Starting phenix.real_space_refine on Sat Jun 7 03:48:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpy_29371/06_2025/8fpy_29371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpy_29371/06_2025/8fpy_29371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpy_29371/06_2025/8fpy_29371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpy_29371/06_2025/8fpy_29371.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpy_29371/06_2025/8fpy_29371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpy_29371/06_2025/8fpy_29371.cif" } resolution = 2.98 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8392 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.93, per 1000 atoms: 0.71 Number of scatterers: 8392 At special positions: 0 Unit cell: (120.54, 93.48, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1608 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 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: 44 helices and 20 sheets defined 41.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.641A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.593A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 695 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: 3.859A 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 removed outlier: 3.554A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 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 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 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 416 through 419 removed outlier: 4.109A 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 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 715 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 662 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 Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.502A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.502A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.668A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 444 removed outlier: 3.732A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 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: 4.028A 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: 6.519A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 439 through 444 removed outlier: 3.537A 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: 3.902A 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: 6.548A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 399 removed outlier: 7.055A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 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 452 through 453 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.099A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.553A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1011 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: 2.37 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2630 1.35 - 1.47: 2036 1.47 - 1.60: 3728 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 1.578 -0.244 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 1.47e+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 C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11327 1.97 - 3.95: 117 3.95 - 5.92: 41 5.92 - 7.90: 24 7.90 - 9.87: 11 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 101.75 111.62 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.52 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.07 -9.32 3.00e+00 1.11e-01 9.66e+00 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.02 -9.27 3.00e+00 1.11e-01 9.55e+00 angle pdb=" O3 CYZ C1302 " pdb=" S2 CYZ C1302 " pdb=" O4 CYZ C1302 " ideal model delta sigma weight residual 118.35 109.33 9.02 3.00e+00 1.11e-01 9.03e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 4627 22.62 - 45.24: 493 45.24 - 67.86: 98 67.86 - 90.48: 20 90.48 - 113.10: 10 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: 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 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+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 93.00 178.71 -85.71 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 155.14 -62.14 1 1.00e+01 1.00e-02 5.11e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1183 0.087 - 0.173: 85 0.173 - 0.260: 0 0.260 - 0.346: 0 0.346 - 0.433: 16 Chirality restraints: 1284 Sorted by residual: 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 2.64 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C8 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" N2 CYZ B1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.60e+00 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 4.57e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 772 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" CD GLU D 772 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU D 772 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 772 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 736 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 737 