Starting phenix.real_space_refine on Fri Aug 22 22:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpy_29371/08_2025/8fpy_29371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpy_29371/08_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_29371/08_2025/8fpy_29371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpy_29371/08_2025/8fpy_29371.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpy_29371/08_2025/8fpy_29371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpy_29371/08_2025/8fpy_29371.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.29, per 1000 atoms: 0.27 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: 0.61 Conformation dependent library (CDL) restraints added in 444.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.34 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: 1.23 Time building geometry restraints manager: 0.79 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 through 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 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 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 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: 3.070 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG D 661 TYR 0.011 0.001 TYR B 673 PHE 0.020 0.001 PHE C 438 TRP 0.007 0.001 TRP C 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.01454 ( 8538) covalent geometry : angle 0.69624 (11520) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.45297 ( 8) hydrogen bonds : bond 0.17719 ( 344) hydrogen bonds : angle 6.26985 ( 1011) *********************** 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 : 0.354 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 0.7491 time to fit residues: 115.4837 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 : 0.351 ------------------------------------------------------------------------------- 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 49 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128709 restraints weight = 10724.368| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.08 r_work: 0.3396 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8542 Z= 0.128 Angle : 0.521 7.718 11528 Z= 0.257 Chirality : 0.044 0.155 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.382 90.072 1292 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.26 % Allowed : 27.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1044 helix: 0.94 (0.25), residues: 438 sheet: -0.37 (0.39), residues: 170 loop : -1.10 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 661 TYR 0.018 0.001 TYR C 673 PHE 0.010 0.001 PHE B 495 TRP 0.006 0.001 TRP C 671 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8538) covalent geometry : angle 0.52095 (11520) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.31211 ( 8) hydrogen bonds : bond 0.03383 ( 344) hydrogen bonds : angle 4.56049 ( 1011) *********************** 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: 47 poor density : 142 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 419 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6767 (tt0) REVERT: A 441 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7850 (tttm) REVERT: A 486 GLU cc_start: 0.7620 (tp30) cc_final: 0.7294 (mm-30) REVERT: B 511 LYS cc_start: 0.6665 (tppp) cc_final: 0.6433 (ptpt) REVERT: C 684 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7160 (mtm180) REVERT: D 427 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6513 (p0) outliers start: 47 outliers final: 20 residues processed: 170 average time/residue: 0.7685 time to fit residues: 137.0337 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 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 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 81 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 C 756 GLN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126734 restraints weight = 10579.036| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.08 r_work: 0.3369 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8542 Z= 0.143 Angle : 0.541 8.112 11528 Z= 0.266 Chirality : 0.044 0.217 1284 Planarity : 0.004 0.039 1422 Dihedral : 9.019 89.555 1277 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.82 % Allowed : 26.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.25), residues: 1044 helix: 0.94 (0.25), residues: 434 sheet: -0.35 (0.38), residues: 168 loop : -1.25 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 684 TYR 0.016 0.002 TYR B 673 PHE 0.011 0.001 PHE B 495 TRP 0.006 0.001 TRP C 460 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8538) covalent geometry : angle 0.54125 (11520) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.28871 ( 8) hydrogen bonds : bond 0.03519 ( 344) hydrogen bonds : angle 4.38598 ( 1011) *********************** 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 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.365 Fit side-chains REVERT: A 393 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.4982 (pmtt) REVERT: A 398 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8046 (m) REVERT: A 419 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: A 441 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7638 (tttm) REVERT: A 486 GLU cc_start: 0.7629 (tp30) cc_final: 0.7262 (mm-30) REVERT: C 393 LYS cc_start: 0.5197 (OUTLIER) cc_final: 0.4755 (pmmt) REVERT: C 751 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8217 (mt) REVERT: D 427 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6308 (p0) REVERT: D 463 MET cc_start: 0.8601 (mtm) cc_final: 0.8400 (mtm) outliers start: 52 outliers final: 20 residues processed: 166 average time/residue: 0.7555 time to fit residues: 131.7422 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 441 LYS Chi-restraints excluded: chain A residue 683 VAL 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 498 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL 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 398 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL 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 666 