Starting phenix.real_space_refine on Sun May 11 21:06:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqh_29388/05_2025/8fqh_29388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqh_29388/05_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_29388/05_2025/8fqh_29388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqh_29388/05_2025/8fqh_29388.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqh_29388/05_2025/8fqh_29388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqh_29388/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.83, per 1000 atoms: 0.70 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: 2.02 Conformation dependent library (CDL) restraints added in 860.8 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: 1.05 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: 2.39 Time building geometry restraints manager: 2.37 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.960 Find NCS groups from input model: 0.440 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 : 0.874 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: 0.1895 time to fit residues: 39.9666 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 : 1.000 ------------------------------------------------------------------------------- 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 = 0.154197 restraints weight = 12661.632| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.77 r_work: 0.3830 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- 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 : 0.888 Fit side-chains REVERT: A 674 MET cc_start: 0.6931 (mpp) cc_final: 0.6397 (mpp) REVERT: A 742 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6360 (mt) REVERT: B 414 MET cc_start: 0.3854 (ppp) cc_final: 0.3612 (ppp) REVERT: C 674 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5471 (tpp) REVERT: C 675 ARG cc_start: 0.6161 (ptt180) cc_final: 0.5535 (tpm170) REVERT: C 751 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (mm) REVERT: D 412 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6429 (p-80) outliers start: 44 outliers final: 23 residues processed: 178 average time/residue: 0.1939 time to fit residues: 47.8964 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 : 0.944 ------------------------------------------------------------------------------- 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: 0.8980 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.177509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155777 restraints weight = 12921.767| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.77 r_work: 0.3849 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8543 Z= 0.160 Angle : 0.578 7.500 11528 Z= 0.283 Chirality : 0.046 0.201 1284 Planarity : 0.004 0.052 1422 Dihedral : 9.766 88.478 1266 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 4.59 % Allowed : 26.62 % Favored : 68.79 % 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: -0.75 (0.25), residues: 1044 helix: 0.37 (0.25), residues: 432 sheet: -0.54 (0.43), residues: 144 loop : -1.25 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 671 HIS 0.006 0.001 HIS B 412 PHE 0.010 0.001 PHE B 659 TYR 0.011 0.001 TYR B 732 ARG 0.002 0.000 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 321) hydrogen bonds : angle 4.94428 ( 948) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.80246 ( 8) covalent geometry : bond 0.00397 ( 8538) covalent geometry : angle 0.57759 (11520) Misc. bond : bond 0.00823 ( 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 191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.962 Fit side-chains REVERT: A 485 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7431 (mtt-85) REVERT: A 660 ARG cc_start: 0.7720 (mtm180) cc_final: 0.7447 (mtt180) REVERT: A 674 MET cc_start: 0.7041 (mpp) cc_final: 0.6550 (mpp) REVERT: A 708 MET cc_start: 0.7450 (ttp) cc_final: 0.6666 (tpt) REVERT: A 772 GLU cc_start: 0.5187 (tt0) cc_final: 0.4748 (tm-30) REVERT: B 414 MET cc_start: 0.3955 (ppp) cc_final: 0.3682 (ppp) REVERT: B 421 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 755 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6720 (mt-10) REVERT: C 674 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5443 (tpp) REVERT: C 675 ARG cc_start: 0.6176 (ptt180) cc_final: 0.5552 (tpm170) REVERT: C 751 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8199 (mm) REVERT: D 502 ILE cc_start: 0.8454 (mm) cc_final: 0.8245 (mm) outliers start: 41 outliers final: 24 residues processed: 179 average time/residue: 0.2029 time to fit residues: 49.7186 Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 B residue 772 GLU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN C 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.180979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159669 restraints weight = 12716.880| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.75 