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 737 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 737 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 438 " 0.006 2.00e-02 2.50e+03 8.60e-03 1.29e+00 pdb=" CG PHE C 438 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 438 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 438 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 438 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 438 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 438 " 0.000 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 90 2.64 - 3.20: 7218 3.20 - 3.77: 13092 3.77 - 4.33: 18567 4.33 - 4.90: 30217 Nonbonded interactions: 69184 Sorted by model distance: nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.069 3.040 nonbonded pdb=" NE2 GLN C 714 " pdb=" O TRP C 767 " model vdw 2.203 3.120 nonbonded pdb=" O PHE A 658 " pdb=" OG SER A 662 " model vdw 2.208 3.040 nonbonded pdb=" N ASP D 427 " pdb=" OD1 ASP D 427 " model vdw 2.216 3.120 nonbonded pdb=" O PHE C 658 " pdb=" OG SER C 662 " model vdw 2.274 3.040 ... (remaining 69179 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.950 Find NCS groups from input model: 0.470 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.244 8542 Z= 0.725 Angle : 0.696 9.871 11528 Z= 0.295 Chirality : 0.061 0.433 1284 Planarity : 0.003 0.030 1422 Dihedral : 19.339 113.100 3288 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.68 % Allowed : 31.99 % Favored : 65.32 % 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: -0.27 (0.25), residues: 1044 helix: 0.86 (0.25), residues: 418 sheet: -0.38 (0.38), residues: 182 loop : -1.05 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 671 HIS 0.005 0.001 HIS B 412 PHE 0.020 0.001 PHE C 438 TYR 0.011 0.001 TYR B 673 ARG 0.007 0.001 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.17719 ( 344) hydrogen bonds : angle 6.26985 ( 1011) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.45297 ( 8) covalent geometry : bond 0.01454 ( 8538) covalent geometry : angle 0.69624 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.928 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 1.5934 time to fit residues: 245.7114 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 625 THR 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: 6.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127435 restraints weight = 10664.005| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.08 r_work: 0.3385 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8542 Z= 0.142 Angle : 0.537 7.705 11528 Z= 0.265 Chirality : 0.044 0.162 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.452 91.303 1292 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.82 % Allowed : 26.62 % Favored : 67.56 % 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: 0.88 (0.25), residues: 438 sheet: -0.39 (0.39), residues: 170 loop : -1.13 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.011 0.001 PHE B 495 TYR 0.018 0.002 TYR C 673 ARG 0.005 0.001 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 344) hydrogen bonds : angle 4.58518 ( 1011) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.32239 ( 8) covalent geometry : bond 0.00345 ( 8538) covalent geometry : angle 0.53730 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.921 Fit side-chains REVERT: A 398 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8047 (m) REVERT: A 419 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: A 441 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7823 (tttm) REVERT: A 486 GLU cc_start: 0.7641 (tp30) cc_final: 0.7311 (mm-30) REVERT: B 511 LYS cc_start: 0.6645 (tppp) cc_final: 0.6429 (ptpt) REVERT: C 684 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7193 (mtm180) REVERT: D 427 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6545 (p0) outliers start: 52 outliers final: 23 residues processed: 171 average time/residue: 1.4589 time to fit residues: 262.7402 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 742 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124310 restraints weight = 10715.350| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.09 r_work: 0.3336 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8542 Z= 0.188 Angle : 0.589 8.801 11528 Z= 0.292 Chirality : 0.047 0.223 1284 Planarity : 0.004 0.040 1422 Dihedral : 9.713 95.888 1278 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 7.49 % Allowed : 25.50 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1044 helix: 0.73 (0.25), residues: 434 sheet: -0.62 (0.40), residues: 158 loop : -1.24 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.005 0.001 HIS B 412 PHE 0.013 0.002 PHE B 495 TYR 0.019 0.002 TYR B 673 ARG 0.006 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 344) hydrogen bonds : angle 4.53391 ( 1011) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.44154 ( 8) covalent geometry : bond 0.00462 ( 8538) covalent geometry : angle 0.58896 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 1.052 Fit side-chains REVERT: A 393 