Starting phenix.real_space_refine on Sat Jun 7 03:28:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqh_29388/06_2025/8fqh_29388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqh_29388/06_2025/8fqh_29388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqh_29388/06_2025/8fqh_29388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqh_29388/06_2025/8fqh_29388.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqh_29388/06_2025/8fqh_29388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqh_29388/06_2025/8fqh_29388.cif" } resolution = 3.43 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 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8384 Number of models: 1 Model: "" Number of chains: 13 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CYZ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.00, per 1000 atoms: 0.72 Number of scatterers: 8384 At special positions: 0 Unit cell: (122.18, 90.2, 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 1600 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 979.5 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: 45 helices and 18 sheets defined 42.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.069A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.549A 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 removed outlier: 3.528A pdb=" N GLY A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.519A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 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 715 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.893A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.589A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.788A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.915A 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 removed outlier: 3.676A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.619A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.978A 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: 3.530A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.572A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.730A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.692A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.551A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.551A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.770A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.011A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.635A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.635A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.454A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.673A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 407 through 408 removed outlier: 3.659A pdb=" N GLU C 422 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 475 through 480 removed outlier: 9.255A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 475 through 480 removed outlier: 9.255A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.934A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AB6, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.597A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.752A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.339A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 948 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: 2.25 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2044 1.48 - 1.60: 3720 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 A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ A1303 " pdb=" C4 CYZ A1303 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " 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 - 2.11: 11304 2.11 - 4.22: 135 4.22 - 6.33: 46 6.33 - 8.44: 24 8.44 - 10.55: 11 Bond angle restraints: 11520 Sorted by residual: angle pdb=" CB MET D 414 " pdb=" CG MET D 414 " pdb=" SD MET D 414 " ideal model delta sigma weight residual 112.70 123.25 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB MET B 414 " pdb=" CG MET B 414 " pdb=" SD MET B 414 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C9 CYZ A1303 " pdb=" S1 CYZ A1303 " pdb=" N1 CYZ A1303 " ideal model delta sigma weight residual 101.75 111.66 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.50 -9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CB MET A 674 " pdb=" CG MET A 674 " pdb=" SD MET A 674 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 4642 22.71 - 45.41: 500 45.41 - 68.12: 75 68.12 - 90.82: 20 90.82 - 113.53: 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 93.00 171.19 -78.19 1 1.00e+01 1.00e-02 7.63e+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 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+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 -147.09 61.09 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1185 0.090 - 0.181: 83 0.181 - 0.271: 0 0.271 - 0.361: 0 0.361 - 0.452: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C1 CYZ A1303 " pdb=" C2 CYZ A1303 " pdb=" C6 CYZ A1303 " pdb=" C8 CYZ A1303 " both_signs ideal model delta sigma weight residual False 2.79 2.34 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C8 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" N2 CYZ B1302 " both_signs ideal model delta sigma weight residual False 2.20 2.65 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" C8 CYZ A1303 " pdb=" C1 CYZ A1303 " pdb=" N1 CYZ A1303 " pdb=" N2 CYZ A1303 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 408 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C MET A 408 " -0.027 2.00e-02 2.50e+03 pdb=" O MET A 408 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 409 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 CYZ A1303 " -0.000 2.00e-02 2.50e+03 9.90e-03 2.45e+00 pdb=" C11 CYZ A1303 " 0.002 2.00e-02 2.50e+03 pdb=" C12 CYZ A1303 " 0.001 2.00e-02 2.50e+03 pdb=" C13 CYZ A1303 " -0.000 2.00e-02 2.50e+03 pdb=" C14 CYZ A1303 " 0.010 2.00e-02 2.50e+03 pdb=" C9 CYZ A1303 " -0.026 2.00e-02 2.50e+03 pdb=" N2 CYZ A1303 " -0.002 2.00e-02 2.50e+03 pdb=" S1 CYZ A1303 " 0.015 2.00e-02 2.50e+03 pdb=" S2 CYZ A1303 " 0.001 2.00e-02 2.50e+03 pdb="CL CYZ A1303 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO C 737 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.019 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 198 2.69 - 3.24: 7956 3.24 - 3.79: 13190 3.79 - 4.35: 17122 4.35 - 4.90: 28813 Nonbonded interactions: 67279 Sorted by model distance: nonbonded pdb=" OG SER A 729 " pdb=" O1 CYZ A1303 " model vdw 2.135 2.432 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.181 3.040 nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 405 " pdb=" OG1 THR C 707 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR B 405 " pdb=" OG1 THR B 707 " model vdw 2.291 3.040 ... (remaining 67274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301)) 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)) selection = (chain 'C' and (resid 393 through 773 or resid 1301)) 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)) } 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: 3.300 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 8543 Z= 0.728 Angle : 0.765 10.552 11528 Z= 0.336 Chirality : 0.064 0.452 1284 Planarity : 0.003 0.034 1422 Dihedral : 18.489 113.528 3288 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.11 % Allowed : 28.19 % Favored : 71.70 % 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: -0.41 (0.25), residues: 1044 helix: 0.90 (0.26), residues: 414 sheet: -0.58 (0.44), residues: 134 loop : -1.19 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 766 HIS 0.005 0.001 HIS B 412 PHE 0.008 0.001 PHE D 495 TYR 0.018 0.001 TYR B 732 ARG 0.002 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.16280 ( 321) hydrogen bonds : angle 6.56755 ( 948) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.83566 ( 8) covalent geometry : bond 0.01463 ( 8538) covalent geometry : angle 0.76492 (11520) Misc. bond : bond 0.00527 ( 1) *********************** 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: 1 poor density : 151 time to evaluate : 0.894 Fit side-chains REVERT: A 503 MET cc_start: 0.6550 (ttp) cc_final: 0.6099 (ttm) REVERT: C 661 ARG cc_start: 0.6116 (mpt-90) cc_final: 0.5269 (ttp-110) REVERT: D 408 MET cc_start: 0.6602 (mmt) cc_final: 0.6348 (mmp) REVERT: D 624 LEU cc_start: 0.6950 (tp) cc_final: 0.6632 (tp) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1981 time to fit residues: 41.5535 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 435 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.176100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154225 restraints weight = 12661.632| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.76 r_work: 0.3831 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 8543 Z= 0.256 Angle : 0.685 8.090 11528 Z= 0.340 Chirality : 0.050 0.196 1284 Planarity : 0.005 0.042 1422 Dihedral : 10.697 93.872 1268 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 4.92 % Allowed : 25.95 % Favored : 69.13 % 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: -0.91 (0.25), residues: 1044 helix: 0.18 (0.25), residues: 432 sheet: -0.60 (0.42), residues: 144 loop : -1.28 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 766 HIS 0.007 0.002 HIS B 412 PHE 0.016 0.002 PHE D 659 TYR 0.013 0.002 TYR A 405 ARG 0.004 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 321) hydrogen bonds : angle 5.24478 ( 948) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.46142 ( 