 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.004 0.001 HIS D 412 PHE 0.012 0.002 PHE B 438 TYR 0.014 0.001 TYR D 673 ARG 0.004 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 344) hydrogen bonds : angle 4.74163 ( 1014) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.73822 ( 8) covalent geometry : bond 0.00335 ( 8538) covalent geometry : angle 0.50288 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.897 Fit side-chains REVERT: A 642 GLN cc_start: 0.6733 (mt0) cc_final: 0.6496 (mp10) REVERT: A 657 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: A 669 LYS cc_start: 0.7078 (tttp) cc_final: 0.6730 (tttp) REVERT: B 414 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6052 (pmm) REVERT: B 628 ARG cc_start: 0.6871 (mtt-85) cc_final: 0.6288 (mtm110) REVERT: C 695 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7457 (mtmt) REVERT: D 466 GLU cc_start: 0.8116 (pp20) cc_final: 0.7662 (pt0) outliers start: 33 outliers final: 21 residues processed: 150 average time/residue: 0.2611 time to fit residues: 50.3783 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 657 GLU 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 644 GLU Chi-restraints excluded: chain B residue 666 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 C residue 723 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER 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 74 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 49 optimal weight: 0.0030 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117728 restraints weight = 10348.885| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.08 r_work: 0.3212 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8542 Z= 0.102 Angle : 0.467 6.443 11528 Z= 0.237 Chirality : 0.043 0.207 1284 Planarity : 0.003 0.044 1422 Dihedral : 9.823 96.160 1266 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.36 % Allowed : 20.81 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1044 helix: 1.00 (0.25), residues: 440 sheet: -1.08 (0.42), residues: 138 loop : -1.03 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS D 412 PHE 0.010 0.001 PHE B 438 TYR 0.011 0.001 TYR D 673 ARG 0.003 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 344) hydrogen bonds : angle 4.58706 ( 1014) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.78635 ( 8) covalent geometry : bond 0.00241 ( 8538) covalent geometry : angle 0.46655 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.873 Fit side-chains REVERT: A 407 MET cc_start: 0.7878 (mpp) cc_final: 0.7527 (mtt) REVERT: A 476 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 634 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6353 (tp30) REVERT: A 657 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: A 669 LYS cc_start: 0.7102 (tttp) cc_final: 0.6710 (tttp) REVERT: B 414 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.6047 (pmm) REVERT: B 628 ARG cc_start: 0.6822 (mtt-85) cc_final: 0.6252 (mtm110) REVERT: C 695 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7405 (mtmt) REVERT: D 466 GLU cc_start: 0.8040 (pp20) cc_final: 0.7666 (pt0) REVERT: D 742 LEU cc_start: 0.7889 (mt) cc_final: 0.7680 (mt) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.2796 time to fit residues: 54.3012 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 657 GLU 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 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 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 407 MET Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 718 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 44 optimal weight: 0.0070 chunk 6 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122327 restraints weight = 10368.552| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.08 r_work: 0.3272 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8542 Z= 0.080 Angle : 0.436 7.068 11528 Z= 0.220 Chirality : 0.042 0.195 1284 Planarity : 0.003 0.039 1422 Dihedral : 8.375 90.310 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 22.26 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1044 helix: 1.21 (0.26), residues: 440 sheet: -0.66 (0.45), residues: 118 loop : -1.01 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 PHE 0.008 0.001 PHE D 438 TYR 0.007 0.001 TYR B 673 ARG 0.004 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.02270 ( 344) hydrogen bonds : angle 4.41141 ( 1014) SS BOND : bond 0.00051 ( 4) SS BOND : angle 0.49940 ( 8) covalent geometry : bond 0.00178 ( 8538) covalent geometry : angle 0.43554 