Starting phenix.real_space_refine on Fri Aug 22 22:54:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpv_29370/08_2025/8fpv_29370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpv_29370/08_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_29370/08_2025/8fpv_29370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpv_29370/08_2025/8fpv_29370.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpv_29370/08_2025/8fpv_29370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpv_29370/08_2025/8fpv_29370.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.24, per 1000 atoms: 0.27 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: 0.68 Conformation dependent library (CDL) restraints added in 465.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 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: 0.29 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: 1.21 Time building geometry restraints manager: 0.87 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 through 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (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 ARG 0.002 0.000 ARG B 420 TYR 0.010 0.001 TYR A 450 PHE 0.012 0.001 PHE B 658 TRP 0.009 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01455 ( 8538) covalent geometry : angle 0.71691 (11520) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.70991 ( 8) hydrogen bonds : bond 0.17241 ( 340) hydrogen bonds : angle 6.74042 ( 1005) *********************** 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 : 0.273 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: 0.1155 time to fit residues: 22.4349 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 : 0.318 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3710 r_free = 0.3710 target = 0.149080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126447 restraints weight = 10560.229| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.95 r_work: 0.3312 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0834 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= 0.105 Angle : 0.493 7.749 11528 Z= 0.248 Chirality : 0.043 0.166 1284 Planarity : 0.004 0.035 1422 Dihedral : 10.690 96.820 1270 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 17.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1044 helix: 1.14 (0.26), residues: 424 sheet: -0.45 (0.39), residues: 172 loop : -1.05 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.009 0.001 TYR D 673 PHE 0.009 0.001 PHE B 495 TRP 0.006 0.001 TRP B 671 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8538) covalent geometry : angle 0.49339 (11520) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.60677 ( 8) hydrogen bonds : bond 0.03115 ( 340) hydrogen bonds : angle 4.99502 ( 1005) *********************** 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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.305 Fit side-chains REVERT: A 718 CYS cc_start: 0.7491 (m) cc_final: 0.7218 (m) REVERT: B 436 CYS cc_start: 0.6407 (p) cc_final: 0.5356 (t) outliers start: 13 outliers final: 9 residues processed: 155 average time/residue: 0.1228 time to fit residues: 24.6882 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 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 C residue 498 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.149688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127837 restraints weight = 10481.565| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.88 r_work: 0.3290 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8542 Z= 0.116 Angle : 0.502 9.039 11528 Z= 0.250 Chirality : 0.043 0.163 1284 Planarity : 0.004 0.032 1422 Dihedral : 10.734 101.649 1266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.02 % Allowed : 16.78 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1044 helix: 1.16 (0.26), residues: 424 sheet: -0.42 (0.39), residues: 172 loop : -1.08 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.010 0.001 TYR D 405 PHE 0.009 0.001 PHE B 495 TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8538) covalent geometry : angle 0.50186 (11520) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.87073 ( 8) hydrogen bonds : bond 0.02980 ( 340) hydrogen bonds : angle 4.78815 ( 1005) *********************** 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.501 Fit side-chains REVERT: A 673 TYR cc_start: 0.7862 (t80) cc_final: 0.7125 (t80) REVERT: A 718 CYS cc_start: 0.7513 (m) cc_final: 0.7241 (m) REVERT: C 444 ILE cc_start: 0.8387 (mm) cc_final: 0.8174 (mt) REVERT: C 673 TYR cc_start: 0.7789 (t80) cc_final: 0.7107 (t80) outliers start: 27 outliers final: 17 residues processed: 159 average time/residue: 0.1268 time to fit residues: 26.3064 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 503 MET Chi-restraints excluded: chain B residue 706 SER 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 105 optimal weight: 0.0010 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.147232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124158 restraints weight = 10762.982| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.99 r_work: 0.3303 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1248 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= 0.096 Angle : 0.487 9.797 11528 Z= 0.240 Chirality : 0.042 0.187 1284 Planarity : 0.003 0.031 1422 Dihedral : 10.299 98.017 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.91 % Allowed : 17.11 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 1044 helix: 1.21 (0.26), residues: 424 sheet: -0.37 (0.39), residues: 172 loop : -1.06 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.008 0.001 TYR D 673 PHE 0.011 0.001 PHE D 438 TRP 0.006 0.001 TRP C 460 HIS 0.002 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8538) covalent geometry : angle 0.48688 (11520) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.62215 ( 8) hydrogen bonds : bond 0.02590 ( 340) hydrogen bonds : angle 4.64259 ( 1005) *********************** 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 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.370 Fit side-chains REVERT: A 673 TYR cc_start: 0.7872 (t80) cc_final: 0.7108 (t80) REVERT: A 718 CYS cc_start: 0.7549 (m) cc_final: 0.7301 (m) REVERT: B 436 CYS cc_start: 0.6536 (OUTLIER) cc_final: 0.5120 (t) REVERT: C 673 TYR cc_start: 