Starting phenix.real_space_refine on Wed Mar 12 23:53:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fph_29364/03_2025/8fph_29364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fph_29364/03_2025/8fph_29364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fph_29364/03_2025/8fph_29364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fph_29364/03_2025/8fph_29364.map" model { file = "/net/cci-nas-00/data/ceres_data/8fph_29364/03_2025/8fph_29364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fph_29364/03_2025/8fph_29364.cif" } resolution = 3.14 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 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.32, per 1000 atoms: 0.75 Number of scatterers: 8388 At special positions: 0 Unit cell: (117.189, 88.506, 84.4085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1604 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 997.0 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 43.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.570A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.005A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.590A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.733A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.929A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.994A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.595A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.592A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.653A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.548A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.573A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.814A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.633A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.507A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.603A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.834A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.628A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.006A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.624A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.386A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.498A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.498A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.522A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.487A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.004A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.661A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.506A pdb=" N LYS D 441 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.296A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.576A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2043 1.48 - 1.60: 3721 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11293 1.95 - 3.89: 152 3.89 - 5.84: 37 5.84 - 7.79: 24 7.79 - 9.74: 14 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.49 -9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.43 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 110.98 -9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 110.98 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.32 9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 4736 22.71 - 45.42: 415 45.42 - 68.12: 72 68.12 - 90.83: 13 90.83 - 113.54: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual -86.00 -149.05 63.05 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual -86.00 -28.29 -57.71 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" N2 CYZ B1302 " pdb=" C8 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" S1 CYZ B1302 " ideal model delta sinusoidal sigma weight residual 55.73 -57.81 113.54 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1175 0.086 - 0.172: 93 0.172 - 0.258: 0 0.258 - 0.344: 0 0.344 - 0.429: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 737 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 494 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 494 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.023 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1349 2.76 - 3.30: 7681 3.30 - 3.83: 13772 3.83 - 4.37: 16252 4.37 - 4.90: 28491 Nonbonded interactions: 67545 Sorted by model distance: nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 654 " pdb=" O HOH B1401 " model vdw 2.245 3.040 nonbonded pdb=" O LEU D 639 " pdb=" NE2 GLN D 642 " model vdw 2.270 3.120 nonbonded pdb=" NH1 ARG D 715 " pdb=" O TRP D 767 " model vdw 2.318 3.120 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.323 3.040 ... (remaining 67540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.410 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.243 8538 Z= 1.034 Angle : 0.722 9.736 11520 Z= 0.313 Chirality : 0.062 0.429 1284 Planarity : 0.004 0.048 1422 Dihedral : 17.886 113.541 3288 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.11 % Allowed : 24.38 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.25), residues: 1044 helix: 0.52 (0.26), residues: 416 sheet: -1.04 (0.38), residues: 172 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.005 0.001 HIS D 412 PHE 0.010 0.001 PHE D 495 TYR 0.010 0.001 TYR D 405 ARG 0.007 0.000 ARG C 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 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.912 Fit side-chains REVERT: A 684 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7516 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2793 time to fit residues: 49.8914 Evaluate side-chains 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140843 restraints weight = 10241.273| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.07 r_work: 0.3482 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8538 Z= 0.169 Angle : 0.499 6.975 11520 Z= 0.248 Chirality : 0.043 0.138 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.096 93.641 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.46 % Allowed : 21.81 % Favored : 75.73 % 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: -0.74 (0.25), residues: 1044 helix: 0.63 (0.25), residues: 436 sheet: -0.98 (0.39), residues: 156 loop : -1.38 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.017 0.001 PHE D 438 TYR 0.009 0.001 TYR D 405 ARG 0.004 0.000 ARG A 684 *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.975 Fit side-chains REVERT: A 408 MET cc_start: 0.7753 (mtp) cc_final: 0.7537 (mtp) REVERT: D 402 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7416 (mm-30) REVERT: D 407 MET cc_start: 0.8207 (mtm) cc_final: 0.8006 (mtp) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.2563 time to fit residues: 53.3375 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.0870 chunk 52 optimal weight: 0.0670 chunk 88 