8) covalent geometry : bond 0.00632 ( 8538) covalent geometry : angle 0.68421 (11520) Misc. bond : bond 0.01121 ( 1) *********************** 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 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.027 Fit side-chains REVERT: A 674 MET cc_start: 0.6932 (mpp) cc_final: 0.6399 (mpp) REVERT: A 742 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6361 (mt) REVERT: B 414 MET cc_start: 0.3856 (ppp) cc_final: 0.3613 (ppp) REVERT: C 674 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5468 (tpp) REVERT: C 675 ARG cc_start: 0.6159 (ptt180) cc_final: 0.5534 (tpm170) REVERT: C 751 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8361 (mm) REVERT: D 412 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6427 (p-80) outliers start: 44 outliers final: 23 residues processed: 178 average time/residue: 0.1942 time to fit residues: 47.9016 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.180900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159425 restraints weight = 12831.746| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.77 r_work: 0.3890 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8543 Z= 0.116 Angle : 0.538 7.771 11528 Z= 0.262 Chirality : 0.045 0.192 1284 Planarity : 0.004 0.052 1422 Dihedral : 9.380 89.103 1266 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.32 % Rotamer: Outliers : 3.69 % Allowed : 27.07 % Favored : 69.24 % 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: -0.56 (0.25), residues: 1044 helix: 0.59 (0.26), residues: 430 sheet: -0.58 (0.39), residues: 172 loop : -1.18 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE B 659 TYR 0.010 0.001 TYR B 732 ARG 0.001 0.000 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.02831 ( 321) hydrogen bonds : angle 4.82951 ( 948) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.55964 ( 8) covalent geometry : bond 0.00285 ( 8538) covalent geometry : angle 0.53754 (11520) Misc. bond : bond 0.00637 ( 1) *********************** 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 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7414 (mtt-85) REVERT: A 660 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7474 (mtt180) REVERT: A 708 MET cc_start: 0.7277 (ttp) cc_final: 0.6498 (tpt) REVERT: A 772 GLU cc_start: 0.5180 (tt0) cc_final: 0.4494 (tm-30) REVERT: B 414 MET cc_start: 0.3895 (ppp) cc_final: 0.3647 (ppp) REVERT: B 421 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: C 674 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.5587 (tpp) REVERT: C 675 ARG cc_start: 0.6130 (ptt180) cc_final: 0.5537 (tpm170) REVERT: C 751 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8238 (mm) REVERT: D 422 GLU cc_start: 0.6193 (mp0) cc_final: 0.5894 (mp0) outliers start: 33 outliers final: 18 residues processed: 176 average time/residue: 0.2133 time to fit residues: 51.1264 Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 13 optimal weight: 9.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157740 restraints weight = 12712.376| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.75 r_work: 0.3873 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8543 Z= 0.135 Angle : 0.541 8.276 11528 Z= 0.265 Chirality : 0.045 0.175 1284 Planarity : 0.004 0.055 1422 Dihedral : 8.710 87.727 1266 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.70 % Allowed : 26.62 % Favored : 68.68 % 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: -0.51 (0.25), residues: 1044 helix: 0.62 (0.26), residues: 434 sheet: -0.59 (0.40), residues: 170 loop : -1.13 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.008 0.001 PHE D 495 TYR 0.014 0.001 TYR A 700 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02871 ( 321) hydrogen bonds : angle 4.74143 ( 948) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.64053 ( 8) covalent geometry : bond 0.00335 ( 8538) covalent geometry : angle 0.54134 (11520) Misc. bond : bond 0.00714 ( 1) *********************** 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 194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.017 Fit side-chains REVERT: A 485 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7463 (mtt-85) REVERT: A 674 MET cc_start: 0.7163 (mpp) cc_final: 0.6736 (mpp) REVERT: A 772 GLU cc_start: 0.5311 (tt0) cc_final: 0.4464 (tm-30) REVERT: B 414 MET cc_start: 0.3873 (ppp) cc_final: 0.3655 (ppp) REVERT: B 421 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: C 504 ILE cc_start: 0.5777 (OUTLIER) cc_final: 0.5451 (pp) REVERT: C 674 MET cc_start: 0.5812 (OUTLIER) cc_final: 0.5527 (tpp) REVERT: C 675 ARG cc_start: 0.6131 (ptt180) cc_final: 0.5552 (tpm170) REVERT: C 714 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: C 751 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8196 (mm) REVERT: D 422 GLU cc_start: 0.6275 (mp0) cc_final: 0.5826 (mp0) outliers start: 42 outliers final: 25 residues processed: 181 average time/residue: 0.1971 time to fit residues: 49.3481 Evaluate side-chains 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 0.0030 chunk 32 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 756 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160114 restraints weight = 12713.910| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.74 r_work: 0.3899 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8543 Z= 0.105 Angle : 0.513 8.833 11528 Z= 0.249 Chirality : 0.044 0.213 1284 Planarity : 0.004 0.057 1422 Dihedral : 7.822 85.912 1266 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.14 % Allowed : 27.63 % Favored : 68.23 % 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: 0.83 (0.26), residues: 430 sheet: -0.58 (0.40), residues: 170 loop : -1.03 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE D 659 TYR 0.012 0.001 TYR A 700 ARG 0.001 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02508 ( 321) hydrogen bonds : angle 4.61457 ( 948) SS BOND : bond 0.00148 ( 4) SS BOND : angle 1.34537 ( 8) covalent geometry : bond 0.00258 ( 8538) covalent geometry : angle 0.51202 (11520) Misc. bond : bond 0.00582 ( 1) *********************** 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 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.895 Fit side-chains REVERT: A 485 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7488 (mtt-85) REVERT: A 674 MET cc_start: 0.7158 (mpp) cc_final: 0.6860 (mpp) REVERT: A 772 GLU cc_start: 0.5366 (tt0) cc_final: 0.4433 (tm-30) REVERT: B 421 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: C 504 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5429 (pp) REVERT: C 661 ARG cc_start: 0.6088 (mpt-90) cc_final: 0.5345 (ptm160) REVERT: C 674 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.5549 (tpp) REVERT: C 675 ARG cc_start: 0.6126 (ptt180) cc_final: 0.5560 (tpm170) REVERT: C 714 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: C 751 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8168 (mm) REVERT: D 422 GLU cc_start: 0.6220 (mp0) cc_final: 0.5772 (mp0) outliers start: 37 outliers final: 23 residues processed: 180 average time/residue: 0.2004 time to fit residues: 49.9074 Evaluate side-chains 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.177738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.156425 restraints weight = 12652.658| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.70 r_work: 0.3854 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8543 Z= 0.165 Angle : 0.569 9.134 11528 Z= 0.279 Chirality : 0.047 0.202 1284 Planarity : 0.004 0.057 1422 Dihedral : 7.819 82.532 1266 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.70 % Allowed : 27.52 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1044 helix: 0.62 (0.26), residues: 432 sheet: -0.44 (0.44), residues: 142 loop : -1.15 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 766 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE D 659 TYR 0.014 0.002 TYR A 700 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 321) hydrogen bonds : angle 4.75678 ( 948) SS BOND : bond 0.00373 ( 4) SS BOND : angle 1.62634 ( 8) covalent geometry : bond 0.00411 ( 8538) covalent geometry : angle 0.56749 (11520) Misc. bond : bond 0.00823 ( 1) *********************** 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 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.207 Fit side-chains REVERT: A 485 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7499 (mtt-85) REVERT: A 661 ARG cc_start: 0.6202 (ptp-170) cc_final: 0.5737 (mpt-90) REVERT: A 674 MET cc_start: 0.7112 (mpp) cc_final: 0.6843 (mpp) REVERT: A 751 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 772 GLU cc_start: 0.5419 (tt0) cc_final: 0.4863 (tm-30) REVERT: B 414 MET cc_start: 0.3739 (ppp) cc_final: 0.3441 (ppp) REVERT: B 421 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 504 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5497 (pp) REVERT: C 674 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5537 (tpp) REVERT: C 675 ARG cc_start: 0.6104 (ptt180) cc_final: 0.5527 (tpm170) REVERT: C 751 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8238 (mm) REVERT: D 412 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6451 (p-80) REVERT: D 422 GLU cc_start: 0.6274 (mp0) cc_final: 0.4956 (mm-30) outliers start: 42 outliers final: 29 residues processed: 181 average time/residue: 0.1996 time to fit residues: 49.8874 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.178580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157169 restraints weight = 