VAL 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 21 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 756 GLN 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 = 0.3789 r_free = 0.3789 target = 0.152296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125281 restraints weight = 10882.029| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.09 r_work: 0.3350 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8542 Z= 0.162 Angle : 0.560 8.860 11528 Z= 0.276 Chirality : 0.045 0.211 1284 Planarity : 0.004 0.042 1422 Dihedral : 8.995 90.926 1277 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.70 % Allowed : 27.18 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.25), residues: 1044 helix: 0.88 (0.25), residues: 434 sheet: -0.57 (0.39), residues: 158 loop : -1.18 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 684 TYR 0.016 0.002 TYR B 673 PHE 0.012 0.002 PHE B 495 TRP 0.006 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8538) covalent geometry : angle 0.56019 (11520) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.47688 ( 8) hydrogen bonds : bond 0.03553 ( 344) hydrogen bonds : angle 4.39584 ( 1011) *********************** 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 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 0.337 Fit side-chains REVERT: A 393 LYS cc_start: 0.5862 (OUTLIER) cc_final: 0.4977 (pmtt) REVERT: A 419 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: A 486 GLU cc_start: 0.7610 (tp30) cc_final: 0.7242 (mm-30) REVERT: A 708 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7454 (mtp) REVERT: C 393 LYS cc_start: 0.5351 (OUTLIER) cc_final: 0.4840 (pmmt) REVERT: C 714 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: C 751 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8208 (mt) REVERT: D 427 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: D 453 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7283 (ttp-170) REVERT: D 463 MET cc_start: 0.8660 (mtm) cc_final: 0.8450 (mtm) REVERT: D 628 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6883 (tpp80) REVERT: D 697 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7388 (mmtm) REVERT: D 715 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.6143 (mtm180) outliers start: 51 outliers final: 23 residues processed: 156 average time/residue: 0.7636 time to fit residues: 125.0029 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 708 MET Chi-restraints excluded: chain A residue 736 THR 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 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 714 GLN 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 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 715 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** D 411 ASN 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 = 0.3776 r_free = 0.3776 target = 0.151178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124465 restraints weight = 10830.179| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.08 r_work: 0.3345 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8542 Z= 0.168 Angle : 0.569 8.816 11528 Z= 0.281 Chirality : 0.046 0.215 1284 Planarity : 0.004 0.044 1422 Dihedral : 8.736 92.888 1275 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.71 % Allowed : 26.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1044 helix: 0.85 (0.26), residues: 434 sheet: -0.60 (0.39), residues: 158 loop : -1.23 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 684 TYR 0.016 0.002 TYR D 673 PHE 0.012 0.002 PHE B 495 TRP 0.006 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8538) covalent geometry : angle 0.56919 (11520) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.58944 ( 8) hydrogen bonds : bond 0.03585 ( 344) hydrogen bonds : angle 4.39712 ( 1011) *********************** 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 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 119 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 393 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.4979 (pmtt) REVERT: A 419 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 486 GLU cc_start: 0.7595 (tp30) cc_final: 0.7221 (mm-30) REVERT: A 684 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7123 (mtp180) REVERT: B 407 MET cc_start: 0.7981 (mtm) cc_final: 0.7706 (mtm) REVERT: C 393 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4809 (pmmt) REVERT: C 751 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (mt) REVERT: D 427 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: D 628 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6887 (tpp80) REVERT: D 697 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7387 (mmtm) outliers start: 60 outliers final: 32 residues processed: 164 average time/residue: 0.7194 time to fit residues: 123.9691 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 684 ARG Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 736 THR 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 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 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 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 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 628 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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** D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123907 restraints weight = 10738.799| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.99 r_work: 0.3334 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8542 Z= 0.229 Angle : 0.633 9.960 11528 Z= 0.314 Chirality : 0.048 0.228 1284 Planarity : 0.005 0.044 1422 Dihedral : 8.916 99.005 1275 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.82 % Allowed : 26.73 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.25), residues: 1044 helix: 0.56 (0.25), residues: 434 sheet: -0.70 (0.39), residues: 158 loop : -1.36 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 684 TYR 0.019 0.002 TYR B 673 PHE 0.014 0.002 PHE B 495 TRP 0.006 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 8538) covalent