Starting phenix.real_space_refine on Sun May 11 21:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq6_29379/05_2025/8fq6_29379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq6_29379/05_2025/8fq6_29379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fq6_29379/05_2025/8fq6_29379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq6_29379/05_2025/8fq6_29379.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq6_29379/05_2025/8fq6_29379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq6_29379/05_2025/8fq6_29379.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 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8398 Number of models: 1 Model: "" Number of chains: 16 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: 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: 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: 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 6.01, per 1000 atoms: 0.72 Number of scatterers: 8398 At special positions: 0 Unit cell: (117.936, 87.633, 83.538, 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 1614 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 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 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 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: 2.01 Conformation dependent library (CDL) restraints added in 949.2 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 41.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.717A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.597A 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: 3.867A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.682A 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 416 through 419 removed outlier: 3.891A 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 463 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.666A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.917A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.847A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.549A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.504A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.531A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.750A 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 757 through 768 removed outlier: 3.526A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.874A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.708A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.926A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'B' and resid 440 through 444 removed outlier: 7.067A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 440 through 444 removed outlier: 7.067A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.493A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.602A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AA7, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.101A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.616A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 440 through 444 removed outlier: 7.113A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.889A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.639A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.603A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB9, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AC1, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.167A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.607A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 942 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: 2.26 Time building geometry restraints manager: 2.34 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: 2042 1.48 - 1.60: 3722 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: 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 C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 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=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CYZ B1302 " pdb=" C6 CYZ B1302 " ideal model delta sigma weight residual 1.553 1.331 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11314 1.93 - 3.85: 133 3.85 - 5.78: 32 5.78 - 7.70: 26 7.70 - 9.63: 15 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.38 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.32 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.26 -9.51 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.22 -9.47 3.00e+00 1.11e-01 9.97e+00 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 109.28 9.07 3.00e+00 1.11e-01 9.15e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 4701 22.94 - 45.88: 454 45.88 - 68.82: 64 68.82 - 91.76: 17 91.76 - 114.70: 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 -174.74 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 177.54 -84.54 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 176.87 -83.87 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1182 0.086 - 0.172: 86 0.172 - 0.258: 0 0.258 - 0.345: 0 0.345 - 0.431: 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 4.64e+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 4.57e+00 chirality pdb=" C2 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" C3 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO C 737 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 477 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO C 478 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO C 494 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " 0.020 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2266 2.80 - 3.33: 7467 3.33 - 3.85: 14006 3.85 - 4.38: 16485 4.38 - 4.90: 28460 Nonbonded interactions: 68684 Sorted by model distance: nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.275 3.040 nonbonded pdb=" O PHE B 495 " pdb=" O HOH B1401 " model vdw 2.309 3.040 nonbonded pdb=" O PHE D 495 " pdb=" O HOH D1402 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.327 3.040 ... (remaining 68679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.730 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 8542 Z= 0.725 Angle : 0.701 9.626 11528 Z= 0.300 Chirality : 0.061 0.431 1284 Planarity : 0.003 0.044 1422 Dihedral : 18.124 114.699 3288 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 22.04 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1044 helix: 1.02 (0.26), residues: 428 sheet: -1.04 (0.38), residues: 168 loop : -1.44 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.001 0.000 HIS C 412 PHE 0.008 0.001 PHE C 495 TYR 0.009 0.001 TYR D 405 ARG 0.004 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.15993 ( 321) hydrogen bonds : angle 6.40832 ( 942) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.36450 ( 8) covalent geometry : bond 0.01453 ( 8538) covalent geometry : angle 0.70145 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.953 Fit side-chains REVERT: B 697 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8010 (pttm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2738 time to fit residues: 47.1668 Evaluate side-chains 132 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116498 restraints weight = 10358.472| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.09 r_work: 0.3208 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8542 Z= 0.212 Angle : 0.587 9.629 11528 Z= 0.291 Chirality : 0.047 0.175 1284 Planarity : 0.004 0.039 1422 Dihedral : 11.225 103.032 1266 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.13 % Allowed : 19.80 % Favored : 77.07 % 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: -0.76 (0.25), residues: 1044 helix: 0.76 (0.26), residues: 432 sheet: -0.99 (0.40), residues: 142 loop : -1.54 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.003 0.001 HIS C 435 PHE 0.015 0.002 PHE A 495 TYR 0.012 0.002 TYR A 673 ARG 0.004 0.001 ARG B 692 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 321) hydrogen bonds : angle 4.96646 ( 942) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.71057 ( 8) covalent geometry : bond 0.00525 ( 8538) covalent geometry : angle 0.58656 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.038 Fit side-chains REVERT: B 438 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.5349 (p90) REVERT: C 454 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5587 (t70) REVERT: C 661 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7720 (mmt180) REVERT: D 438 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5488 (p90) REVERT: A 440 TYR cc_start: 0.8626 (p90) cc_final: 0.8402 (p90) REVERT: A 454 ASP cc_start: 0.6139 (OUTLIER) cc_final: 0.5754 (t70) REVERT: A 486 GLU cc_start: 0.8469 (tp30) cc_final: 0.8023 (tp30) outliers start: 28 outliers final: 12 residues processed: 155 average time/residue: 0.2738 time to fit residues: 54.1525 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 758 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.0770 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.150817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125892 restraints weight = 10430.892| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.00 r_work: 0.3231 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.104 Angle : 0.484 7.159 11528 Z= 0.240 Chirality : 0.042 0.143 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.596 97.882 1266 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.80 % Allowed : 19.91 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1044 helix: 1.06 (0.26), residues: 434 sheet: -0.85 (0.38), residues: 152 loop : -1.52 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 PHE 0.009 0.001 PHE D 495 TYR 0.010 0.001 TYR A 673 ARG 0.002 0.000 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 321) hydrogen bonds : angle 4.59100 ( 942) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.34030 ( 8) covalent geometry : bond 0.00246 ( 8538) covalent geometry : angle 0.48406 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.981 Fit side-chains REVERT: B 697 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8229 (pttm) REVERT: C 661 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7630 (mmt180) outliers start: 25 outliers final: 12 residues processed: 157 average time/residue: 0.2743 time to fit residues: 55.3823 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 0.0020 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 0.0010 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119027 restraints weight = 10403.766| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.02 r_work: 0.3190 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8542 Z= 0.174 Angle : 0.544 7.005 11528 Z= 0.268 Chirality : 0.045 0.162 1284 Planarity : 0.004 0.046 1422 Dihedral : 10.821 101.670 1266 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.58 % Allowed : 20.36 % Favored : 76.06 % 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: -0.61 (0.25), residues: 1044 helix: 0.95 (0.26), residues: 432 sheet: -0.75 (0.41), residues: 124 loop : -1.59 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.002 0.001 HIS B 412 PHE 0.013 0.002 PHE A 495 TYR 0.012 0.001 TYR A 673 ARG 0.003 0.000 ARG B 692 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 321) hydrogen bonds : angle 4.67153 ( 942) SS BOND : bond 0.00191 ( 4) SS BOND : angle 0.80472 ( 8) covalent geometry : bond 0.00432 ( 8538) covalent geometry : angle 0.54348 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.020 Fit side-chains REVERT: C 454 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5524 (t70) REVERT: C 661 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7699 (mmt180) REVERT: C 708 MET cc_start: 0.8354 (mtt) cc_final: 0.8119 (mtt) REVERT: D 438 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.5375 (p90) REVERT: D 705 