Starting phenix.real_space_refine on Sat Jun 7 03:31:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpv_29370/06_2025/8fpv_29370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpv_29370/06_2025/8fpv_29370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpv_29370/06_2025/8fpv_29370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpv_29370/06_2025/8fpv_29370.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpv_29370/06_2025/8fpv_29370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpv_29370/06_2025/8fpv_29370.cif" } resolution = 3.08 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 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8394 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.28, per 1000 atoms: 0.75 Number of scatterers: 8394 At special positions: 0 Unit cell: (123, 94.3, 83.64, 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 1610 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 916.6 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 19 sheets defined 43.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.738A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.532A 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: 4.088A 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 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.502A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 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: 3.675A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 654 through 662 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 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.962A 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: 3.671A 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: 3.540A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.629A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.558A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.235A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (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: 3.982A 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: 6.490A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 500 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 725 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.627A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) 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 489 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.944A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.646A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.449A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.935A 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: 6.355A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.297A 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: 3.544A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 removed outlier: 3.544A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.471A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 509 through 510 removed outlier: 3.596A pdb=" N ARG D 628 " --> pdb=" O SER D 510 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1005 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: 2.33 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2630 1.35 - 1.48: 2038 1.48 - 1.60: 3726 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.329 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11317 1.95 - 3.90: 129 3.90 - 5.85: 31 5.85 - 7.80: 30 7.80 - 9.76: 13 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C GLU C 634 " pdb=" CA GLU C 634 " pdb=" CB GLU C 634 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" CA GLU C 634 " pdb=" C GLU C 634 " pdb=" N SER C 635 " ideal model delta sigma weight residual 119.63 116.66 2.97 8.10e-01 1.52e+00 1.34e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 122.46 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.30 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 108.97 9.38 3.00e+00 1.11e-01 9.78e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 4763 23.14 - 46.28: 404 46.28 - 69.43: 55 69.43 - 92.57: 15 92.57 - 115.71: 11 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 93.00 -178.44 -88.56 1 1.00e+01 1.00e-02 9.36e+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 93.00 176.77 -83.77 1 1.00e+01 1.00e-02 8.56e+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 -86.00 -167.00 81.00 1 1.00e+01 1.00e-02 8.10e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1176 0.086 - 0.171: 90 0.171 - 0.257: 2 0.257 - 0.342: 0 0.342 - 0.428: 16 Chirality restraints: 1284 Sorted by residual: 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=" C8 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" N2 CYZ D1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.57e+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 2.88 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 493 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 494 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 494 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 494 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 625 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C THR B 625 " 0.025 2.00e-02 2.50e+03 pdb=" O THR B 625 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 626 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 