geometry : angle 0.63295 (11520) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.81543 ( 8) hydrogen bonds : bond 0.04116 ( 344) hydrogen bonds : angle 4.56310 ( 1011) *********************** 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 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 393 LYS cc_start: 0.5864 (OUTLIER) cc_final: 0.4988 (pmtt) REVERT: A 486 GLU cc_start: 0.7653 (tp30) cc_final: 0.7353 (mm-30) REVERT: A 684 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7165 (mtp180) REVERT: A 708 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7520 (mtp) REVERT: B 407 MET cc_start: 0.7985 (mtm) cc_final: 0.7779 (mtm) REVERT: B 486 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: C 393 LYS cc_start: 0.5441 (OUTLIER) cc_final: 0.4838 (pmmt) REVERT: C 751 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8251 (mt) REVERT: C 761 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8159 (pttm) REVERT: D 463 MET cc_start: 0.8682 (mtm) cc_final: 0.8477 (mtm) REVERT: D 511 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6641 (mmtt) REVERT: D 628 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6880 (tpp80) outliers start: 61 outliers final: 33 residues processed: 167 average time/residue: 0.7104 time to fit residues: 124.8215 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 681 VAL 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 721 MET Chi-restraints excluded: chain A residue 736 THR 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 486 GLU 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 685 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 683 VAL 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 C residue 761 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127690 restraints weight = 10861.734| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.01 r_work: 0.3385 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.110 Angle : 0.506 7.940 11528 Z= 0.255 Chirality : 0.043 0.185 1284 Planarity : 0.004 0.045 1422 Dihedral : 7.758 88.118 1273 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.70 % Allowed : 28.86 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.25), residues: 1044 helix: 0.85 (0.26), residues: 438 sheet: -0.30 (0.43), residues: 112 loop : -1.40 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 684 TYR 0.011 0.001 TYR D 673 PHE 0.010 0.001 PHE D 495 TRP 0.007 0.001 TRP A 460 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8538) covalent geometry : angle 0.50659 (11520) SS BOND : bond 0.00303 ( 4) SS BOND : angle 0.32141 ( 8) hydrogen bonds : bond 0.03013 ( 344) hydrogen bonds : angle 4.32962 ( 1011) *********************** 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: 42 poor density : 129 time to evaluate : 0.352 Fit side-chains REVERT: A 419 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: A 486 GLU cc_start: 0.7456 (tp30) cc_final: 0.7108 (mm-30) REVERT: A 684 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: A 703 LEU cc_start: 0.8067 (mt) cc_final: 0.7848 (mt) REVERT: A 708 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7439 (mtp) REVERT: B 407 MET cc_start: 0.7945 (mtm) cc_final: 0.7623 (mtm) REVERT: B 511 LYS cc_start: 0.6245 (ptpt) cc_final: 0.5979 (mptt) REVERT: C 393 LYS cc_start: 0.5414 (OUTLIER) cc_final: 0.4755 (pmmt) REVERT: D 454 ASP cc_start: 0.5765 (t0) cc_final: 0.5332 (m-30) outliers start: 42 outliers final: 18 residues processed: 159 average time/residue: 0.7716 time to fit residues: 128.6260 Evaluate side-chains 139 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 684 ARG Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 773 CYS 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 720 THR Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 508 GLN 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 = 0.3804 r_free = 0.3804 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128216 restraints weight = 10732.532| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.99 r_work: 0.3380 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2045 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= 0.116 Angle : 0.517 7.787 11528 Z= 0.260 Chirality : 0.043 0.182 1284 Planarity : 0.004 0.048 1422 Dihedral : 7.396 85.314 1270 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.47 % Allowed : 30.20 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.25), residues: 1044 helix: 0.93 (0.26), residues: 436 sheet: -0.19 (0.38), residues: 150 loop : -1.42 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 684 TYR 0.013 0.001 TYR D 673 PHE 0.025 0.001 PHE A 438 TRP 0.007 0.001 TRP C 766 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8538) covalent geometry : angle 0.51709 (11520) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.26356 ( 8) hydrogen bonds : bond 0.02987 ( 344) hydrogen bonds : angle 4.28861 ( 1011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.346 Fit side-chains REVERT: A 419 GLU cc_start: 0.7575 (tp30) cc_final: 0.7262 (tt0) REVERT: A 486 GLU cc_start: 0.7474 (tp30) cc_final: 0.7122 (mm-30) REVERT: A 684 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7094 (mtp180) REVERT: A 703 LEU cc_start: 0.8096 (mt) cc_final: 0.7854 (mt) REVERT: A 708 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7466 (mtp) REVERT: C 393 LYS cc_start: 0.5254 (OUTLIER) cc_final: 0.4626 (pmmt) REVERT: C 715 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6092 (ttm110) REVERT: D 454 ASP cc_start: 0.5505 (t0) cc_final: 0.5175 (m-30) REVERT: D 463 MET cc_start: 0.8726 (mtm) cc_final: 0.8485 (mtm) REVERT: D 628 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6837 (tpp80) outliers start: 31 outliers final: 18 residues processed: 146 average time/residue: 0.7430 time to fit residues: 113.7548 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR 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 B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR 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 B residue 773 CYS 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 715 ARG Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 672 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 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 = 0.3794 r_free = 0.3794 target = 0.152841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126973 restraints weight = 10831.930| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.02 r_work: 0.3378 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8542 Z= 0.134 Angle : 0.544 8.051 11528 Z= 0.273 Chirality : 0.044 0.188 1284 Planarity : 0.004 0.051 1422 Dihedral : 7.413 82.689 1270 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.03 % Allowed : 29.