Starting phenix.real_space_refine on Fri Nov 15 06:19:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fph_29364/11_2024/8fph_29364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fph_29364/11_2024/8fph_29364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fph_29364/11_2024/8fph_29364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fph_29364/11_2024/8fph_29364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fph_29364/11_2024/8fph_29364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fph_29364/11_2024/8fph_29364.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.30, per 1000 atoms: 0.75 Number of scatterers: 8388 At special positions: 0 Unit cell: (117.189, 88.506, 84.4085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1604 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 43.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.570A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.005A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.590A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.733A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.929A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.994A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.595A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.592A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.653A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.548A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.573A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.814A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.633A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.507A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.603A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.834A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.628A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.006A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.624A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.386A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.498A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.498A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.522A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.487A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.004A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.661A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.506A pdb=" N LYS D 441 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.296A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.576A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2043 1.48 - 1.60: 3721 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11293 1.95 - 3.89: 152 3.89 - 5.84: 37 5.84 - 7.79: 24 7.79 - 9.74: 14 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.49 -9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.43 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 110.98 -9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 110.98 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.32 9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 4736 22.71 - 45.42: 415 45.42 - 68.12: 72 68.12 - 90.83: 13 90.83 - 113.54: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual -86.00 -149.05 63.05 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual -86.00 -28.29 -57.71 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" N2 CYZ B1302 " pdb=" C8 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" S1 CYZ B1302 " ideal model delta sinusoidal sigma weight residual 55.73 -57.81 113.54 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1175 0.086 - 0.172: 93 0.172 - 0.258: 0 0.258 - 0.344: 0 0.344 - 0.429: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 737 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 494 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 494 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.023 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1349 2.76 - 3.30: 7681 3.30 - 3.83: 13772 3.83 - 4.37: 16252 4.37 - 4.90: 28491 Nonbonded interactions: 67545 Sorted by model distance: nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 654 " pdb=" O HOH B1401 " model vdw 2.245 3.040 nonbonded pdb=" O LEU D 639 " pdb=" NE2 GLN D 642 " model vdw 2.270 3.120 nonbonded pdb=" NH1 ARG D 715 " pdb=" O TRP D 767 " model vdw 2.318 3.120 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.323 3.040 ... (remaining 67540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.243 8538 Z= 1.034 Angle : 0.722 9.736 11520 Z= 0.313 Chirality : 0.062 0.429 1284 Planarity : 0.004 0.048 1422 Dihedral : 17.886 113.541 3288 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.11 % Allowed : 24.38 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1044 helix: 0.52 (0.26), residues: 416 sheet: -1.04 (0.38), residues: 172 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.005 0.001 HIS D 412 PHE 0.010 0.001 PHE D 495 TYR 0.010 0.001 TYR D 405 ARG 0.007 0.000 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.981 Fit side-chains REVERT: A 684 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7516 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2822 time to fit residues: 50.3623 Evaluate side-chains 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8538 Z= 0.169 Angle : 0.499 6.975 11520 Z= 0.248 Chirality : 0.043 0.138 1284 Planarity : 0.004 0.039 1422 Dihedral : 10.095 93.638 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.46 % Allowed : 21.81 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1044 helix: 0.63 (0.25), residues: 436 sheet: -0.98 (0.39), residues: 156 loop : -1.38 