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.975 Fit side-chains REVERT: A 407 MET cc_start: 0.7677 (mpp) cc_final: 0.7389 (mtt) REVERT: A 634 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6326 (tp30) REVERT: A 642 GLN cc_start: 0.6760 (mp10) cc_final: 0.6533 (mp10) REVERT: A 669 LYS cc_start: 0.7070 (tttp) cc_final: 0.6657 (tttp) REVERT: B 628 ARG cc_start: 0.6564 (mtt-85) cc_final: 0.6127 (mtm110) REVERT: B 637 GLU cc_start: 0.8041 (tp30) cc_final: 0.7610 (tp30) REVERT: B 676 SER cc_start: 0.7217 (m) cc_final: 0.6874 (p) REVERT: B 765 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7749 (pttp) REVERT: C 695 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7381 (mtmt) REVERT: D 438 PHE cc_start: 0.6037 (p90) cc_final: 0.5565 (p90) REVERT: D 466 GLU cc_start: 0.7957 (pp20) cc_final: 0.7646 (pt0) REVERT: D 490 ASP cc_start: 0.8469 (m-30) cc_final: 0.8058 (m-30) REVERT: D 628 ARG cc_start: 0.7065 (mtt-85) cc_final: 0.6308 (mtm110) REVERT: D 742 LEU cc_start: 0.7836 (mt) cc_final: 0.7548 (mt) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 0.2864 time to fit residues: 58.5003 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL 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 D residue 414 MET 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 718 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.142551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116216 restraints weight = 10294.967| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.09 r_work: 0.3198 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1541 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= 0.135 Angle : 0.492 8.097 11528 Z= 0.250 Chirality : 0.044 0.201 1284 Planarity : 0.004 0.040 1422 Dihedral : 8.866 100.711 1266 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.58 % Allowed : 21.48 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1044 helix: 1.06 (0.25), residues: 440 sheet: -1.06 (0.40), residues: 146 loop : -0.92 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.004 0.001 HIS D 412 PHE 0.012 0.002 PHE B 438 TYR 0.013 0.001 TYR D 673 ARG 0.007 0.000 ARG B 675 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 344) hydrogen bonds : angle 4.52972 ( 1014) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.94900 ( 8) covalent geometry : bond 0.00325 ( 8538) covalent geometry : angle 0.49201 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.232 Fit side-chains REVERT: A 407 MET cc_start: 0.7819 (mpp) cc_final: 0.7588 (mtt) REVERT: A 634 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6361 (tp30) REVERT: A 669 LYS cc_start: 0.7135 (tttp) cc_final: 0.6778 (tttp) REVERT: B 414 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6062 (pmm) REVERT: B 765 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7747 (pttp) REVERT: C 695 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7553 (mtmt) REVERT: D 399 THR cc_start: 0.8560 (m) cc_final: 0.8279 (m) REVERT: D 466 GLU cc_start: 0.8014 (pp20) cc_final: 0.7699 (pt0) outliers start: 32 outliers final: 23 residues processed: 147 average time/residue: 0.3261 time to fit residues: 62.5478 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 681 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 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 C residue 736 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 626 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.0050 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 overall best weight: 0.5916 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117739 restraints weight = 10412.078| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.11 r_work: 0.3220 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8542 Z= 0.095 Angle : 0.453 7.754 11528 Z= 0.231 Chirality : 0.042 0.224 1284 Planarity : 0.003 0.038 1422 Dihedral : 8.320 94.332 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.80 % Allowed : 22.26 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1044 helix: 1.12 (0.25), residues: 440 sheet: -0.63 (0.44), residues: 118 loop : -1.00 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.003 0.001 HIS D 412 PHE 0.010 0.001 PHE B 438 TYR 0.011 0.001 TYR D 673 ARG 0.002 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 344) hydrogen bonds : angle 4.43752 ( 1014) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.67219 ( 8) covalent geometry : bond 0.00223 ( 8538) covalent geometry : angle 0.45244 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.022 Fit side-chains REVERT: A 407 MET cc_start: 0.7767 (mpp) cc_final: 