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1044 helix: 0.87 (0.26), residues: 436 sheet: -0.23 (0.39), residues: 138 loop : -1.37 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 684 TYR 0.014 0.001 TYR D 673 PHE 0.011 0.001 PHE B 495 TRP 0.007 0.001 TRP C 766 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8538) covalent geometry : angle 0.54398 (11520) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.26183 ( 8) hydrogen bonds : bond 0.03159 ( 344) hydrogen bonds : angle 4.31469 ( 1011) *********************** 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 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.244 Fit side-chains REVERT: A 419 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 486 GLU cc_start: 0.7502 (tp30) cc_final: 0.7155 (mm-30) REVERT: A 661 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6372 (mtt90) REVERT: A 684 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7144 (mtp180) REVERT: A 708 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7451 (mtp) REVERT: B 511 LYS cc_start: 0.6317 (ptpt) cc_final: 0.5976 (mptt) REVERT: C 393 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4657 (pmmt) REVERT: C 421 TYR cc_start: 0.8315 (m-80) cc_final: 0.8114 (m-80) REVERT: C 719 ASP cc_start: 0.6587 (p0) cc_final: 0.6091 (p0) REVERT: D 454 ASP cc_start: 0.5541 (t0) cc_final: 0.5192 (m-30) REVERT: D 463 MET cc_start: 0.8716 (mtm) cc_final: 0.8482 (mtm) outliers start: 36 outliers final: 20 residues processed: 155 average time/residue: 0.6541 time to fit residues: 106.7004 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 684 ARG Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR 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 B residue 773 CYS 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 D residue 436 CYS 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 41 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.152035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126405 restraints weight = 10856.630| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.00 r_work: 0.3369 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2120 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= 0.144 Angle : 0.560 8.444 11528 Z= 0.280 Chirality : 0.044 0.195 1284 Planarity : 0.004 0.055 1422 Dihedral : 7.384 78.201 1270 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 30.65 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.25), residues: 1044 helix: 0.81 (0.26), residues: 436 sheet: -0.19 (0.38), residues: 150 loop : -1.45 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 684 TYR 0.015 0.001 TYR D 673 PHE 0.029 0.002 PHE A 438 TRP 0.006 0.001 TRP C 766 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8538) covalent geometry : angle 0.56038 (11520) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.27488 ( 8) hydrogen bonds : bond 0.03270 ( 344) hydrogen bonds : angle 4.33469 ( 1011) ********************** 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 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.368 Fit side-chains REVERT: A 419 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 486 GLU cc_start: 0.7522 (tp30) cc_final: 0.7164 (mm-30) REVERT: A 651 ASP cc_start: 0.6328 (t70) cc_final: 0.5447 (p0) REVERT: A 684 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7138 (mtp180) REVERT: A 708 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7441 (mtp) REVERT: B 511 LYS cc_start: 0.6338 (ptpt) cc_final: 0.5987 (mptt) REVERT: C 393 LYS cc_start: 0.5276 (OUTLIER) cc_final: 0.4637 (pmmt) REVERT: C 715 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6237 (ttm110) REVERT: C 719 ASP cc_start: 0.6602 (p0) cc_final: 0.6112 (p0) REVERT: C 751 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8239 (mt) REVERT: D 454 ASP cc_start: 0.5517 (t0) cc_final: 0.5155 (m-30) outliers start: 30 outliers final: 21 residues processed: 148 average time/residue: 0.7319 time to fit residues: 113.7532 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 B residue 445 VAL Chi-restraints excluded: chain B residue 625 THR 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 B residue 773 CYS 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 715 ARG Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 436 CYS 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 8 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.152024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126465 restraints weight = 10768.995| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.99 r_work: 0.3379 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8542 Z= 0.136 Angle : 0.554 8.276 11528 Z= 0.276 Chirality : 0.044 0.201 1284 Planarity : 0.004 0.054 1422 Dihedral : 6.968 62.537 1270 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.91 % Allowed : 30.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.25), residues: 1044 helix: 0.85 (0.26), residues: 436 sheet: -0.17 (0.38), residues: 150 loop : -1.45 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 684 TYR 0.022 0.001 TYR C 673 PHE 0.027 0.002 PHE A 438 TRP 0.006 0.001 TRP C 766 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8538) covalent geometry : angle 0.55418 (11520) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.38568 ( 8) hydrogen bonds : bond 0.03183 ( 344) hydrogen bonds : angle 4.32070 ( 1011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.77 seconds wall clock time: 55 minutes 34.24 seconds (3334.24 seconds total)