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.017 0.001 PHE D 438 TYR 0.009 0.001 TYR D 405 ARG 0.004 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.942 Fit side-chains REVERT: D 402 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7386 (mm-30) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.2626 time to fit residues: 54.8816 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8538 Z= 0.214 Angle : 0.532 7.590 11520 Z= 0.261 Chirality : 0.045 0.172 1284 Planarity : 0.004 0.037 1422 Dihedral : 9.481 92.242 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.58 % Allowed : 22.82 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1044 helix: 0.83 (0.25), residues: 428 sheet: -1.06 (0.38), residues: 156 loop : -1.44 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.005 0.002 HIS B 412 PHE 0.010 0.001 PHE A 495 TYR 0.018 0.001 TYR C 450 ARG 0.003 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.950 Fit side-chains REVERT: A 760 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: C 408 MET cc_start: 0.8144 (tpp) cc_final: 0.7817 (tpp) REVERT: D 402 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7432 (mm-30) outliers start: 32 outliers final: 23 residues processed: 154 average time/residue: 0.2656 time to fit residues: 53.0918 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.0050 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8538 Z= 0.181 Angle : 0.503 7.409 11520 Z= 0.246 Chirality : 0.044 0.215 1284 Planarity : 0.003 0.035 1422 Dihedral : 8.268 88.437 1266 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.59 % Allowed : 21.92 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1044 helix: 0.98 (0.25), residues: 428 sheet: -1.06 (0.38), residues: 156 loop : -1.46 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.008 0.001 TYR B 673 ARG 0.006 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.974 Fit side-chains REVERT: A 684 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7518 (mtm180) REVERT: A 760 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: C 408 MET cc_start: 0.8105 (tpp) cc_final: 0.7797 (tpp) REVERT: D 402 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7420 (mm-30) REVERT: D 422 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7733 (pt0) outliers start: 41 outliers final: 22 residues processed: 168 average time/residue: 0.2599 time to fit residues: 56.6424 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8538 Z= 0.318 Angle : 0.586 8.575 11520 Z= 0.293 Chirality : 0.047 0.229 1284 Planarity : 0.004 0.037 1422 Dihedral : 8.129 96.873 1266 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.26 % Allowed : 22.48 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1044 helix: 0.73 (0.25), residues: 426 sheet: -1.46 (0.35), residues: 176 loop : -1.60 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.015 0.002 PHE A 495 TYR 0.012 0.002 TYR D 405 ARG 0.004 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.967 Fit side-chains REVERT: A 760 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: B 466 GLU cc_start: 0.8178 (pp20) cc_final: 0.7766 (pt0) REVERT: B 634 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7236 (mt-10) REVERT: D 402 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7517 (mm-30) outliers start: 47 outliers final: 33 residues processed: 174 average time/residue: 0.2739 time to fit residues: 61.2076 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 439 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8538 Z= 0.145 Angle : 0.479 6.801 11520 Z= 0.239 Chirality : 0.043 0.196 1284 Planarity : 0.003 0.037 1422 Dihedral : 7.248 90.053 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.03 % Allowed : 23.49 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1044 helix: 1.06 (0.25), residues: 426 sheet: -1.16 (0.35), residues: 182 loop : -1.45 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.007 0.001 TYR B 673 ARG 0.001 0.000 ARG D 660 *********************** 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 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.998 Fit side-chains REVERT: A 695 LYS cc_start: 0.7550 (tppt) cc_final: 0.7224 (tptt) REVERT: A 760 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: D 402 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7494 (mm-30) REVERT: D 405 TYR cc_start: 0.8505 (m-80) cc_final: 0.8168 (m-80) REVERT: D 422 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: D 675 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7730 (ttm-80) REVERT: D 761 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7881 (tmmt) outliers start: 36 outliers final: 22 residues processed: 158 average time/residue: 0.2612 time to fit residues: 53.8694 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 678 GLU Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 57 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8538 Z= 0.141 Angle : 0.470 6.452 11520 Z= 0.235 Chirality : 0.043 0.147 1284 Planarity : 0.003 0.036 1422 Dihedral : 6.543 79.307 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.36 % Allowed : 23.38 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1044 helix: 1.20 (0.26), residues: 428 sheet: -1.09 (0.35), residues: 182 loop : -1.35 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.008 0.001 PHE D 495 TYR 0.011 0.001 TYR C 450 ARG 0.001 0.000 ARG D 660 *********************** 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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.026 Fit side-chains REVERT: A 695 LYS cc_start: 0.7609 (tppt) cc_final: 0.7275 (tptt) REVERT: A 760 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: D 402 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7478 (mm-30) REVERT: D 408 MET cc_start: 0.7340 (mmt) cc_final: 0.6982 (mmt) REVERT: D 414 MET cc_start: 0.5773 (ppp) cc_final: 0.5136 (ppp) REVERT: D 642 GLN cc_start: 0.7404 (pp30) cc_final: 0.7131 (pp30) REVERT: D 660 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8269 (ttm110) REVERT: D 761 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7868 (tmmt) outliers start: 30 outliers final: 21 residues processed: 152 average time/residue: 0.2547 time to fit residues: 50.2875 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 678 GLU Chi-restraints excluded: chain D residue 684 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8538 Z= 0.367 Angle : 0.614 8.761 11520 Z= 0.308 Chirality : 0.049 0.187 1284 Planarity : 0.004 0.038 1422 Dihedral : 7.249 85.502 1266 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.59 % Allowed : 22.82 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1044 helix: 0.73 (0.25), residues: 426 sheet: -1.63 (0.35), residues: 176 loop : -1.62 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 460 HIS 0.004 0.001 HIS D 412 PHE 0.014 0.002 PHE A 495 TYR 0.013 0.002 TYR D 405 ARG 0.003 0.001 ARG A 692 *********************** 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 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 760 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 634 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 402 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7635 (mm-30) REVERT: D 408 MET cc_start: 0.7548 (mmt) cc_final: 0.7272 (mmt) REVERT: D 684 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6549 (tpm170) REVERT: D 761 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7893 (tmmt) outliers start: 41 outliers final: 30 residues processed: 156 average time/residue: 0.2772 time to fit residues: 55.1006 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8538 Z= 0.174 Angle : 0.504 7.074 11520 Z= 0.252 Chirality : 0.044 0.144 1284 Planarity : 0.003 0.037 1422 Dihedral : 6.754 78.699 1266 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.91 % Allowed : 24.27 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1044 helix: 1.01 (0.25), residues: 426 sheet: -1.49 (0.36), residues: 156 loop : -1.47 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.009 0.001 PHE D 495 TYR 0.010 0.001 TYR A 450 ARG 0.003 0.000 ARG A 692 *********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 695 LYS cc_start: 0.7585 (tppt) cc_final: 0.7221 (tptt) REVERT: A 760 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: B 422 GLU cc_start: 0.7711 (pt0) cc_final: 0.7479 (pt0) REVERT: C 408 MET cc_start: 0.8146 (tpp) cc_final: 0.7812 (tpp) REVERT: C 486 GLU cc_start: 0.7470 (tp30) cc_final: 0.7181 (tp30) REVERT: D 402 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7528 (mm-30) REVERT: D 408 MET cc_start: 0.7320 (mmt) cc_final: 0.7011 (mmt) REVERT: D 414 MET cc_start: 0.5739 (ppp) cc_final: 0.5230 (ppp) REVERT: D 684 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6518 (tpm170) REVERT: D 761 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7885 (tmmt) outliers start: 26 outliers final: 21 residues processed: 152 average time/residue: 0.2644 time to fit residues: 51.8455 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8538 Z= 0.375 Angle : 0.623 8.515 11520 Z= 0.312 Chirality : 0.049 0.189 1284 Planarity : 0.004 0.040 1422 Dihedral : 7.149 82.108 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.58 % Allowed : 23.83 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1044 helix: 0.68 (0.25), residues: 424 sheet: -1.68 (0.35), residues: 174 loop : -1.68 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 460 HIS 0.005 0.002 HIS D 412 PHE 0.016 0.002 PHE C 495 TYR 0.019 0.002 TYR C 647 ARG 0.003 0.001 ARG A 692 ********************** 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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: B 422 GLU cc_start: 0.7681 (pt0) cc_final: 0.7412 (pt0) REVERT: B 634 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7115 (mt-10) REVERT: C 408 MET cc_start: 0.8287 (tpp) cc_final: 0.7987 (tpp) REVERT: C 486 GLU cc_start: 0.7619 (tp30) cc_final: 0.7317 (tp30) REVERT: D 402 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 642 GLN cc_start: 0.7436 (pp30) cc_final: 0.6994 (pp30) REVERT: D 684 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6628 (tpm170) REVERT: D 761 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7902 (tmmt) outliers start: 32 outliers final: 27 residues processed: 157 average time/residue: 0.2744 time to fit residues: 55.0857 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 416 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 441 LYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136729 restraints weight = 10292.334| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.03 r_work: 0.3440 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8538 Z= 0.191 Angle : 0.522 7.209 11520 Z= 0.261 Chirality : 0.044 0.165 1284 Planarity : 0.004 0.038 1422 Dihedral : 6.679 74.285 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.13 % Allowed : 24.72 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1044 helix: 0.94 (0.25), residues: 424 sheet: -1.52 (0.36), residues: 154 loop : -1.56 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.004 0.001 HIS D 412 PHE 0.010 0.001 PHE D 495 TYR 0.013 0.001 TYR C 647 ARG 0.003 0.000 ARG C 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.98 seconds wall clock time: 40 minutes 55.69 seconds (2455.69 seconds total)