r_work: 0.3897 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8543 Z= 0.106 Angle : 0.515 8.340 11528 Z= 0.252 Chirality : 0.044 0.175 1284 Planarity : 0.004 0.055 1422 Dihedral : 8.644 89.547 1266 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.58 % Allowed : 28.41 % Favored : 68.01 % 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 (0.26), residues: 1044 helix: 0.76 (0.26), residues: 428 sheet: -0.59 (0.40), residues: 170 loop : -1.11 (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 0.007 0.001 PHE D 495 TYR 0.009 0.001 TYR B 732 ARG 0.001 0.000 ARG D 694 Details of bonding type rmsd hydrogen bonds : bond 0.02570 ( 321) hydrogen bonds : angle 4.69018 ( 948) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.44501 ( 8) covalent geometry : bond 0.00260 ( 8538) covalent geometry : angle 0.51482 (11520) Misc. bond : bond 0.00600 ( 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 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.917 Fit side-chains REVERT: A 485 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7489 (mtt-85) REVERT: A 660 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7460 (mtt180) REVERT: A 674 MET cc_start: 0.7138 (mpp) cc_final: 0.6723 (mpp) REVERT: A 772 GLU cc_start: 0.5290 (tt0) cc_final: 0.4403 (tm-30) REVERT: B 414 MET cc_start: 0.3897 (ppp) cc_final: 0.3681 (ppp) REVERT: B 421 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 504 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5433 (pp) REVERT: C 674 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5539 (tpp) REVERT: C 675 ARG cc_start: 0.6118 (ptt180) cc_final: 0.5566 (tpm170) REVERT: C 714 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: C 751 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8182 (mm) outliers start: 32 outliers final: 18 residues processed: 182 average time/residue: 0.1988 time to fit residues: 49.7320 Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 485 ARG Chi-restraints excluded: chain A residue 489 ILE 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 B residue 758 VAL Chi-restraints excluded: chain C residue 445 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 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: 3.9990 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.180529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.159213 restraints weight = 12741.051| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.72 r_work: 0.3887 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2125 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= 0.118 Angle : 0.520 8.638 11528 Z= 0.255 Chirality : 0.045 0.200 1284 Planarity : 0.004 0.056 1422 Dihedral : 8.025 87.360 1266 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.70 % Allowed : 27.74 % 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: 0.74 (0.26), residues: 434 sheet: -0.63 (0.40), residues: 170 loop : -1.00 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.009 0.001 PHE B 659 TYR 0.009 0.001 TYR B 732 ARG 0.001 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 321) hydrogen bonds : angle 4.64566 ( 948) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.42907 ( 8) covalent geometry : bond 0.00292 ( 8538) covalent geometry : angle 0.51900 (11520) Misc. bond : bond 0.00639 ( 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 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.930 Fit side-chains REVERT: A 485 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: A 674 MET cc_start: 0.7113 (mpp) cc_final: 0.6832 (mpp) REVERT: A 675 ARG cc_start: 0.5523 (tpm170) cc_final: 0.5277 (tpm170) REVERT: A 751 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 772 GLU cc_start: 0.5410 (tt0) cc_final: 0.4465 (tm-30) REVERT: B 414 MET cc_start: 0.3818 (ppp) cc_final: 0.3608 (ppp) REVERT: B 421 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: C 504 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5454 (pp) REVERT: C 674 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5530 (tpp) REVERT: C 675 ARG cc_start: 0.6138 (ptt180) cc_final: 0.5564 (tpm170) REVERT: C 714 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: C 751 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8178 (mm) REVERT: D 412 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6408 (p-80) outliers start: 42 outliers final: 25 residues processed: 181 average time/residue: 0.1991 time to fit residues: 49.6115 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 412 HIS Chi-restraints excluded: chain D residue 432 ILE 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: 7.