Starting phenix.real_space_refine on Fri Nov 15 06:24:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpv_29370/11_2024/8fpv_29370.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpv_29370/11_2024/8fpv_29370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpv_29370/11_2024/8fpv_29370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpv_29370/11_2024/8fpv_29370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpv_29370/11_2024/8fpv_29370.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpv_29370/11_2024/8fpv_29370.cif" } resolution = 3.08 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 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8394 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.15, per 1000 atoms: 0.73 Number of scatterers: 8394 At special positions: 0 Unit cell: (123, 94.3, 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 1610 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 43.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.738A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.088A 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 removed outlier: 3.502A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.675A 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: 3.962A 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: 3.671A 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 removed outlier: 3.540A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.629A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) 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 715 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.558A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) 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: 6.235A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.982A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.490A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 500 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 725 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.627A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (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 489 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.944A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.646A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.449A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.935A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.355A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.544A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.544A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.471A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 509 through 510 removed outlier: 3.596A pdb=" N ARG D 628 " --> pdb=" O SER D 510 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1005 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: 2.36 Time building geometry restraints manager: 2.67 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 - 1.48: 2038 1.48 - 1.60: 3726 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " 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 B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.329 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11317 1.95 - 3.90: 129 3.90 - 5.85: 31 5.85 - 7.80: 30 7.80 - 9.76: 13 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C GLU C 634 " pdb=" CA GLU C 634 " pdb=" CB GLU C 634 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" CA GLU C 634 " pdb=" C GLU C 634 " pdb=" N SER C 635 " ideal model delta sigma weight residual 119.63 116.66 2.97 8.10e-01 1.52e+00 1.34e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 122.46 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.30 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 108.97 9.38 3.00e+00 1.11e-01 9.78e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 4763 23.14 - 46.28: 404 46.28 - 69.43: 55 69.43 - 92.57: 15 92.57 - 115.71: 11 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 -178.44 -88.56 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 176.77 -83.77 1 1.00e+01 1.00e-02 8.56e+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 -86.00 -167.00 81.00 1 1.00e+01 1.00e-02 8.10e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1176 0.086 - 0.171: 90 0.171 - 0.257: 2 0.257 - 0.342: 0 0.342 - 0.428: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C8 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" N2 CYZ D1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.57e+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 2.88 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 493 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 494 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 494 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 494 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 625 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C THR B 625 " 0.025 2.00e-02 2.50e+03 pdb=" O THR B 625 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 626 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 477 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 478 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.018 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1895 2.78 - 3.31: 7602 3.31 - 3.84: 14232 3.84 - 4.37: 16638 4.37 - 4.90: 29221 Nonbonded interactions: 69588 Sorted by model distance: nonbonded pdb=" OH TYR D 424 " pdb=" O HOH D1401 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 424 " pdb=" O HOH B1401 " model vdw 2.270 3.040 nonbonded pdb=" NZ LYS A 409 " pdb=" O GLU A 419 " model vdw 2.282 3.120 ... (remaining 69583 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: 3.220 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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= 0.991 Angle : 0.717 9.755 11520 Z= 0.314 Chirality : 0.062 0.428 1284 Planarity : 0.003 0.043 1422 Dihedral : 17.490 115.711 3288 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.22 % Allowed : 18.90 % Favored : 80.87 % 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: -0.33 (0.25), residues: 1044 helix: 0.85 (0.25), residues: 422 sheet: -0.53 (0.39), residues: 174 loop : -1.07 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.012 0.001 PHE B 658 TYR 0.010 0.001 TYR A 450 ARG 0.002 0.000 ARG B 420 *********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.985 Fit side-chains REVERT: A 718 CYS cc_start: 0.7138 (m) cc_final: 0.6813 (m) REVERT: C 673 TYR cc_start: 0.7954 (t80) cc_final: 0.7296 (t80) REVERT: D 453 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6826 (ttm110) outliers start: 2 outliers final: 2 residues processed: 150 average time/residue: 0.2698 time to fit residues: 52.6069 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.0570 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0840 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= 0.142 Angle : 0.485 7.408 11520 Z= 0.244 Chirality : 0.042 0.163 1284 Planarity : 0.004 0.035 1422 Dihedral : 10.590 95.313 1270 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.12 % Allowed : 17.34 % Favored : 81.54 % 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: -0.08 (0.26), residues: 1044 helix: 1.16 (0.26), residues: 424 sheet: -0.42 (0.39), residues: 172 loop : -1.05 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.008 0.001 PHE B 495 TYR 0.009 0.001 TYR D 673 ARG 0.003 0.000 ARG B 420 *********************** 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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.017 Fit side-chains REVERT: A 718 CYS cc_start: 0.7181 (m) cc_final: 0.6886 (m) REVERT: B 436 CYS cc_start: 0.6296 (p) cc_final: 0.5392 (t) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.2617 time to fit residues: 54.8362 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8538 Z= 0.425 Angle : 0.672 13.086 11520 Z= 0.334 Chirality : 0.050 0.184 1284 Planarity : 0.005 0.047 1422 Dihedral : 12.177 114.489 1266 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.69 % Allowed : 17.56 % Favored : 78.75 % 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: -0.73 (0.25), residues: 1044 helix: 0.62 (0.25), residues: 422 sheet: -1.35 (0.38), residues: 158 loop : -1.14 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 460 HIS 0.004 0.001 HIS D 435 PHE 0.018 0.003 PHE B 659 TYR 0.015 0.002 TYR D 673 ARG 0.004 0.001 ARG C 694 *********************** 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 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: D 651 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6543 (m-30) outliers start: 33 outliers final: 20 residues processed: 159 average time/residue: 0.2917 time to fit residues: 58.8736 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 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 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8538 Z= 0.164 Angle : 0.506 9.836 11520 Z= 0.253 Chirality : 0.043 0.140 1284 Planarity : 0.003 0.033 1422 Dihedral : 11.017 100.504 1266 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.35 % Allowed : 19.02 % Favored : 78.64 % 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: -0.32 (0.26), residues: 1044 helix: 0.98 (0.26), residues: 422 sheet: -0.70 (0.38), residues: 176 loop : -1.13 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 766 HIS 0.002 0.001 HIS C 412 PHE 0.013 0.001 PHE D 438 TYR 0.009 0.001 TYR C 673 ARG 0.003 0.000 ARG A 661 *********************** 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 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.966 Fit side-chains REVERT: A 673 TYR cc_start: 0.7868 (t80) cc_final: 0.7138 (t80) REVERT: A 718 CYS cc_start: 0.7272 (m) cc_final: 0.7015 (m) REVERT: C 673 TYR cc_start: 0.7838 (t80) cc_final: 0.7055 (t80) REVERT: D 453 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6826 (ttm110) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 0.2708 time to fit residues: 52.0880 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8538 Z= 0.290 Angle : 0.581 10.762 11520 Z= 0.288 Chirality : 0.046 0.162 1284 Planarity : 0.004 0.035 1422 Dihedral : 11.746 110.799 1266 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.69 % Allowed : 18.01 % Favored : 78.30 % 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: -0.56 (0.25), residues: 1044 helix: 0.82 (0.26), residues: 422 sheet: -1.20 (0.37), residues: 156 loop : -1.14 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 PHE 0.015 0.002 PHE D 438 TYR 0.012 0.002 TYR D 673 ARG 0.006 0.000 ARG D 684 *********************** 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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.975 Fit side-chains REVERT: A 673 TYR cc_start: 0.7872 (t80) cc_final: 0.7146 (t80) REVERT: A 705 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: A 718 CYS cc_start: 0.7377 (m) cc_final: 0.7128 (m) REVERT: D 453 ARG cc_start: 0.7193 (ttm110) cc_final: 0.6821 (ttm110) outliers start: 33 outliers final: 26 residues processed: 155 average time/residue: 0.2883 time to fit residues: 57.2767 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 726 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8538 Z= 0.172 Angle : 0.512 11.503 11520 Z= 0.254 Chirality : 0.043 0.141 1284 Planarity : 0.003 0.033 1422 Dihedral : 11.111 102.709 1266 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.47 % Allowed : 19.13 % Favored : 77.40 % 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: -0.33 (0.26), residues: 1044 helix: 1.00 (0.26), residues: 422 sheet: -0.77 (0.38), residues: 176 loop : -1.13 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.002 0.001 HIS C 412 PHE 0.012 0.002 PHE D 438 TYR 0.009 0.001 TYR C 673 ARG 0.005 0.000 ARG D 684 *********************** 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 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.094 Fit side-chains REVERT: A 673 TYR cc_start: 0.7861 (t80) cc_final: 0.7166 (t80) REVERT: A 718 CYS cc_start: 0.7337 (m) cc_final: 0.7094 (m) REVERT: C 