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: A 454 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5699 (t70) REVERT: A 708 MET cc_start: 0.8343 (mtt) cc_final: 0.8104 (mtt) outliers start: 32 outliers final: 18 residues processed: 163 average time/residue: 0.2624 time to fit residues: 54.9627 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP 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 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 454 ASP 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 758 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119722 restraints weight = 10316.652| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.01 r_work: 0.3165 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8542 Z= 0.127 Angle : 0.506 6.371 11528 Z= 0.248 Chirality : 0.043 0.147 1284 Planarity : 0.004 0.046 1422 Dihedral : 10.444 98.843 1266 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.24 % Allowed : 21.14 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1044 helix: 1.00 (0.26), residues: 436 sheet: -0.73 (0.41), residues: 124 loop : -1.55 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.001 0.001 HIS B 412 PHE 0.010 0.001 PHE A 495 TYR 0.011 0.001 TYR A 673 ARG 0.003 0.000 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 321) hydrogen bonds : angle 4.54223 ( 942) SS BOND : bond 0.00166 ( 4) SS BOND : angle 0.59246 ( 8) covalent geometry : bond 0.00310 ( 8538) covalent geometry : angle 0.50556 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.033 Fit side-chains REVERT: B 697 LYS cc_start: 0.8486 (ptpp) cc_final: 0.8254 (pttm) REVERT: C 454 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5433 (t70) REVERT: C 661 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7712 (mmt180) REVERT: C 708 MET cc_start: 0.8319 (mtt) cc_final: 0.7901 (mtt) REVERT: A 454 ASP cc_start: 0.6091 (OUTLIER) cc_final: 0.5673 (t70) REVERT: A 708 MET cc_start: 0.8310 (mtt) cc_final: 0.7966 (mtt) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 0.2749 time to fit residues: 57.1252 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 454 ASP 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 758 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114848 restraints weight = 10482.882| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.07 r_work: 0.3237 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8542 Z= 0.155 Angle : 0.536 7.201 11528 Z= 0.261 Chirality : 0.044 0.189 1284 Planarity : 0.004 0.046 1422 Dihedral : 10.267 100.236 1266 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.58 % Allowed : 21.14 % Favored : 75.28 % 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: 1.00 (0.26), residues: 432 sheet: -0.79 (0.41), residues: 124 loop : -1.55 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS A 435 PHE 0.013 0.002 PHE A 495 TYR 0.011 0.001 TYR A 673 ARG 0.003 0.000 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 321) hydrogen bonds : angle 4.57006 ( 942) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.64495 ( 8) covalent geometry : bond 0.00384 ( 8538) covalent geometry : angle 0.53590 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.033 Fit side-chains REVERT: C 454 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5845 (t70) REVERT: C 661 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7746 (mmt180) REVERT: C 708 MET cc_start: 0.8339 (mtt) cc_final: 0.8009 (mtt) REVERT: D 438 PHE cc_start: 0.5795 (OUTLIER) cc_final: 0.5314 (p90) REVERT: D 705 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: A 454 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5640 (t70) outliers start: 32 outliers final: 21 residues processed: 160 average time/residue: 0.2687 time to fit residues: 55.0689 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 454 ASP 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 758 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117194 restraints weight = 10472.889| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.08 r_work: 0.3256 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8542 Z= 0.108 Angle : 0.490 7.220 11528 Z= 0.240 Chirality : 0.043 0.216 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.145 95.991 1266 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.02 % Allowed : 21.70 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1044 helix: 1.15 (0.26), residues: 434 sheet: -0.72 (0.41), residues: 124 loop : -1.51 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 PHE 0.009 0.001 PHE A 495 TYR 0.009 0.001 TYR A 673 ARG 0.003 0.000 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 321) hydrogen bonds : angle 4.41978 ( 942) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.44130 ( 8) covalent geometry : bond 0.00260 ( 8538) covalent geometry : angle 0.49007 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.929 Fit side-chains REVERT: C 454 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5572 (t70) REVERT: C 459 ILE cc_start: 0.6634 (mm) cc_final: 0.6424 (mm) REVERT: C 661 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7695 (mmt180) REVERT: C 708 MET cc_start: 0.8312 (mtt) cc_final: 0.8000 (mtt) outliers start: 27 outliers final: 21 residues processed: 167 average time/residue: 0.2649 time to fit residues: 56.7916 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 736 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 758 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114375 restraints weight = 10543.598| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.09 r_work: 0.3222 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8542 Z= 0.174 Angle : 0.544 8.301 11528 Z= 0.267 Chirality : 0.045 0.192 1284 Planarity : 0.004 0.045 1422 Dihedral : 9.198 101.027 1266 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.80 % Allowed : 21.25 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1044 