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.4967 (pmtt) REVERT: A 419 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: A 486 GLU cc_start: 0.7669 (tp30) cc_final: 0.7355 (mm-30) REVERT: A 715 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6572 (ttm110) REVERT: A 761 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8260 (pttm) REVERT: C 393 LYS cc_start: 0.5375 (OUTLIER) cc_final: 0.4925 (pmmt) REVERT: C 751 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8227 (mt) REVERT: D 427 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: D 628 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6887 (tpp80) REVERT: D 697 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7400 (mmtm) outliers start: 67 outliers final: 27 residues processed: 177 average time/residue: 1.5309 time to fit residues: 285.1979 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.151968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125793 restraints weight = 10704.274| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.01 r_work: 0.3353 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8542 Z= 0.151 Angle : 0.545 8.636 11528 Z= 0.270 Chirality : 0.045 0.211 1284 Planarity : 0.004 0.043 1422 Dihedral : 9.369 93.024 1277 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.71 % Allowed : 25.95 % Favored : 67.34 % 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: -0.42 (0.25), residues: 1044 helix: 0.84 (0.25), residues: 434 sheet: -0.62 (0.38), residues: 166 loop : -1.23 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 766 HIS 0.005 0.001 HIS B 412 PHE 0.012 0.002 PHE B 495 TYR 0.015 0.002 TYR D 673 ARG 0.007 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 344) hydrogen bonds : angle 4.40705 ( 1011) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.62465 ( 8) covalent geometry : bond 0.00370 ( 8538) covalent geometry : angle 0.54462 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 0.957 Fit side-chains REVERT: A 393 LYS cc_start: 0.5855 (OUTLIER) cc_final: 0.4960 (pmtt) REVERT: A 486 GLU cc_start: 0.7587 (tp30) cc_final: 0.7215 (mm-30) REVERT: A 761 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8270 (pttm) REVERT: C 393 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.4890 (pmmt) REVERT: C 751 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8219 (mt) REVERT: D 427 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: D 697 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7108 (mmmm) outliers start: 60 outliers final: 28 residues processed: 173 average time/residue: 1.6045 time to fit residues: 292.3039 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 697 LYS 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 78 optimal weight: 0.0030 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 overall best weight: 0.5732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128878 restraints weight = 10748.463| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.03 r_work: 0.3401 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8542 Z= 0.098 Angle : 0.490 7.422 11528 Z= 0.243 Chirality : 0.043 0.170 1284 Planarity : 0.004 0.043 1422 Dihedral : 8.274 84.161 1276 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.03 % Allowed : 28.52 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1044 helix: 1.05 (0.26), residues: 434 sheet: -0.34 (0.37), residues: 168 loop : -1.29 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.009 0.001 PHE B 495 TYR 0.011 0.001 TYR B 673 ARG 0.008 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 344) hydrogen bonds : angle 4.24699 ( 1011) SS BOND : bond 0.00507 ( 4) SS BOND : angle 0.44409 ( 8) covalent geometry : bond 0.00229 ( 8538) covalent geometry : angle 0.49005 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.025 Fit side-chains REVERT: A 419 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 486 GLU cc_start: 0.7473 (tp30) cc_final: 0.7181 (mm-30) REVERT: A 703 LEU cc_start: 0.8066 (mt) cc_final: 0.7862 (mt) REVERT: A 708 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7403 (mtp) REVERT: C 708 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7552 (mtp) REVERT: C 719 ASP cc_start: 0.6406 (p0) cc_final: 0.5941 (p0) REVERT: D 454 ASP cc_start: 0.5557 (t0) cc_final: 0.5234 (m-30) outliers start: 36 outliers final: 15 residues processed: 160 average time/residue: 1.5935 time to fit residues: 270.1085 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 87 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128243 restraints weight = 10640.909| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.01 r_work: 0.3392 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8542 Z= 0.118 Angle : 0.511 7.588 11528 Z= 0.254 Chirality : 0.043 0.213 1284 Planarity : 0.004 0.043 1422 Dihedral : 7.391 80.146 1270 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.47 % Allowed : 28.86 % Favored : 66.67 % 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: -0.25 (0.25), residues: 1044 helix: 0.97 (0.26), residues: 438 sheet: -0.17 (0.38), residues: 