12907.205| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.75 r_work: 0.3864 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8543 Z= 0.139 Angle : 0.560 9.982 11528 Z= 0.275 Chirality : 0.046 0.336 1284 Planarity : 0.004 0.058 1422 Dihedral : 7.581 67.415 1266 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.81 % Allowed : 27.40 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1044 helix: 0.71 (0.26), residues: 428 sheet: -0.57 (0.40), residues: 170 loop : -1.09 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE B 659 TYR 0.012 0.001 TYR A 700 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 321) hydrogen bonds : angle 4.71519 ( 948) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.37935 ( 8) covalent geometry : bond 0.00342 ( 8538) covalent geometry : angle 0.55913 (11520) Misc. bond : bond 0.01205 ( 1) *********************** 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 196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7522 (mtt180) REVERT: A 661 ARG cc_start: 0.6155 (ptp-170) cc_final: 0.5697 (mpt-90) REVERT: A 674 MET cc_start: 0.7171 (mpp) cc_final: 0.6904 (mpp) REVERT: A 751 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 772 GLU cc_start: 0.5413 (tt0) cc_final: 0.4865 (tm-30) REVERT: B 414 MET cc_start: 0.3797 (ppp) cc_final: 0.3468 (ppp) REVERT: B 421 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: C 504 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.5451 (pp) REVERT: C 674 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5543 (tpp) REVERT: C 675 ARG cc_start: 0.6112 (ptt180) cc_final: 0.5532 (tpm170) REVERT: C 751 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8221 (mm) REVERT: D 412 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6459 (p-80) outliers start: 43 outliers final: 30 residues processed: 185 average time/residue: 0.2000 time to fit residues: 50.9072 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.179448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158137 restraints weight = 12920.570| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.76 r_work: 0.3873 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8543 Z= 0.124 Angle : 0.537 9.403 11528 Z= 0.263 Chirality : 0.045 0.251 1284 Planarity : 0.004 0.058 1422 Dihedral : 7.041 66.209 1266 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.92 % Allowed : 27.52 % Favored : 67.56 % 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: -0.37 (0.26), residues: 1044 helix: 0.79 (0.26), residues: 428 sheet: -0.57 (0.41), residues: 170 loop : -1.08 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE D 659 TYR 0.013 0.001 TYR D 732 ARG 0.002 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.02643 ( 321) hydrogen bonds : angle 4.65534 ( 948) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.22240 ( 8) covalent geometry : bond 0.00305 ( 8538) covalent geometry : angle 0.53634 (11520) Misc. bond : bond 0.01103 ( 1) *********************** 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 191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7417 (mtt-85) REVERT: A 661 ARG cc_start: 0.6205 (ptp-170) cc_final: 0.5779 (mpt-90) REVERT: A 751 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 414 MET cc_start: 0.3848 (ppp) cc_final: 0.3520 (ppp) REVERT: B 421 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: C 504 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5471 (pp) REVERT: C 674 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5557 (tpp) REVERT: C 675 ARG cc_start: 0.6088 (ptt180) cc_final: 0.5619 (tpm170) REVERT: C 751 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (mm) REVERT: D 412 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6446 (p-80) REVERT: D 422 GLU cc_start: 0.6220 (mp0) cc_final: 0.4934 (mm-30) outliers start: 44 outliers final: 28 residues processed: 180 average time/residue: 0.1926 time to fit residues: 47.7325 Evaluate side-chains 176 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.180993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159941 restraints weight = 12852.740| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.74 r_work: 0.3894 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8543 Z= 0.107 Angle : 0.527 10.384 11528 Z= 0.259 Chirality : 0.045 0.237 1284 Planarity : 0.004 0.059 1422 Dihedral : 6.763 66.371 1266 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.14 % Allowed : 27.96 % Favored : 67.90 % 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: 0.85 (0.26), residues: 428 sheet: -0.56 (0.41), residues: 170 loop : -1.06 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.006 0.001 PHE D 659 TYR 0.010 0.001 TYR A 700 ARG 0.001 0.000 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.02467 ( 321) hydrogen bonds : angle 