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 0.0010 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144437 restraints weight = 10312.102| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.08 r_work: 0.3538 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8538 Z= 0.110 Angle : 0.466 7.100 11520 Z= 0.226 Chirality : 0.042 0.180 1284 Planarity : 0.003 0.036 1422 Dihedral : 8.387 77.304 1266 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.46 % Allowed : 22.60 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1044 helix: 1.04 (0.25), residues: 434 sheet: -0.64 (0.42), residues: 144 loop : -1.34 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 PHE 0.007 0.001 PHE D 495 TYR 0.011 0.001 TYR C 450 ARG 0.002 0.000 ARG D 715 *********************** 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 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.954 Fit side-chains REVERT: A 674 MET cc_start: 0.7393 (mtp) cc_final: 0.7062 (mtt) REVERT: A 695 LYS cc_start: 0.7348 (tppt) cc_final: 0.6974 (tttm) REVERT: A 760 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: C 408 MET cc_start: 0.8161 (tpp) cc_final: 0.7853 (tpp) REVERT: D 402 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7421 (mm-30) outliers start: 22 outliers final: 9 residues processed: 151 average time/residue: 0.2615 time to fit residues: 51.2494 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.161146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137151 restraints weight = 10413.459| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.07 r_work: 0.3424 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8538 Z= 0.284 Angle : 0.573 8.137 11520 Z= 0.284 Chirality : 0.047 0.239 1284 Planarity : 0.004 0.034 1422 Dihedral : 7.310 72.186 1266 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.80 % Allowed : 22.04 % 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: -0.69 (0.25), residues: 1044 helix: 0.83 (0.25), residues: 430 sheet: -0.91 (0.40), residues: 146 loop : -1.53 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 PHE 0.014 0.002 PHE A 495 TYR 0.012 0.001 TYR D 405 ARG 0.006 0.001 ARG A 684 *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.981 Fit side-chains REVERT: A 674 MET cc_start: 0.7509 (mtp) cc_final: 0.7275 (mtp) REVERT: C 408 MET cc_start: 0.8350 (tpp) cc_final: 0.8122 (tpp) REVERT: C 497 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8602 (p) REVERT: D 642 GLN cc_start: 0.7395 (pp30) cc_final: 0.7122 (pp30) outliers start: 34 outliers final: 21 residues processed: 157 average time/residue: 0.2694 time to fit residues: 54.5443 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0010 chunk 94 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 78 optimal weight: 0.0030 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138201 restraints weight = 10266.202| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.06 r_work: 0.3447 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8538 Z= 0.194 Angle : 0.506 7.635 11520 Z= 0.251 Chirality : 0.044 0.226 1284 Planarity : 0.003 0.035 1422 Dihedral : 6.386 56.880 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.03 % Allowed : 22.48 % Favored : 73.49 % 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: -0.62 (0.25), residues: 1044 helix: 0.98 (0.25), residues: 428 sheet: -1.09 (0.35), residues: 182 loop : -1.49 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 PHE 0.010 0.001 PHE D 495 TYR 0.016 0.001 TYR C 450 ARG 0.006 0.000 ARG A 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 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.966 Fit side-chains REVERT: A 674 MET cc_start: 0.7587 (mtp) cc_final: 0.7353 (mtp) REVERT: A 684 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7838 (mtm180) REVERT: A 695 LYS cc_start: 0.7532 (tppt) cc_final: 0.7161 (tptt) REVERT: C 408 MET cc_start: 0.8242 (tpp) cc_final: 0.8038 (tpp) REVERT: C 450 TYR cc_start: 0.8462 (m-80) cc_final: 0.8257 (m-80) REVERT: C 497 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (p) REVERT: D 402 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7467 (mm-30) REVERT: D 466 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: D 695 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7063 (tptt) outliers start: 36 outliers final: 16 residues processed: 161 average time/residue: 0.2596 time to fit residues: 54.3682 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 99 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141523 restraints weight = 10310.942| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.01 r_work: 0.3464 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8538 Z= 0.165 Angle : 0.484 6.884 11520 Z= 0.242 Chirality : 0.043 0.165 1284 Planarity : 0.003 0.036 1422 Dihedral : 5.711 49.305 1266 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.91 % Allowed : 22.60 % Favored : 73.49 % 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: -0.49 (0.25), residues: 1044 helix: 1.08 (0.25), residues: 428 sheet: -1.13 (0.38), residues: 156 loop : -1.37 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.014 0.001 TYR C 450 ARG 0.004 0.000 ARG A 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 176 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.000 Fit side-chains REVERT: A 684 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7835 (mtm180) REVERT: A 695 LYS cc_start: 0.7611 (tppt) cc_final: 0.7248 (tptt) REVERT: A 760 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: C 497 SER cc_start: 0.8837 (t) cc_final: 0.8620 (p) REVERT: D 402 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7481 (mm-30) REVERT: D 660 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8365 (ttm110) REVERT: D 761 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7983 (tmmt) outliers start: 35 outliers final: 24 residues processed: 166 average time/residue: 0.2482 time to fit residues: 54.1858 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.8278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138633 restraints weight = 10369.145| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.09 r_work: 0.3450 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1513 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= 0.180 Angle : 0.494 6.947 11520 Z= 0.248 Chirality : 0.044 0.141 1284 Planarity : 0.003 0.036 1422 Dihedral : 5.583 44.929 1266 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.80 % Allowed : 22.48 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.25), residues: 1044 helix: 1.08 (0.25), residues: 428 sheet: -1.19 (0.37), residues: 156 loop : -1.38 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.009 0.001 TYR B 673 ARG 0.004 0.000 ARG A 