0.7803 (t80) cc_final: 0.7092 (t80) REVERT: D 453 ARG cc_start: 0.7095 (ttm110) cc_final: 0.6687 (ttm110) REVERT: D 651 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: D 684 ARG cc_start: 0.8024 (mmp-170) cc_final: 0.7799 (mtp85) outliers start: 26 outliers final: 20 residues processed: 165 average time/residue: 0.1213 time to fit residues: 26.1246 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 706 SER 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 498 LEU Chi-restraints excluded: chain D residue 503 MET 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 46 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.148717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126601 restraints weight = 10580.527| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.89 r_work: 0.3319 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8542 Z= 0.095 Angle : 0.489 10.391 11528 Z= 0.239 Chirality : 0.043 0.194 1284 Planarity : 0.003 0.032 1422 Dihedral : 9.878 98.167 1266 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.13 % Allowed : 17.79 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1044 helix: 1.14 (0.26), residues: 436 sheet: -0.34 (0.39), residues: 172 loop : -1.16 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.013 0.001 TYR A 732 PHE 0.010 0.001 PHE D 438 TRP 0.006 0.001 TRP C 460 HIS 0.002 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8538) covalent geometry : angle 0.48857 (11520) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.55216 ( 8) hydrogen bonds : bond 0.02531 ( 340) hydrogen bonds : angle 4.57685 ( 1005) *********************** 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 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.378 Fit side-chains REVERT: A 673 TYR cc_start: 0.7867 (t80) cc_final: 0.7207 (t80) REVERT: A 718 CYS cc_start: 0.7508 (m) cc_final: 0.7268 (m) REVERT: D 453 ARG cc_start: 0.7077 (ttm110) cc_final: 0.6649 (ttm110) REVERT: D 651 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6744 (m-30) outliers start: 28 outliers final: 21 residues processed: 172 average time/residue: 0.1183 time to fit residues: 26.5134 Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE 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 706 SER Chi-restraints excluded: chain B residue 718 CYS 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 634 GLU Chi-restraints excluded: chain D residue 651 ASP 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 22 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.152348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130985 restraints weight = 10526.329| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.85 r_work: 0.3373 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8542 Z= 0.082 Angle : 0.470 10.587 11528 Z= 0.231 Chirality : 0.042 0.211 1284 Planarity : 0.003 0.032 1422 Dihedral : 8.652 91.874 1266 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.57 % Allowed : 18.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.26), residues: 1044 helix: 1.23 (0.26), residues: 436 sheet: -0.23 (0.42), residues: 152 loop : -1.12 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 684 TYR 0.007 0.001 TYR C 405 PHE 0.009 0.001 PHE D 438 TRP 0.006 0.001 TRP A 766 HIS 0.002 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 8538) covalent geometry : angle 0.47008 (11520) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.49176 ( 8) hydrogen bonds : bond 0.02214 ( 340) hydrogen bonds : angle 4.51138 ( 1005) *********************** 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 174 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.363 Fit side-chains REVERT: A 673 TYR cc_start: 0.7811 (t80) cc_final: 0.7220 (t80) REVERT: A 718 CYS cc_start: 0.7458 (m) cc_final: 0.7224 (m) REVERT: B 436 CYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5167 (t) REVERT: C 673 TYR cc_start: 0.7769 (t80) cc_final: 0.7187 (t80) REVERT: D 453 ARG cc_start: 0.7016 (ttm110) cc_final: 0.6563 (ttm110) outliers start: 23 outliers final: 17 residues processed: 168 average time/residue: 0.1187 time to fit residues: 26.1557 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 : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 645 ILE 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 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 B residue 718 CYS Chi-restraints excluded: chain C residue 498 LEU 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 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 26 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.0030 chunk 61 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 overall best weight: 1.0606 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.149702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127939 restraints weight = 10643.863| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.86 r_work: 0.3311 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8542 Z= 0.122 Angle : 0.515 11.594 11528 Z= 0.253 Chirality : 0.045 0.229 1284 Planarity : 0.003 0.032 1422 Dihedral : 9.072 102.144 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 19.35 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1044 helix: 1.08 (0.26), residues: 436 sheet: -0.51 (0.41), residues: 156 loop : -1.13 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 684 TYR 0.009 0.001 TYR D 673 PHE 0.011 0.002 PHE D 438 TRP 0.005 0.001 TRP C 460 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8538) covalent geometry : angle 0.51502 (11520) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.65809 ( 8) hydrogen bonds : bond 0.02794 ( 340) hydrogen bonds : angle 4.60152 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.227 Fit side-chains REVERT: A 673 TYR cc_start: 0.7814 (t80) cc_final: 0.7205 (t80) REVERT: A 718 CYS cc_start: 0.7523 (m) cc_final: 0.7277 (m) REVERT: C 673 TYR cc_start: 0.7835 (t80) cc_final: 0.7187 (t80) outliers start: 23 outliers final: 21 residues processed: 164 average time/residue: 0.1180 time to fit residues: 24.8984 Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU 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 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 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 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 22 