0.7490 (mtt) REVERT: A 634 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6360 (tp30) REVERT: A 642 GLN cc_start: 0.6501 (mp10) cc_final: 0.6205 (mp10) REVERT: A 669 LYS cc_start: 0.7142 (tttp) cc_final: 0.6773 (tttp) REVERT: B 414 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.6046 (pmm) REVERT: B 637 GLU cc_start: 0.8097 (tp30) cc_final: 0.7666 (tp30) REVERT: B 765 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7742 (pttp) REVERT: C 695 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7552 (mtmt) REVERT: D 399 THR cc_start: 0.8517 (m) cc_final: 0.8208 (m) REVERT: D 438 PHE cc_start: 0.5958 (p90) cc_final: 0.5527 (p90) REVERT: D 466 GLU cc_start: 0.8014 (pp20) cc_final: 0.7771 (pt0) REVERT: D 742 LEU cc_start: 0.7840 (mt) cc_final: 0.7605 (mt) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.2747 time to fit residues: 48.8230 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 : 0.977 ------------------------------------------------------------------------------- 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 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 765 LYS 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 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 718 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 59 optimal weight: 0.0040 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.143673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118344 restraints weight = 10406.564| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.01 r_work: 0.3234 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1676 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= 0.101 Angle : 0.460 8.433 11528 Z= 0.234 Chirality : 0.043 0.225 1284 Planarity : 0.003 0.040 1422 Dihedral : 8.266 95.461 1266 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.24 % Allowed : 21.81 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1044 helix: 1.14 (0.25), residues: 440 sheet: -0.91 (0.40), residues: 144 loop : -0.91 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.003 0.001 HIS D 412 PHE 0.010 0.001 PHE B 438 TYR 0.011 0.001 TYR D 673 ARG 0.003 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02633 ( 344) hydrogen bonds : angle 4.43360 ( 1014) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.67721 ( 8) covalent geometry : bond 0.00240 ( 8538) covalent geometry : angle 0.45994 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.025 Fit side-chains REVERT: A 407 MET cc_start: 0.7730 (mpp) cc_final: 0.7490 (mtt) REVERT: A 634 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6357 (tp30) REVERT: A 669 LYS cc_start: 0.7163 (tttp) cc_final: 0.6781 (tttp) REVERT: B 414 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6098 (pmm) REVERT: B 637 GLU cc_start: 0.8102 (tp30) cc_final: 0.7676 (tp30) REVERT: B 765 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7705 (pttp) REVERT: C 695 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7544 (mtmt) REVERT: D 399 THR cc_start: 0.8543 (m) cc_final: 0.8242 (m) REVERT: D 438 PHE cc_start: 0.6040 (p90) cc_final: 0.5631 (p90) REVERT: D 466 GLU cc_start: 0.7996 (pp20) cc_final: 0.7757 (pt0) outliers start: 29 outliers final: 21 residues processed: 141 average time/residue: 0.2757 time to fit residues: 50.0818 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 736 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 498 LEU 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 C residue 736 THR Chi-restraints excluded: chain D residue 414 MET 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 718 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.145020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118833 restraints weight = 10385.011| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.10 r_work: 0.3234 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8542 Z= 0.097 Angle : 0.453 7.850 11528 Z= 0.231 Chirality : 0.042 0.246 1284 Planarity : 0.003 0.039 1422 Dihedral : 8.130 94.580 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.47 % Allowed : 21.59 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1044 helix: 1.14 (0.25), residues: 442 sheet: -0.56 (0.45), residues: 118 loop : -0.97 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.003 0.001 HIS D 412 PHE 0.011 0.001 PHE D 438 TYR 0.010 0.001 TYR D 673 ARG 0.003 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02573 ( 344) hydrogen bonds : angle 4.41368 ( 1014) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.65763 ( 8) covalent geometry : bond 0.00230 ( 8538) covalent geometry : angle 0.45327 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.071 Fit side-chains REVERT: A 407 MET cc_start: 0.7717 (mpp) cc_final: 0.7472 (mtt) REVERT: A 634 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6338 (tp30) REVERT: A 642 GLN cc_start: 0.6439 (mp10) cc_final: 0.6213 (mp10) REVERT: A 669 LYS cc_start: 0.7158 (tttp) cc_final: 0.6761 (tttp) REVERT: B 414 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6068 (pmm) REVERT: B 637 GLU cc_start: 0.8126 (tp30) cc_final: 0.7702 (tp30) REVERT: C 695 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7552 (mtmt) REVERT: D 399 THR cc_start: 0.8553 (m) cc_final: 0.8258 (m) REVERT: D 416 GLU cc_start: 0.5972 (tp30) cc_final: 0.5292 (tt0) REVERT: D 438 PHE cc_start: 0.6066 (p90) cc_final: 0.5642 (p90) REVERT: D 466 GLU cc_start: 0.7989 (pp20) cc_final: 0.7747 (pt0) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.2699 time to fit residues: 51.7541 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 498 LEU 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 C residue 736 THR Chi-restraints excluded: chain D residue 414 MET 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 503 MET Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 718 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN B 756 GLN C 714 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114685 restraints weight = 10362.684| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.10 r_work: 0.3178 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8542 Z= 0.144 Angle : 0.505 9.241 11528 Z= 0.257 Chirality : 0.045 0.233 1284 Planarity : 0.003 0.040 1422 Dihedral : 8.955 102.505 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.02 % Allowed : 21.59 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1044 helix: 0.98 (0.25), residues: 442 sheet: -1.03 (0.40), residues: 146 loop : -0.93 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.004 0.001 HIS D 435 PHE 0.014 0.002 PHE D 438 TYR 0.018 0.001 TYR D 673 ARG 0.003 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 344) hydrogen bonds : angle 4.58415 ( 1014) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.92960 ( 8) covalent geometry : bond 0.00351 ( 8538) covalent geometry : angle 0.50425 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.934 Fit side-chains REVERT: A 407 MET cc_start: 0.7857 (mpp) cc_final: 0.7590 (mtt) REVERT: A 634 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6370 (tp30) REVERT: A 642 GLN cc_start: 0.6310 (mp10) cc_final: 0.5938 (mp10) REVERT: A 669 LYS cc_start: 0.7122 (tttp) cc_final: 0.6703 (tttp) REVERT: B 414 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.6078 (pmm) REVERT: C 441 LYS cc_start: 0.8493 (ttpp) cc_final: 0.8211 (ttmt) REVERT: C 447 ASP cc_start: 0.6763 (p0) cc_final: 0.6549 (p0) REVERT: C 695 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7486 (mtmt) REVERT: D 399 THR cc_start: 0.8549 (m) cc_final: 0.8269 (m) REVERT: D 416 GLU cc_start: 0.5785 (tp30) cc_final: 0.5474 (tp30) REVERT: D 466 GLU cc_start: 0.8079 (pp20) cc_final: 0.7799 (pt0) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.3150 time to fit residues: 57.6339 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 498 LEU 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 C residue 736 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 718 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.0040 chunk 92 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN B 756 GLN C 714 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113304 restraints weight = 10555.394| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.13 r_work: 0.3174 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8542 Z= 0.152 Angle : 0.514 8.918 11528 Z= 0.263 Chirality : 0.045 0.258 1284 Planarity : 0.004 0.040 1422 Dihedral : 9.206 104.309 1266 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.68 % Allowed : 21.92 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1044 helix: 0.89 (0.25), residues: 442 sheet: -1.20 (0.38), residues: 156 loop : -0.93 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.004 0.001 HIS D 435 PHE 0.016 0.002 PHE D 438 TYR 0.018 0.002 TYR D 673 ARG 0.003 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 344) hydrogen bonds : angle 4.62666 ( 1014) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.98376 ( 8) covalent geometry : bond 0.00369 ( 8538) covalent geometry : angle 0.51394 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4849.28 seconds wall clock time: 85 minutes 6.97 seconds (5106.97 seconds total)