477 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 478 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.018 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1895 2.78 - 3.31: 7602 3.31 - 3.84: 14232 3.84 - 4.37: 16638 4.37 - 4.90: 29221 Nonbonded interactions: 69588 Sorted by model distance: nonbonded pdb=" OH TYR D 424 " pdb=" O HOH D1401 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 424 " pdb=" O HOH B1401 " model vdw 2.270 3.040 nonbonded pdb=" NZ LYS A 409 " pdb=" O GLU A 419 " model vdw 2.282 3.120 ... (remaining 69583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.290 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.717 9.755 11528 Z= 0.314 Chirality : 0.062 0.428 1284 Planarity : 0.003 0.043 1422 Dihedral : 17.490 115.711 3288 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.22 % Allowed : 18.90 % Favored : 80.87 % 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: -0.33 (0.25), residues: 1044 helix: 0.85 (0.25), residues: 422 sheet: -0.53 (0.39), residues: 174 loop : -1.07 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.012 0.001 PHE B 658 TYR 0.010 0.001 TYR A 450 ARG 0.002 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.17241 ( 340) hydrogen bonds : angle 6.74042 ( 1005) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.70991 ( 8) covalent geometry : bond 0.01455 ( 8538) covalent geometry : angle 0.71691 (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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.886 Fit side-chains REVERT: A 718 CYS cc_start: 0.7138 (m) cc_final: 0.6813 (m) REVERT: C 673 TYR cc_start: 0.7954 (t80) cc_final: 0.7296 (t80) REVERT: D 453 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6826 (ttm110) outliers start: 2 outliers final: 2 residues processed: 150 average time/residue: 0.2512 time to fit residues: 48.9411 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU 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: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.0570 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128242 restraints weight = 10478.864| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.86 r_work: 0.3349 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8542 Z= 0.097 Angle : 0.485 7.408 11528 Z= 0.244 Chirality : 0.042 0.163 1284 Planarity : 0.004 0.035 1422 Dihedral : 10.590 95.313 1270 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.12 % Allowed : 17.34 % Favored : 81.54 % 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: -0.08 (0.26), residues: 1044 helix: 1.16 (0.26), residues: 424 sheet: -0.42 (0.39), residues: 172 loop : -1.05 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.008 0.001 PHE B 495 TYR 0.009 0.001 TYR D 673 ARG 0.003 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 340) hydrogen bonds : angle 4.99073 ( 1005) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.57741 ( 8) covalent geometry : bond 0.00224 ( 8538) covalent geometry : angle 0.48458 (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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.956 Fit side-chains REVERT: A 718 CYS cc_start: 0.7429 (m) cc_final: 0.7149 (m) REVERT: B 436 CYS cc_start: 0.6382 (p) cc_final: 0.5394 (t) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.2435 time to fit residues: 50.9043 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127476 restraints weight = 10619.471| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.97 r_work: 0.3339 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8542 Z= 0.087 Angle : 0.473 7.732 11528 Z= 0.234 Chirality : 0.042 0.165 1284 Planarity : 0.003 0.032 1422 Dihedral : 9.828 93.383 1266 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.24 % Allowed : 17.34 % Favored : 80.43 % 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: 0.04 (0.26), residues: 1044 helix: 1.29 (0.26), residues: 424 sheet: -0.26 (0.39), residues: 172 loop : -1.06 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 460 HIS 0.002 0.000 HIS C 412 PHE 0.010 0.001 PHE D 438 TYR 0.007 0.001 TYR D 673 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02554 ( 340) hydrogen bonds : angle 4.72741 ( 1005) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.66901 ( 8) covalent geometry : bond 0.00198 ( 8538) covalent geometry : angle 0.47281 (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 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.898 Fit side-chains REVERT: A 673 TYR cc_start: 0.7857 (t80) cc_final: 0.7176 (t80) REVERT: A 718 CYS cc_start: 0.7525 (m) cc_final: 0.7268 (m) REVERT: B 642 GLN cc_start: 0.8341 (pp30) cc_final: 0.8132 (pp30) REVERT: C 673 TYR cc_start: 0.7770 (t80) cc_final: 0.7097 (t80) REVERT: D 453 ARG cc_start: 0.7055 (ttm110) cc_final: 0.6628 (ttm110) REVERT: D 715 ARG cc_start: 0.7141 (mmm-85) cc_final: 0.6817 (mmm-85) outliers start: 20 outliers final: 11 residues processed: 164 average time/residue: 0.2421 time to fit residues: 51.9954 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 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 747 ASN B 756 GLN D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119041 restraints weight = 10620.384| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.00 r_work: 0.3220 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8542 Z= 0.205 Angle : 0.606 11.996 