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.174206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152337 restraints weight = 12817.867| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.74 r_work: 0.3800 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 8543 Z= 0.237 Angle : 0.648 8.794 11528 Z= 0.319 Chirality : 0.049 0.199 1284 Planarity : 0.005 0.056 1422 Dihedral : 8.518 84.384 1266 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.15 % Allowed : 28.19 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1044 helix: 0.30 (0.25), residues: 432 sheet: -0.57 (0.44), residues: 142 loop : -1.25 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 767 HIS 0.006 0.002 HIS B 412 PHE 0.013 0.002 PHE D 659 TYR 0.015 0.002 TYR B 732 ARG 0.004 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 321) hydrogen bonds : angle 4.98807 ( 948) SS BOND : bond 0.00389 ( 4) SS BOND : angle 2.01859 ( 8) covalent geometry : bond 0.00588 ( 8538) covalent geometry : angle 0.64562 (11520) Misc. bond : bond 0.01046 ( 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 199 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.864 Fit side-chains REVERT: A 485 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7472 (mtt-85) REVERT: A 661 ARG cc_start: 0.6195 (ptp-170) cc_final: 0.5815 (mpt-90) REVERT: A 751 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 772 GLU cc_start: 0.5326 (tt0) cc_final: 0.4747 (tm-30) REVERT: B 414 MET cc_start: 0.3845 (ppp) cc_final: 0.3620 (ppp) REVERT: C 504 ILE cc_start: 0.5660 (OUTLIER) cc_final: 0.5362 (pp) REVERT: C 674 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5441 (tpp) REVERT: C 675 ARG cc_start: 0.6308 (ptt180) cc_final: 0.5778 (tpm170) REVERT: C 751 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8268 (mm) REVERT: D 412 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6648 (p-80) outliers start: 46 outliers final: 34 residues processed: 185 average time/residue: 0.1942 time to fit residues: 49.2846 Evaluate side-chains 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 503 MET 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 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 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 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 772 GLU 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 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: 3.9990 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 98 optimal weight: 0.0000 chunk 83 optimal weight: 0.0470 chunk 93 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN C 714 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 = 0.181310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160131 restraints weight = 12842.751| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.74 r_work: 0.3900 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8543 Z= 0.100 Angle : 0.541 10.100 11528 Z= 0.264 Chirality : 0.045 0.306 1284 Planarity : 0.004 0.058 1422 Dihedral : 7.617 75.764 1266 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.25 % Allowed : 28.08 % Favored : 67.67 % 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: 0.80 (0.26), residues: 428 sheet: -0.57 (0.41), residues: 170 loop : -1.09 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.008 0.001 PHE B 659 TYR 0.014 0.001 TYR B 732 ARG 0.001 0.000 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.02438 ( 321) hydrogen bonds : angle 4.63601 ( 948) SS BOND : bond 0.00109 ( 4) SS BOND : angle 1.03027 ( 8) covalent geometry : bond 0.00233 ( 8538) covalent geometry : angle 0.54014 (11520) Misc. bond : bond 0.01307 ( 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 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.6234 (ptp-170) cc_final: 0.5923 (mpt-90) REVERT: B 421 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 755 GLU cc_start: 0.6754 (mt-10) cc_final: 0.5739 (mt-10) REVERT: C 504 ILE cc_start: 0.5755 (OUTLIER) cc_final: 0.5435 (pp) REVERT: C 661 ARG cc_start: 0.5993 (mpt-90) cc_final: 0.5259 (ptm160) REVERT: C 674 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5675 (tpp) REVERT: C 675 ARG cc_start: 0.6032 (ptt180) cc_final: 0.5605 (tpm170) REVERT: C 751 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8161 (mm) outliers start: 38 outliers final: 22 residues processed: 171 average time/residue: 0.2009 time to fit residues: 46.9673 Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 729 SER 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 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 407 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL 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 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: 5.