4.59489 ( 948) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.02071 ( 8) covalent geometry : bond 0.00259 ( 8538) covalent geometry : angle 0.52613 (11520) Misc. bond : bond 0.00907 ( 1) *********************** 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 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.6209 (ptp-170) cc_final: 0.5760 (mpt-90) REVERT: A 748 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7644 (mp) REVERT: A 751 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8288 (mt) REVERT: B 414 MET cc_start: 0.3806 (ppp) cc_final: 0.3494 (ppp) REVERT: B 421 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: B 626 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6502 (m) REVERT: C 504 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5478 (pp) REVERT: C 661 ARG cc_start: 0.6381 (mpt-90) cc_final: 0.5634 (ptm160) REVERT: C 674 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5564 (tpp) REVERT: C 675 ARG cc_start: 0.6044 (ptt180) cc_final: 0.5610 (tpm170) REVERT: C 751 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8134 (mm) REVERT: D 412 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6477 (p-80) REVERT: D 422 GLU cc_start: 0.6181 (mp0) cc_final: 0.5205 (mm-30) outliers start: 37 outliers final: 24 residues processed: 174 average time/residue: 0.2091 time to fit residues: 50.9196 Evaluate side-chains 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160544 restraints weight = 12602.178| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.69 r_work: 0.3906 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8543 Z= 0.110 Angle : 0.526 10.862 11528 Z= 0.260 Chirality : 0.045 0.221 1284 Planarity : 0.004 0.058 1422 Dihedral : 6.606 67.253 1266 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.25 % Allowed : 27.52 % Favored : 68.23 % 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: -0.26 (0.26), residues: 1044 helix: 0.88 (0.26), residues: 428 sheet: -0.37 (0.39), residues: 184 loop : -1.09 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.006 0.001 PHE D 495 TYR 0.010 0.001 TYR A 700 ARG 0.001 0.000 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.02520 ( 321) hydrogen bonds : angle 4.57839 ( 948) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.04424 ( 8) covalent geometry : bond 0.00269 ( 8538) covalent geometry : angle 0.52565 (11520) Misc. bond : bond 0.00870 ( 1) ********************** 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 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7474 (mtt-85) REVERT: A 661 ARG cc_start: 0.6240 (ptp-170) cc_final: 0.5757 (mpt-90) REVERT: A 751 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8268 (mt) REVERT: B 414 MET cc_start: 0.3827 (ppp) cc_final: 0.3522 (ppp) REVERT: B 421 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: B 626 VAL cc_start: 0.6730 (OUTLIER) cc_final: 0.6509 (m) REVERT: C 504 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5487 (pp) REVERT: C 661 ARG cc_start: 0.6319 (mpt-90) cc_final: 0.5616 (ptm160) REVERT: C 674 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5601 (tpp) REVERT: C 675 ARG cc_start: 0.6049 (ptt180) cc_final: 0.5616 (tpm170) REVERT: C 751 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8165 (mm) REVERT: D 412 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.5647 (p-80) REVERT: D 422 GLU cc_start: 0.6197 (mp0) cc_final: 0.5194 (mm-30) outliers start: 38 outliers final: 28 residues processed: 174 average time/residue: 0.2106 time to fit residues: 50.3553 Evaluate side-chains 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 94 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.177170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155777 restraints weight = 12930.737| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.76 r_work: 0.3843 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8543 Z= 0.173 Angle : 0.597 10.811 11528 Z= 0.296 Chirality : 0.048 0.223 1284 Planarity : 0.004 0.058 1422 Dihedral : 6.958 74.035 1266 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.25 % Allowed : 27.63 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1044 helix: 0.57 (0.25), residues: 432 sheet: -0.23 (0.42), residues: 156 loop : -1.21 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 766 HIS 0.005 0.001 HIS B 412 PHE 0.010 0.001 PHE D 659 TYR 0.012 0.002 TYR A 700 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 321) hydrogen bonds : angle 4.75797 ( 948) SS BOND : bond 0.00255 ( 4) SS BOND : angle 1.56776 ( 8) covalent geometry : bond 0.00432 ( 8538) covalent geometry : angle 0.59621 (11520) Misc. bond : bond 0.01060 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3627.81 seconds wall clock time: 63 minutes 54.21 seconds (3834.21 seconds total)