11528 Z= 0.300 Chirality : 0.047 0.180 1284 Planarity : 0.004 0.038 1422 Dihedral : 11.683 111.185 1266 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.24 % Allowed : 17.45 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1044 helix: 0.91 (0.26), residues: 424 sheet: -1.00 (0.38), residues: 154 loop : -1.14 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 PHE 0.014 0.002 PHE B 659 TYR 0.013 0.002 TYR D 673 ARG 0.004 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 340) hydrogen bonds : angle 4.86860 ( 1005) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.92847 ( 8) covalent geometry : bond 0.00498 ( 8538) covalent geometry : angle 0.60580 (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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.932 Fit side-chains REVERT: D 651 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6794 (m-30) outliers start: 29 outliers final: 19 residues processed: 156 average time/residue: 0.2875 time to fit residues: 57.1342 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127476 restraints weight = 10507.221| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.88 r_work: 0.3328 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8542 Z= 0.086 Angle : 0.478 9.551 11528 Z= 0.237 Chirality : 0.042 0.142 1284 Planarity : 0.003 0.033 1422 Dihedral : 10.179 91.201 1266 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.35 % Allowed : 19.02 % Favored : 78.64 % 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: -0.10 (0.26), residues: 1044 helix: 1.17 (0.26), residues: 424 sheet: -0.40 (0.39), residues: 172 loop : -1.11 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.002 0.000 HIS C 412 PHE 0.011 0.001 PHE D 438 TYR 0.008 0.001 TYR A 673 ARG 0.003 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.02373 ( 340) hydrogen bonds : angle 4.62042 ( 1005) SS BOND : bond 0.00113 ( 4) SS BOND : angle 1.26911 ( 8) covalent geometry : bond 0.00194 ( 8538) covalent geometry : angle 0.47707 (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 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.025 Fit side-chains REVERT: A 673 TYR cc_start: 0.7870 (t80) cc_final: 0.7129 (t80) REVERT: C 673 TYR cc_start: 0.7797 (t80) cc_final: 0.7152 (t80) outliers start: 21 outliers final: 18 residues processed: 164 average time/residue: 0.2637 time to fit residues: 56.0427 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN D 726 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124612 restraints weight = 10551.917| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.90 r_work: 0.3305 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.128 Angle : 0.540 10.902 11528 Z= 0.265 Chirality : 0.044 0.148 1284 Planarity : 0.004 0.033 1422 Dihedral : 10.760 103.427 1266 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 18.34 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1044 helix: 1.12 (0.26), residues: 424 sheet: -0.66 (0.41), residues: 156 loop : -1.19 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 PHE 0.011 0.002 PHE B 438 TYR 0.010 0.001 TYR D 673 ARG 0.006 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 340) hydrogen bonds : angle 4.63425 ( 1005) SS BOND : bond 0.00165 ( 4) SS BOND : angle 2.27802 ( 8) covalent geometry : bond 0.00306 ( 8538) covalent geometry : angle 0.53659 (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 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.158 Fit side-chains REVERT: A 673 TYR cc_start: 0.7898 (t80) cc_final: 0.7267 (t80) REVERT: C 673 TYR cc_start: 0.7823 (t80) cc_final: 0.7120 (t80) outliers start: 27 outliers final: 26 residues processed: 161 average time/residue: 0.2675 time to fit residues: 55.5000 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128001 restraints weight = 10561.165| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.91 r_work: 0.3319 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1582 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= 0.107 Angle : 0.518 11.758 11528 Z= 0.253 Chirality : 0.043 0.180 1284 Planarity : 0.003 0.034 1422 Dihedral : 10.361 99.768 1266 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.47 % Allowed : 18.90 % Favored : 77.63 % 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: -0.17 (0.26), residues: 1044 helix: 1.17 (0.26), residues: 424 sheet: -0.54 (0.42), residues: 148 loop : -1.15 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS B 412 PHE 0.011 0.001 PHE B 438 TYR 0.010 0.001 TYR C 732 ARG 0.006 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 340) hydrogen bonds : angle 4.56987 ( 1005) SS BOND : bond 0.00098 ( 4) SS BOND : angle 2.00356 ( 8) covalent geometry : bond 0.00253 ( 8538) covalent geometry : angle 0.51509 (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 174 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.005 Fit side-chains REVERT: A 673 TYR cc_start: 0.7878 (t80) cc_final: 0.7260 (t80) REVERT: B 641 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7279 (mmtm) REVERT: C 673 TYR cc_start: 0.7788 (t80) cc_final: 0.7086 (t80) outliers start: 31 outliers final: 24 residues processed: 165 average time/residue: 0.2618 time to fit residues: 55.9738 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 0.0070 chunk 68 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123219 restraints