150 loop : -1.28 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.004 0.001 HIS B 412 PHE 0.027 0.001 PHE A 438 TYR 0.012 0.001 TYR D 673 ARG 0.009 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 344) hydrogen bonds : angle 4.24654 ( 1011) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.38649 ( 8) covalent geometry : bond 0.00284 ( 8538) covalent geometry : angle 0.51092 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.863 Fit side-chains REVERT: A 419 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: A 486 GLU cc_start: 0.7511 (tp30) cc_final: 0.7225 (mm-30) REVERT: A 684 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7112 (mtp180) REVERT: A 703 LEU cc_start: 0.8071 (mt) cc_final: 0.7837 (mt) REVERT: A 708 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7449 (mtp) REVERT: B 714 GLN cc_start: 0.7541 (tp40) cc_final: 0.6853 (tp40) REVERT: C 393 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4642 (pmmt) REVERT: C 708 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7480 (mtp) outliers start: 40 outliers final: 24 residues processed: 156 average time/residue: 1.4913 time to fit residues: 244.9127 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 ARG Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124258 restraints weight = 10809.881| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.06 r_work: 0.3338 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8542 Z= 0.188 Angle : 0.593 9.182 11528 Z= 0.296 Chirality : 0.047 0.213 1284 Planarity : 0.004 0.043 1422 Dihedral : 7.791 82.112 1270 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.70 % Allowed : 28.08 % Favored : 66.22 % 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: -0.42 (0.25), residues: 1044 helix: 0.81 (0.26), residues: 434 sheet: -0.60 (0.38), residues: 158 loop : -1.20 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.004 0.001 HIS B 412 PHE 0.013 0.002 PHE B 495 TYR 0.018 0.002 TYR D 673 ARG 0.009 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 344) hydrogen bonds : angle 4.43665 ( 1011) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.63521 ( 8) covalent geometry : bond 0.00464 ( 8538) covalent geometry : angle 0.59333 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.009 Fit side-chains REVERT: A 419 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: A 486 GLU cc_start: 0.7599 (tp30) cc_final: 0.7324 (mm-30) REVERT: A 708 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7467 (mtp) REVERT: A 761 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8343 (pttm) REVERT: B 486 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: B 511 LYS cc_start: 0.6368 (ptpt) cc_final: 0.6013 (mptt) REVERT: C 393 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.4713 (pmmt) REVERT: C 708 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7470 (mtp) REVERT: C 751 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8211 (mt) REVERT: C 761 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8324 (pttm) REVERT: D 511 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6669 (mmtt) REVERT: D 628 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6842 (tpp80) outliers start: 51 outliers final: 28 residues processed: 161 average time/residue: 1.5564 time to fit residues: 263.9235 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126205 restraints weight = 10813.445| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.00 r_work: 0.3368 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8542 Z= 0.145 Angle : 0.551 8.490 11528 Z= 0.275 Chirality : 0.045 0.197 1284 Planarity : 0.004 0.046 1422 Dihedral : 7.477 78.357 1270 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.03 % Allowed : 29.19 % Favored : 65.77 % 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: -0.43 (0.25), residues: 1044 helix: 0.79 (0.26), residues: 438 sheet: -0.25 (0.39), residues: 138 loop : -1.33 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 PHE 0.012 0.002 PHE B 495 TYR 0.014 0.001 TYR B 673 ARG 0.011 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 344) hydrogen bonds : angle 4.36086 ( 1011) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.52255 ( 8) covalent geometry : bond 0.00353 ( 8538) covalent geometry : angle 0.55096 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.857 Fit side-chains REVERT: A 393 LYS cc_start: 0.5535 (OUTLIER) cc_final: 0.5133 (pmmt) REVERT: A 419 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: A 486 GLU cc_start: 0.7517 (tp30) cc_final: 0.7208 (mm-30) REVERT: A 708 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7459 (mtp) REVERT: C 393 LYS cc_start: 0.5271 (OUTLIER) cc_final: 0.4714 (pmmt) REVERT: C 708 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7497 (mtp) REVERT: C 719 ASP cc_start: 0.6612 (p0) cc_final: 0.6169 (p0) REVERT: C 751 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (mt) REVERT: C 761 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8391 (pttm) REVERT: D 628 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6816 (tpp80) outliers start: 45 outliers final: 28 residues processed: 154 average time/residue: 1.7549 time to fit residues: 283.7758 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125515 restraints weight = 10824.056| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.04 r_work: 0.3357 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8542 Z= 0.156 Angle : 0.571 8.811 11528 Z= 0.284 Chirality : 0.045 0.201 1284 Planarity : 0.004 0.051 1422 Dihedral : 7.252 67.686 1270 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.92 % Allowed : 29.64 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1044 helix: 0.81 (0.26), residues: 434 sheet: -0.24 (0.39), residues: 138 loop : -1.36 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.005 0.001 HIS B 412 PHE 0.012 0.002 PHE B 495 TYR 0.016 0.002 TYR D 673 ARG 0.012 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 344) hydrogen bonds : angle 4.38833 ( 1011) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.61996 ( 8) covalent geometry : bond 0.00383 ( 8538) covalent geometry : angle 0.57100 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.964 Fit side-chains REVERT: A 393 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.5011 (pmmt) REVERT: A 419 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: A 486 GLU cc_start: 0.7537 (tp30) cc_final: 0.7184 (mm-30) REVERT: A 708 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7456 (mtp) REVERT: B 486 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: B 511 LYS cc_start: 0.6344 (ptpt) cc_final: 0.5991 (mptt) REVERT: C 393 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.4805 (pmmt) REVERT: C 751 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8222 (mt) REVERT: C 761 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8374 (pttm) REVERT: D 454 ASP cc_start: 0.5561 (t0) cc_final: 0.5218 (m-30) outliers start: 44 outliers final: 31 residues processed: 151 average time/residue: 1.4912 time to fit residues: 238.3269 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 0.0000 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127371 restraints weight = 10718.272| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.05 r_work: 0.3388 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8542 Z= 0.118 Angle : 0.528 7.688 11528 Z= 0.264 Chirality : 0.044 0.217 1284 Planarity : 0.004 0.055 1422 Dihedral : 6.479 50.692 1270 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.69 % Allowed : 30.65 % Favored : 65.66 % 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: -0.39 (0.25), residues: 1044 helix: 0.87 (0.26), residues: 438 sheet: -0.10 (0.41), residues: 124 loop : -1.38 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.005 0.001 HIS B 412 PHE 0.010 0.001 PHE B 495 TYR 0.012 0.001 TYR D 673 ARG 0.013 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 344) hydrogen bonds : angle 4.31447 ( 1011) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.48616 ( 8) covalent geometry : bond 0.00281 ( 8538) covalent geometry : angle 0.52761 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.005 Fit side-chains REVERT: A 419 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: A 486 GLU cc_start: 0.7480 (tp30) cc_final: 0.7140 (mm-30) REVERT: A 708 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7417 (mtp) REVERT: B 511 LYS cc_start: 0.6318 (ptpt) cc_final: 0.5971 (mptt) REVERT: B 695 LYS cc_start: 0.7912 (mptt) cc_final: 0.7684 (mppt) REVERT: C 393 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4667 (pmmt) REVERT: C 751 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8203 (mt) REVERT: D 454 ASP cc_start: 0.5550 (t0) cc_final: 0.5220 (m-30) REVERT: D 628 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6763 (tpp80) outliers start: 33 outliers final: 23 residues processed: 148 average time/residue: 1.4442 time to fit residues: 225.9323 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN D 642 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130140 restraints weight = 10884.604| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.05 r_work: 0.3429 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8542 Z= 0.103 Angle : 0.510 7.652 11528 Z= 0.258 Chirality : 0.043 0.157 1284 Planarity : 0.004 0.055 1422 Dihedral : 5.896 48.682 1270 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.24 % Allowed : 31.32 % Favored : 65.44 % 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: -0.25 (0.25), residues: 1044 helix: 1.00 (0.26), residues: 436 sheet: 0.05 (0.42), residues: 124 loop : -1.34 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.005 0.001 HIS B 412 PHE 0.027 0.002 PHE A 438 TYR 0.022 0.001 TYR C 673 ARG 0.013 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 344) hydrogen bonds : angle 4.23352 ( 1011) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.54800 ( 8) covalent geometry : bond 0.00242 ( 8538) covalent geometry : angle 0.51018 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8208.02 seconds wall clock time: 144 minutes 50.19 seconds (8690.19 seconds total)