Starting phenix.real_space_refine on Fri Nov 15 06:25:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqg_29387/11_2024/8fqg_29387.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqg_29387/11_2024/8fqg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqg_29387/11_2024/8fqg_29387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqg_29387/11_2024/8fqg_29387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqg_29387/11_2024/8fqg_29387.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqg_29387/11_2024/8fqg_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.34, per 1000 atoms: 0.76 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 17 sheets defined 43.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 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: 2.03 Time building geometry restraints manager: 2.72 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 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: 3.490 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.080 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- 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 8538 Z= 0.985 Angle : 0.730 10.883 11520 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 *********************** 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 : 1.076 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: 0.3015 time to fit residues: 47.1860 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 : 1.022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 8538 Z= 0.204 Angle : 0.507 7.359 11520 Z= 0.261 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 *********************** 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 : 1.043 Fit side-chains REVERT: A 669 LYS cc_start: 0.7070 (tttp) cc_final: 0.6859 (tttp) REVERT: B 628 ARG cc_start: 0.6682 (mtt-85) cc_final: 0.6264 (mtm110) REVERT: D 453 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7781 (ttp-170) REVERT: D 466 GLU cc_start: 0.8166 (pp20) cc_final: 0.7741 (pp20) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.2770 time to fit residues: 49.8276 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 : 1.041 ------------------------------------------------------------------------------- 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 53 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8538 Z= 0.330 Angle : 0.577 6.954 11520 Z= 0.295 Chirality : 0.047 0.213 1284 Planarity : 0.004 0.044 1422 Dihedral : 11.697 107.736 1266 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.80 % Allowed : 20.58 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1044 helix: 0.66 (0.25), residues: 438 sheet: -1.43 (0.37), residues: 156 loop : -1.07 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 671 HIS 0.005 0.001 HIS D 435 PHE 0.017 0.002 PHE D 659 TYR 0.018 0.002 TYR D 673 ARG 0.004 0.001 ARG B 628 *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.058 Fit side-chains REVERT: A 642 GLN cc_start: 0.6692 (mt0) cc_final: 0.6465 (mp10) REVERT: A 657 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: A 669 LYS cc_start: 0.7108 (tttp) cc_final: 0.6881 (tttp) REVERT: B 414 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6165 (pmm) REVERT: B 628 ARG cc_start: 0.6743 (mtt-85) cc_final: 0.6288 (mtm110) REVERT: C 441 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8190 (ttmt) REVERT: C 660 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8019 (ttm170) REVERT: C 695 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7498 (mtmt) REVERT: D 466 GLU cc_start: 0.8179 (pp20) cc_final: 0.7702 (pt0) outliers start: 34 outliers final: 23 residues processed: 155 average time/residue: 0.3122 time to fit residues: 60.8385 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LYS 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 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 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 Chi-restraints excluded: chain D residue 762 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8538 Z= 0.207 Angle : 0.506 7.314 11520 Z= 0.258 Chirality : 0.044 0.183 1284 Planarity : 0.004 0.047 1422 Dihedral : 10.931 100.255 1266 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.91 % Allowed : 20.69 % 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: -0.47 (0.25), residues: 1044 helix: 0.85 (0.25), residues: 436 sheet: -1.33 (0.38), residues: 156 loop : -1.02 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 671 HIS 0.004 0.001 HIS D 412 PHE 0.011 0.002 PHE B 438 TYR 0.014 0.001 TYR D 673 ARG 0.003 0.000 ARG B 628 *********************** 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 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.076 Fit side-chains REVERT: A 634 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6323 (tp30) REVERT: A 657 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 669 LYS cc_start: 0.7136 (tttp) cc_final: 0.6831 (tttp) REVERT: B 414 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6092 (pmm) REVERT: B 628 ARG cc_start: 0.6744 (mtt-85) cc_final: 0.6289 (mtm110) REVERT: B 765 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7594 (pttp) REVERT: C 695 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7509 (mtmt) REVERT: D 466 GLU cc_start: 0.8105 (pp20) cc_final: 0.7681 (pt0) outliers start: 35 outliers final: 25 residues processed: 160 average time/residue: 0.2778 time to fit residues: 57.3461 