helix: 0.99 (0.26), residues: 432 sheet: -1.13 (0.38), residues: 144 loop : -1.48 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS A 435 PHE 0.014 0.002 PHE A 495 TYR 0.011 0.001 TYR A 673 ARG 0.003 0.000 ARG B 692 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 321) hydrogen bonds : angle 4.58561 ( 942) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.77575 ( 8) covalent geometry : bond 0.00431 ( 8538) covalent geometry : angle 0.54340 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.064 Fit side-chains REVERT: C 454 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5562 (t70) REVERT: C 459 ILE cc_start: 0.6564 (mm) cc_final: 0.6356 (mm) REVERT: C 661 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7725 (mmt180) REVERT: C 708 MET cc_start: 0.8363 (mtt) cc_final: 0.8018 (mtt) REVERT: C 715 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6704 (mtp85) REVERT: D 438 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5221 (p90) REVERT: D 466 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8151 (pp20) REVERT: A 454 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5815 (t70) REVERT: A 708 MET cc_start: 0.8368 (mtt) cc_final: 0.8126 (mtt) outliers start: 34 outliers final: 24 residues processed: 160 average time/residue: 0.2892 time to fit residues: 58.7527 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 454 ASP 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 758 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 76 optimal weight: 0.0670 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117832 restraints weight = 10506.368| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.10 r_work: 0.3270 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8542 Z= 0.099 Angle : 0.476 8.413 11528 Z= 0.236 Chirality : 0.042 0.134 1284 Planarity : 0.004 0.045 1422 Dihedral : 8.517 94.355 1266 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 22.37 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1044 helix: 1.14 (0.26), residues: 434 sheet: -0.81 (0.42), residues: 124 loop : -1.50 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 766 HIS 0.002 0.000 HIS B 412 PHE 0.009 0.001 PHE B 495 TYR 0.008 0.001 TYR B 405 ARG 0.002 0.000 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 321) hydrogen bonds : angle 4.41308 ( 942) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.43789 ( 8) covalent geometry : bond 0.00234 ( 8538) covalent geometry : angle 0.47648 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.969 Fit side-chains REVERT: C 454 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5826 (t70) REVERT: C 459 ILE cc_start: 0.6658 (mm) cc_final: 0.6429 (mm) REVERT: C 661 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7691 (mmt180) REVERT: C 708 MET cc_start: 0.8286 (mtt) cc_final: 0.7881 (mtt) REVERT: C 715 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6523 (mtp85) REVERT: A 668 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6048 (m-30) outliers start: 23 outliers final: 17 residues processed: 155 average time/residue: 0.2780 time to fit residues: 54.7666 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.0370 chunk 3 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121093 restraints weight = 10316.784| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.07 r_work: 0.3189 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8542 Z= 0.090 Angle : 0.465 8.691 11528 Z= 0.229 Chirality : 0.041 0.135 1284 Planarity : 0.004 0.043 1422 Dihedral : 7.906 88.692 1266 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.13 % Allowed : 23.04 % Favored : 74.83 % 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: -0.31 (0.26), residues: 1044 helix: 1.27 (0.26), residues: 434 sheet: -0.73 (0.42), residues: 124 loop : -1.46 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 766 HIS 0.001 0.000 HIS C 435 PHE 0.007 0.001 PHE B 495 TYR 0.007 0.001 TYR B 405 ARG 0.002 0.000 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 321) hydrogen bonds : angle 4.28563 ( 942) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.40990 ( 8) covalent geometry : bond 0.00214 ( 8538) covalent geometry : angle 0.46553 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.911 Fit side-chains REVERT: C 454 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5647 (t0) REVERT: C 459 ILE cc_start: 0.6566 (mm) cc_final: 0.6338 (mm) REVERT: C 661 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7659 (mmt180) REVERT: C 715 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6498 (mtp85) REVERT: D 454 ASP cc_start: 0.7274 (p0) cc_final: 0.6835 (m-30) REVERT: A 668 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6197 (m-30) outliers start: 19 outliers final: 15 residues processed: 161 average time/residue: 0.2685 time to fit residues: 55.4128 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118604 restraints weight = 10496.302| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8542 Z= 0.118 Angle : 0.498 8.854 11528 Z= 0.245 Chirality : 0.043 0.136 1284 Planarity : 0.004 0.041 1422 Dihedral : 8.160 90.061 1266 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.80 % Allowed : 22.15 % Favored : 75.06 % 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: -0.38 (0.26), residues: 1044 helix: 1.21 (0.26), residues: 434 sheet: -0.77 (0.42), residues: 124 loop : -1.48 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 766 HIS 0.001 0.001 HIS B 412 PHE 0.009 0.001 PHE B 495 TYR 0.008 0.001 TYR C 440 ARG 0.003 0.000 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 321) hydrogen bonds : angle 4.36369 ( 942) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.51999 ( 8) covalent geometry : bond 0.00289 ( 8538) covalent geometry : angle 0.49749 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4622.15 seconds wall clock time: 81 minutes 16.63 seconds (4876.63 seconds total)