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.146798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124444 restraints weight = 10508.987| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.90 r_work: 0.3312 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1543 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 : 0.508 12.296 11528 Z= 0.250 Chirality : 0.044 0.199 1284 Planarity : 0.003 0.033 1422 Dihedral : 8.979 100.129 1266 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.80 % Allowed : 19.35 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 1044 helix: 1.02 (0.25), residues: 436 sheet: -0.55 (0.41), residues: 156 loop : -1.13 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 684 TYR 0.012 0.001 TYR C 732 PHE 0.010 0.001 PHE D 438 TRP 0.006 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8538) covalent geometry : angle 0.50803 (11520) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.64282 ( 8) hydrogen bonds : bond 0.02694 ( 340) hydrogen bonds : angle 4.61580 ( 1005) *********************** 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 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.342 Fit side-chains REVERT: A 673 TYR cc_start: 0.7829 (t80) cc_final: 0.7384 (t80) REVERT: A 718 CYS cc_start: 0.7509 (m) cc_final: 0.7267 (m) REVERT: C 673 TYR cc_start: 0.7793 (t80) cc_final: 0.7115 (t80) outliers start: 25 outliers final: 21 residues processed: 166 average time/residue: 0.1260 time to fit residues: 26.9267 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU 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 706 SER Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 746 VAL 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 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 62 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 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 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 = 0.3666 r_free = 0.3666 target = 0.145515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122729 restraints weight = 10687.223| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.93 r_work: 0.3284 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1599 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= 0.128 Angle : 0.531 12.709 11528 Z= 0.262 Chirality : 0.044 0.186 1284 Planarity : 0.004 0.033 1422 Dihedral : 9.237 102.939 1266 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.26), residues: 1044 helix: 1.08 (0.26), residues: 424 sheet: -0.52 (0.41), residues: 148 loop : -1.01 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 684 TYR 0.019 0.001 TYR A 732 PHE 0.011 0.002 PHE B 438 TRP 0.007 0.001 TRP B 671 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8538) covalent geometry : angle 0.53049 (11520) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.71618 ( 8) hydrogen bonds : bond 0.02911 ( 340) hydrogen bonds : angle 4.65214 ( 1005) *********************** 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 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.332 Fit side-chains REVERT: A 673 TYR cc_start: 0.7843 (t80) cc_final: 0.7355 (t80) REVERT: A 718 CYS cc_start: 0.7507 (m) cc_final: 0.7271 (m) outliers start: 25 outliers final: 23 residues processed: 164 average time/residue: 0.1354 time to fit residues: 28.2757 Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU 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 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 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.144145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120816 restraints weight = 10623.969| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.99 r_work: 0.3284 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1680 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= 0.135 Angle : 0.542 13.106 11528 Z= 0.267 Chirality : 0.045 0.192 1284 Planarity : 0.004 0.033 1422 Dihedral : 9.326 104.045 1266 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.80 % Allowed : 19.69 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1044 helix: 1.03 (0.26), residues: 424 sheet: -0.58 (0.41), residues: 148 loop : -1.03 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 684 TYR 0.009 0.001 TYR D 673 PHE 0.012 0.002 PHE D 438 TRP 0.005 0.001 TRP B 671 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8538) covalent geometry : angle 0.54174 (11520) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.78905 ( 8) hydrogen bonds : bond 0.02980 ( 340) hydrogen bonds : angle 4.65749 ( 1005) ********************** 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 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.357 Fit side-chains REVERT: A 673 TYR cc_start: 0.7836 (t80) cc_final: 0.7247 (t80) REVERT: A 718 CYS cc_start: 0.7584 (m) cc_final: 0.7350 (m) REVERT: C 673 TYR cc_start: 0.7807 (t80) cc_final: 0.7175 (t80) outliers start: 25 outliers final: 24 residues processed: 162 average time/residue: 0.1372 time to fit residues: 28.3050 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU 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 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 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 98 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.146656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124247 restraints weight = 10614.115| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.90 r_work: 0.3338 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1726 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= 0.115 Angle : 0.521 13.241 11528 Z= 0.258 Chirality : 0.043 0.174 1284 Planarity : 0.003 0.033 1422 Dihedral : 9.043 100.866 1266 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1044 helix: 1.07 (0.26), residues: 424 sheet: -0.57 (0.41), residues: 148 loop : -1.04 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 684 TYR 0.013 0.001 TYR C 732 PHE 0.011 0.002 PHE D 438 TRP 0.005 0.001 TRP B 671 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8538) covalent geometry : angle 0.52117 (11520) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.82901 ( 8) hydrogen bonds : bond 0.02764 ( 340) hydrogen bonds : angle 4.61970 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.12 seconds wall clock time: 42 minutes 6.54 seconds (2526.54 seconds total)