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 644 GLU 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 58 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8538 Z= 0.327 Angle : 0.577 7.948 11520 Z= 0.294 Chirality : 0.047 0.229 1284 Planarity : 0.004 0.047 1422 Dihedral : 11.381 107.558 1266 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.91 % Allowed : 21.92 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1044 helix: 0.69 (0.25), residues: 436 sheet: -1.43 (0.37), residues: 156 loop : -1.06 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS D 435 PHE 0.016 0.002 PHE D 659 TYR 0.017 0.002 TYR D 673 ARG 0.003 0.001 ARG A 715 *********************** 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 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.219 Fit side-chains REVERT: A 634 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6370 (tp30) REVERT: B 414 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6149 (pmm) REVERT: B 628 ARG cc_start: 0.6796 (mtt-85) cc_final: 0.6376 (mtm110) REVERT: B 765 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7653 (pttp) REVERT: C 441 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8174 (ttmt) REVERT: C 695 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7500 (mtmt) REVERT: D 466 GLU cc_start: 0.8114 (pp20) cc_final: 0.7760 (pt0) outliers start: 35 outliers final: 26 residues processed: 149 average time/residue: 0.3030 time to fit residues: 57.2395 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8538 Z= 0.139 Angle : 0.470 7.074 11520 Z= 0.240 Chirality : 0.042 0.204 1284 Planarity : 0.003 0.049 1422 Dihedral : 9.803 93.844 1266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.02 % Allowed : 22.60 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.26), residues: 1044 helix: 0.95 (0.26), residues: 440 sheet: -1.16 (0.39), residues: 154 loop : -1.03 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 766 HIS 0.003 0.001 HIS D 412 PHE 0.007 0.001 PHE B 438 TYR 0.011 0.001 TYR B 673 ARG 0.004 0.000 ARG C 715 *********************** 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 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.044 Fit side-chains REVERT: A 407 MET cc_start: 0.7939 (mpp) cc_final: 0.7576 (mtt) REVERT: A 634 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6246 (tp30) REVERT: A 669 LYS cc_start: 0.7317 (tttp) cc_final: 0.6815 (tttp) REVERT: B 414 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6087 (pmm) REVERT: B 628 ARG cc_start: 0.6737 (mtt-85) cc_final: 0.6335 (mtm110) REVERT: C 695 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7516 (mtmt) REVERT: C 713 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: D 466 GLU cc_start: 0.8036 (pp20) cc_final: 0.7726 (pt0) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 0.2731 time to fit residues: 49.7832 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 644 GLU 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 713 GLU Chi-restraints excluded: chain C residue 723 VAL 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 Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8538 Z= 0.161 Angle : 0.474 6.891 11520 Z= 0.241 Chirality : 0.043 0.179 1284 Planarity : 0.003 0.048 1422 Dihedral : 9.587 97.629 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.36 % Allowed : 22.26 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.26), residues: 1044 helix: 1.17 (0.26), residues: 428 sheet: -1.20 (0.39), residues: 156 loop : -0.85 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS D 412 PHE 0.011 0.001 PHE B 438 TYR 0.012 0.001 TYR D 673 ARG 0.003 0.000 ARG D 628 *********************** 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 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.980 Fit side-chains REVERT: A 634 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6254 (tp30) REVERT: B 414 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6099 (pmm) REVERT: B 416 GLU cc_start: 0.5710 (tp30) cc_final: 0.5432 (tt0) REVERT: B 628 ARG cc_start: 0.6592 (mtt-85) cc_final: 0.6225 (mtm110) REVERT: C 695 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7502 (mtmt) REVERT: D 399 THR cc_start: 0.8604 (m) cc_final: 0.8358 (m) REVERT: D 466 GLU cc_start: 0.8045 (pp20) cc_final: 0.7751 (pt0) outliers start: 30 outliers final: 24 residues processed: 135 average time/residue: 0.2726 time to fit residues: 48.1369 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 406 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 644 GLU 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 486 GLU 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 Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8538 Z= 0.260 Angle : 0.538 8.144 11520 Z= 0.272 Chirality : 0.046 0.215 1284 Planarity : 0.004 0.048 1422 Dihedral : 10.019 104.557 1266 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 21.92 % Favored : 74.61 % 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: -0.26 (0.26), residues: 1044 helix: 1.04 (0.26), residues: 426 sheet: -1.26 (0.38), residues: 156 loop : -0.86 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.004 0.001 HIS D 435 PHE 0.014 0.002 PHE B 438 TYR 0.015 0.001 TYR D 673 ARG 0.004 0.000 ARG D 628 *********************** 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: 31 poor density : 121 time to evaluate : 1.056 Fit side-chains REVERT: A 634 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6313 (tp30) REVERT: B 414 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6141 (pmm) REVERT: C 441 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8142 (ttmt) REVERT: C 695 LYS cc_start: 0.7733 (mtpt) cc_final: 0.7415 (mtmt) REVERT: D 399 THR cc_start: 0.8636 (m) cc_final: 0.8407 (m) REVERT: D 466 GLU cc_start: 0.8108 (pp20) cc_final: 0.7825 (pt0) REVERT: D 628 ARG cc_start: 0.6839 (mtt-85) cc_final: 0.6076 (ptp-110) outliers start: 31 outliers final: 26 residues processed: 142 average time/residue: 0.2834 time to fit residues: 51.9131 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 406 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 644 GLU 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 681 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 395 VAL 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 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 95 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8538 Z= 0.168 Angle : 0.484 7.283 11520 Z= 0.245 Chirality : 0.043 0.216 1284 Planarity : 0.003 0.049 1422 Dihedral : 8.938 95.965 1266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.36 % Allowed : 22.26 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.26), residues: 1044 helix: 1.11 (0.26), residues: 428 sheet: -1.09 (0.39), residues: 154 loop : -0.86 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.012 0.001 PHE B 438 TYR 0.012 0.001 TYR B 673 ARG 0.003 0.000 ARG D 628 *********************** 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 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.961 Fit side-chains REVERT: A 634 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6255 (tp30) REVERT: A 642 GLN cc_start: 0.6386 (mp10) cc_final: 0.6035 (mp10) REVERT: B 414 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.6094 (pmm) REVERT: B 416 GLU cc_start: 0.5644 (tp30) cc_final: 0.5407 (tt0) REVERT: C 695 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7443 (mtmt) REVERT: D 399 THR cc_start: 0.8582 (m) cc_final: 0.8279 (m) REVERT: D 416 GLU cc_start: 0.5759 (tp30) cc_final: 0.5395 (tp30) REVERT: D 466 GLU cc_start: 0.8049 (pp20) cc_final: 0.7792 (pt0) outliers start: 30 outliers final: 25 residues processed: 144 average time/residue: 0.2752 time to fit residues: 51.2607 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 406 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 644 GLU 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 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 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 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 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8538 Z= 0.159 Angle : 0.469 7.156 11520 Z= 0.240 Chirality : 0.042 0.146 1284 Planarity : 0.003 0.049 1422 Dihedral : 8.575 96.703 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.13 % Allowed : 22.71 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1044 helix: 1.19 (0.26), residues: 428 sheet: -1.01 (0.40), residues: 154 loop : -0.81 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 PHE 0.012 0.001 PHE B 438 TYR 0.012 0.001 TYR B 673 ARG 0.003 0.000 ARG D 628 ********************** 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: 28 poor density : 125 time to evaluate : 0.951 Fit side-chains REVERT: A 634 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6234 (tp30) REVERT: A 642 GLN cc_start: 0.6436 (mp10) cc_final: 0.6100 (mp10) REVERT: B 414 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.6113 (pmm) REVERT: B 416 GLU cc_start: 0.5629 (tp30) cc_final: 0.5415 (tt0) REVERT: B 719 ASP cc_start: 0.8414 (p0) cc_final: 0.8205 (p0) REVERT: C 657 GLU cc_start: 0.8224 (mp0) cc_final: 0.7766 (mp0) REVERT: C 695 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7431 (mtmt) REVERT: D 399 THR cc_start: 0.8590 (m) cc_final: 0.8294 (m) REVERT: D 416 GLU cc_start: 0.5822 (tp30) cc_final: 0.5492 (tp30) REVERT: D 466 GLU cc_start: 0.8033 (pp20) cc_final: 0.7796 (pt0) outliers start: 28 outliers final: 23 residues processed: 144 average time/residue: 0.2704 time to fit residues: 50.4771 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 406 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 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 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 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 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 25 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 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 C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113789 restraints weight = 10329.842| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.08 r_work: 0.3165 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8538 Z= 0.221 Angle : 0.509 7.921 11520 Z= 0.259 Chirality : 0.045 0.277 1284 Planarity : 0.004 0.048 1422 Dihedral : 9.085 102.044 1266 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.13 % Allowed : 22.82 % Favored : 74.05 % 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: -0.20 (0.26), residues: 1044 helix: 1.07 (0.26), residues: 430 sheet: -1.25 (0.39), residues: 160 loop : -0.80 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.004 0.001 HIS D 435 PHE 0.015 0.002 PHE B 438 TYR 0.014 0.001 TYR B 673 ARG 0.003 0.000 ARG D 628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.81 seconds wall clock time: 41 minutes 1.59 seconds (2461.59 seconds total)