weight = 10689.564| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.94 r_work: 0.3301 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8542 Z= 0.111 Angle : 0.519 12.482 11528 Z= 0.255 Chirality : 0.043 0.225 1284 Planarity : 0.004 0.033 1422 Dihedral : 10.103 100.771 1266 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.02 % Allowed : 19.24 % Favored : 77.74 % 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: -0.21 (0.26), residues: 1044 helix: 1.15 (0.26), residues: 424 sheet: -0.65 (0.40), residues: 156 loop : -1.16 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS B 412 PHE 0.011 0.001 PHE B 438 TYR 0.013 0.001 TYR A 732 ARG 0.006 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02743 ( 340) hydrogen bonds : angle 4.57231 ( 1005) SS BOND : bond 0.00134 ( 4) SS BOND : angle 1.77105 ( 8) covalent geometry : bond 0.00265 ( 8538) covalent geometry : angle 0.51710 (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 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.906 Fit side-chains REVERT: A 673 TYR cc_start: 0.7877 (t80) cc_final: 0.7328 (t80) REVERT: B 641 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7333 (mmtm) outliers start: 27 outliers final: 25 residues processed: 152 average time/residue: 0.3143 time to fit residues: 60.8835 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125400 restraints weight = 10655.575| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.90 r_work: 0.3313 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.116 Angle : 0.526 13.185 11528 Z= 0.259 Chirality : 0.044 0.203 1284 Planarity : 0.003 0.033 1422 Dihedral : 10.050 100.919 1266 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 19.24 % Favored : 77.74 % 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: -0.22 (0.26), residues: 1044 helix: 1.12 (0.26), residues: 424 sheet: -0.66 (0.40), residues: 156 loop : -1.14 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS B 412 PHE 0.011 0.002 PHE D 438 TYR 0.011 0.001 TYR A 732 ARG 0.007 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 340) hydrogen bonds : angle 4.58762 ( 1005) SS BOND : bond 0.00100 ( 4) SS BOND : angle 1.71892 ( 8) covalent geometry : bond 0.00276 ( 8538) covalent geometry : angle 0.52376 (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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.016 Fit side-chains REVERT: A 673 TYR cc_start: 0.7842 (t80) cc_final: 0.7202 (t80) REVERT: B 641 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7286 (mmtm) REVERT: C 673 TYR cc_start: 0.7836 (t80) cc_final: 0.7217 (t80) outliers start: 27 outliers final: 26 residues processed: 152 average time/residue: 0.2860 time to fit residues: 55.4498 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121460 restraints weight = 10548.920| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.99 r_work: 0.3252 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.140 Angle : 0.539 9.047 11528 Z= 0.268 Chirality : 0.045 0.204 1284 Planarity : 0.004 0.033 1422 Dihedral : 10.416 105.163 1266 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.91 % Allowed : 19.13 % 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: -0.29 (0.26), residues: 1044 helix: 1.04 (0.26), residues: 424 sheet: -0.68 (0.41), residues: 148 loop : -1.15 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 PHE 0.012 0.002 PHE D 438 TYR 0.010 0.001 TYR D 673 ARG 0.007 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 340) hydrogen bonds : angle 4.65261 ( 1005) SS BOND : bond 0.00123 ( 4) SS BOND : angle 1.72987 ( 8) covalent geometry : bond 0.00336 ( 8538) covalent geometry : angle 0.53692 (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 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.921 Fit side-chains REVERT: A 673 TYR cc_start: 0.7806 (t80) cc_final: 0.7084 (t80) REVERT: B 641 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7270 (mmtt) REVERT: C 673 TYR cc_start: 0.7824 (t80) cc_final: 0.7157 (t80) REVERT: D 642 GLN cc_start: 0.8549 (pp30) cc_final: 0.8307 (pp30) outliers start: 26 outliers final: 26 residues processed: 152 average time/residue: 0.3389 time to fit residues: 66.3429 Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 747 ASN B 756 GLN C 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125726 restraints weight = 10647.441| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.92 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.137 Angle : 0.553 13.487 11528 Z= 0.272 Chirality : 0.044 0.201 1284 Planarity : 0.004 0.033 1422 Dihedral : 10.371 104.320 1266 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.13 % Allowed : 19.13 % Favored : 77.74 % 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: -0.32 (0.26), residues: 1044 helix: 1.00 (0.26), residues: 424 sheet: -0.71 (0.41), residues: 148 loop : -1.15 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 460 HIS 0.004 0.001 HIS B 412 PHE 0.012 0.002 PHE D 438 TYR 0.016 0.001 TYR C 732 ARG 0.007 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 340) hydrogen bonds : angle 4.63609 ( 1005) SS BOND : bond 0.00140 ( 4) SS BOND : angle 1.75713 ( 8) covalent geometry : bond 0.00331 ( 8538) covalent geometry : angle 0.55155 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.57 seconds wall clock time: 82 minutes 13.03 seconds (4933.03 seconds total)