673 TYR cc_start: 0.7814 (t80) cc_final: 0.7013 (t80) REVERT: D 453 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6758 (ttm110) outliers start: 31 outliers final: 25 residues processed: 155 average time/residue: 0.2777 time to fit residues: 55.1739 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR 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 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN D 726 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8538 Z= 0.163 Angle : 0.509 11.886 11520 Z= 0.251 Chirality : 0.043 0.138 1284 Planarity : 0.003 0.034 1422 Dihedral : 10.892 101.270 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.24 % Allowed : 19.57 % Favored : 77.18 % 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: -0.30 (0.26), residues: 1044 helix: 1.07 (0.26), residues: 424 sheet: -0.75 (0.41), residues: 148 loop : -1.16 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.002 0.001 HIS C 412 PHE 0.012 0.001 PHE D 438 TYR 0.009 0.001 TYR C 732 ARG 0.006 0.000 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.970 Fit side-chains REVERT: A 673 TYR cc_start: 0.7852 (t80) cc_final: 0.7197 (t80) REVERT: A 718 CYS cc_start: 0.7268 (m) cc_final: 0.7026 (m) REVERT: C 673 TYR cc_start: 0.7759 (t80) cc_final: 0.7076 (t80) REVERT: D 453 ARG cc_start: 0.7079 (ttm110) cc_final: 0.6691 (ttm110) outliers start: 29 outliers final: 23 residues processed: 159 average time/residue: 0.2803 time to fit residues: 57.4636 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS 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: 0.9980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8538 Z= 0.247 Angle : 0.561 12.224 11520 Z= 0.276 Chirality : 0.045 0.186 1284 Planarity : 0.004 0.033 1422 Dihedral : 11.511 108.435 1266 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.58 % Allowed : 18.90 % Favored : 77.52 % 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: -0.46 (0.25), residues: 1044 helix: 0.97 (0.26), residues: 422 sheet: -1.32 (0.41), residues: 128 loop : -1.13 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.003 0.001 HIS D 435 PHE 0.014 0.002 PHE D 438 TYR 0.010 0.001 TYR C 732 ARG 0.007 0.000 ARG D 684 *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.955 Fit side-chains REVERT: A 673 TYR cc_start: 0.7852 (t80) cc_final: 0.7178 (t80) REVERT: A 705 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: A 718 CYS cc_start: 0.7306 (m) cc_final: 0.7065 (m) REVERT: B 641 LYS cc_start: 0.7479 (mtmt) cc_final: 0.7252 (mmtt) REVERT: D 453 ARG cc_start: 0.7115 (ttm110) cc_final: 0.6722 (ttm110) outliers start: 32 outliers final: 26 residues processed: 159 average time/residue: 0.2928 time to fit residues: 58.9943 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8538 Z= 0.237 Angle : 0.559 12.759 11520 Z= 0.275 Chirality : 0.045 0.175 1284 Planarity : 0.004 0.034 1422 Dihedral : 11.448 106.893 1266 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.02 % Allowed : 19.69 % Favored : 77.29 % 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: -0.48 (0.25), residues: 1044 helix: 0.93 (0.26), residues: 422 sheet: -1.24 (0.37), residues: 156 loop : -1.10 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.002 0.001 HIS D 435 PHE 0.014 0.002 PHE D 438 TYR 0.010 0.001 TYR C 732 ARG 0.002 0.000 ARG D 684 *********************** 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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.881 Fit side-chains REVERT: A 673 TYR cc_start: 0.7839 (t80) cc_final: 0.7081 (t80) REVERT: A 718 CYS cc_start: 0.7378 (m) cc_final: 0.7148 (m) REVERT: B 641 LYS cc_start: 0.7479 (mtmt) cc_final: 0.7249 (mmtt) REVERT: C 673 TYR cc_start: 0.7766 (t80) cc_final: 0.7122 (t80) REVERT: C 715 ARG cc_start: 0.6823 (mpt180) cc_final: 0.6470 (mpt180) REVERT: D 453 ARG cc_start: 0.7108 (ttm110) cc_final: 0.6710 (ttm110) outliers start: 27 outliers final: 26 residues processed: 155 average time/residue: 0.2963 time to fit residues: 57.8357 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8538 Z= 0.274 Angle : 0.587 13.028 11520 Z= 0.289 Chirality : 0.046 0.178 1284 Planarity : 0.004 0.034 1422 Dihedral : 11.649 109.407 1266 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 19.80 % Favored : 76.96 % 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: -0.56 (0.25), residues: 1044 helix: 0.84 (0.26), residues: 422 sheet: -1.28 (0.37), residues: 156 loop : -1.13 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.003 0.001 HIS D 435 PHE 0.014 0.002 PHE D 438 TYR 0.021 0.002 TYR C 732 ARG 0.002 0.000 ARG C 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.897 Fit side-chains REVERT: A 705 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: A 718 CYS cc_start: 0.7446 (m) cc_final: 0.7218 (m) REVERT: B 641 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7265 (mmtt) REVERT: C 673 TYR cc_start: 0.7833 (t80) cc_final: 0.7146 (t80) REVERT: D 453 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6720 (ttm110) outliers start: 29 outliers final: 25 residues processed: 150 average time/residue: 0.3105 time to fit residues: 58.3548 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126445 restraints weight = 10454.584| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.87 r_work: 0.3290 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8538 Z= 0.135 Angle : 0.506 12.886 11520 Z= 0.249 Chirality : 0.042 0.137 1284 Planarity : 0.003 0.033 1422 Dihedral : 10.497 95.259 1266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.68 % Allowed : 20.69 % Favored : 76.62 % 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: -0.26 (0.26), residues: 1044 helix: 1.06 (0.26), residues: 424 sheet: -0.72 (0.37), residues: 174 loop : -1.11 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.002 0.000 HIS C 412 PHE 0.012 0.001 PHE D 438 TYR 0.008 0.001 TYR A 732 ARG 0.002 0.000 ARG A 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.84 seconds wall clock time: 39 minutes 10.78 seconds (2350.78 seconds total)