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.035 Fit side-chains REVERT: A 674 MET cc_start: 0.7610 (mtp) cc_final: 0.7217 (mtt) REVERT: A 684 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7811 (mtm180) REVERT: A 695 LYS cc_start: 0.7742 (tppt) cc_final: 0.7331 (tptt) REVERT: A 760 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: B 705 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8406 (mm-30) REVERT: C 497 SER cc_start: 0.8892 (t) cc_final: 0.8669 (p) REVERT: D 402 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 466 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7629 (pp20) REVERT: D 660 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8342 (ttm110) REVERT: D 761 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7970 (tmmt) outliers start: 34 outliers final: 26 residues processed: 158 average time/residue: 0.2549 time to fit residues: 52.3731 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 6 optimal weight: 0.0770 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.166368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143761 restraints weight = 10271.919| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.92 r_work: 0.3488 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8538 Z= 0.146 Angle : 0.472 6.368 11520 Z= 0.237 Chirality : 0.043 0.128 1284 Planarity : 0.003 0.035 1422 Dihedral : 5.320 42.002 1266 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.91 % Allowed : 23.49 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1044 helix: 1.19 (0.25), residues: 428 sheet: -1.03 (0.35), residues: 180 loop : -1.31 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.010 0.001 TYR C 647 ARG 0.004 0.000 ARG A 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 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.024 Fit side-chains REVERT: A 674 MET cc_start: 0.7624 (mtp) cc_final: 0.7208 (mtt) REVERT: A 684 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7780 (mtm180) REVERT: A 695 LYS cc_start: 0.7705 (tppt) cc_final: 0.7310 (tptt) REVERT: A 760 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: C 497 SER cc_start: 0.8837 (t) cc_final: 0.8618 (p) REVERT: D 402 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 466 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: D 761 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7966 (tmmt) outliers start: 26 outliers final: 20 residues processed: 153 average time/residue: 0.2705 time to fit residues: 54.2131 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 0.0020 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.0470 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142743 restraints weight = 10359.478| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.07 r_work: 0.3507 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8538 Z= 0.123 Angle : 0.454 6.326 11520 Z= 0.229 Chirality : 0.042 0.127 1284 Planarity : 0.003 0.035 1422 Dihedral : 4.935 38.874 1266 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.46 % Allowed : 23.94 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.25), residues: 1044 helix: 1.32 (0.26), residues: 430 sheet: -0.79 (0.37), residues: 170 loop : -1.28 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.007 0.001 PHE D 495 TYR 0.011 0.001 TYR C 450 ARG 0.003 0.000 ARG A 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 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.056 Fit side-chains REVERT: A 674 MET cc_start: 0.7622 (mtp) cc_final: 0.7213 (mtt) REVERT: A 684 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7803 (mtm180) REVERT: A 695 LYS cc_start: 0.7655 (tppt) cc_final: 0.7240 (tptt) REVERT: A 760 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: A 773 CYS cc_start: 0.4834 (t) cc_final: 0.4575 (t) REVERT: C 450 TYR cc_start: 0.8443 (m-80) cc_final: 0.8225 (m-80) REVERT: C 497 SER cc_start: 0.8816 (t) cc_final: 0.8607 (p) REVERT: D 402 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7588 (mm-30) REVERT: D 466 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7632 (pp20) REVERT: D 761 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7866 (tmmt) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.2553 time to fit residues: 48.3689 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.3980 chunk 80 optimal weight: 30.0000 chunk 2 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140345 restraints weight = 10307.964| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.05 r_work: 0.3474 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8538 Z= 0.167 Angle : 0.489 6.609 11520 Z= 0.245 Chirality : 0.043 0.128 1284 Planarity : 0.003 0.035 1422 Dihedral : 5.188 41.719 1266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.13 % Allowed : 24.16 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1044 helix: 1.26 (0.25), residues: 428 sheet: -1.03 (0.37), residues: 156 loop : -1.23 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 PHE 0.009 0.001 PHE B 438 TYR 0.013 0.001 TYR C 450 ARG 0.003 0.000 ARG A 684 ********************** 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 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.107 Fit side-chains REVERT: A 674 MET cc_start: 0.7616 (mtp) cc_final: 0.7207 (mtt) REVERT: A 684 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7815 (mtm180) REVERT: A 695 LYS cc_start: 0.7748 (tppt) cc_final: 0.7330 (tptt) REVERT: A 760 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: C 450 TYR cc_start: 0.8481 (m-80) cc_final: 0.8266 (m-80) REVERT: D 402 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 684 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6546 (tpm170) REVERT: D 761 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7864 (tmmt) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.2826 time to fit residues: 51.6149 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.0370 chunk 75 optimal weight: 0.7980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141579 restraints weight = 10374.809| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.04 r_work: 0.3493 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8538 Z= 0.137 Angle : 0.470 6.340 11520 Z= 0.237 Chirality : 0.042 0.127 1284 Planarity : 0.003 0.034 1422 Dihedral : 5.033 40.051 1266 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.13 % Allowed : 23.94 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1044 helix: 1.35 (0.26), residues: 428 sheet: -0.92 (0.35), residues: 180 loop : -1.19 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.008 0.001 PHE D 495 TYR 0.011 0.001 TYR C 450 ARG 0.003 0.000 ARG A 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4963.14 seconds wall clock time: 86 minutes 43.69 seconds (5203.69 seconds total)