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.176547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154917 restraints weight = 12980.337| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.77 r_work: 0.3833 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8543 Z= 0.173 Angle : 0.614 11.654 11528 Z= 0.301 Chirality : 0.048 0.298 1284 Planarity : 0.004 0.057 1422 Dihedral : 7.610 65.422 1266 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.59 % Allowed : 28.41 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1044 helix: 0.51 (0.25), residues: 432 sheet: -0.49 (0.44), residues: 142 loop : -1.20 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 767 HIS 0.005 0.001 HIS B 412 PHE 0.012 0.001 PHE D 659 TYR 0.010 0.002 TYR D 424 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 321) hydrogen bonds : angle 4.79710 ( 948) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.54732 ( 8) covalent geometry : bond 0.00431 ( 8538) covalent geometry : angle 0.61335 (11520) Misc. bond : bond 0.01276 ( 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 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.975 Fit side-chains REVERT: A 485 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7501 (mtt-85) REVERT: A 661 ARG cc_start: 0.6231 (ptp-170) cc_final: 0.5892 (mpt-90) REVERT: A 751 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8399 (mm) REVERT: A 772 GLU cc_start: 0.5671 (tt0) cc_final: 0.4803 (tm-30) REVERT: B 414 MET cc_start: 0.3795 (ppp) cc_final: 0.3500 (ppp) REVERT: C 408 MET cc_start: 0.6269 (tpp) cc_final: 0.5816 (tpp) REVERT: C 504 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5415 (pp) REVERT: C 674 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5493 (tpp) REVERT: C 675 ARG cc_start: 0.6142 (ptt180) cc_final: 0.5648 (tpm170) REVERT: C 751 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8255 (mm) REVERT: C 772 GLU cc_start: 0.5544 (tt0) cc_final: 0.5054 (tt0) REVERT: D 412 HIS cc_start: 0.7082 (OUTLIER) cc_final: 0.6447 (p-80) REVERT: D 422 GLU cc_start: 0.6329 (mp0) cc_final: 0.4974 (mm-30) outliers start: 41 outliers final: 27 residues processed: 180 average time/residue: 0.2133 time to fit residues: 52.5358 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 503 MET 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 751 LEU Chi-restraints excluded: chain B residue 416 GLU 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 407 MET 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 681 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS 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: 0.0370 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.182040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.161037 restraints weight = 12933.290| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.75 r_work: 0.3912 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8543 Z= 0.098 Angle : 0.536 10.664 11528 Z= 0.261 Chirality : 0.045 0.273 1284 Planarity : 0.004 0.058 1422 Dihedral : 6.954 69.289 1266 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.91 % Allowed : 29.19 % Favored : 66.89 % 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: -0.35 (0.26), residues: 1044 helix: 0.80 (0.26), residues: 428 sheet: -0.55 (0.41), residues: 170 loop : -1.07 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.007 0.001 PHE D 495 TYR 0.009 0.001 TYR C 424 ARG 0.001 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02370 ( 321) hydrogen bonds : angle 4.60507 ( 948) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.83283 ( 8) covalent geometry : bond 0.00229 ( 8538) covalent geometry : angle 0.53573 (11520) Misc. bond : bond 0.00882 ( 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 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7400 (mtt-85) REVERT: A 661 ARG cc_start: 0.6222 (ptp-170) cc_final: 0.5826 (mpt-90) REVERT: A 751 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 414 MET cc_start: 0.3817 (ppp) cc_final: 0.3531 (ppp) REVERT: B 421 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: B 755 GLU cc_start: 0.6711 (mt-10) cc_final: 0.5586 (mt-10) REVERT: C 504 ILE cc_start: 0.5756 (OUTLIER) cc_final: 0.5435 (pp) REVERT: C 661 ARG cc_start: 0.6103 (mpt-90) cc_final: 0.5507 (ptm160) REVERT: C 674 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5734 (tpp) REVERT: C 675 ARG cc_start: 0.6052 (ptt180) cc_final: 0.5648 (tpm170) REVERT: C 708 MET cc_start: 0.7388 (ttp) cc_final: 0.6491 (tpt) REVERT: C 751 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8134 (mm) REVERT: D 422 GLU cc_start: 0.6175 (mp0) cc_final: 0.4944 (mm-30) outliers start: 35 outliers final: 23 residues processed: 180 average time/residue: 0.2070 time to fit residues: 50.5445 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 751 LEU 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 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 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 681 VAL Chi-restraints excluded: chain C residue 751 LEU 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 27 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.181882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.161129 restraints weight = 12701.985| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.70 r_work: 0.3911 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8543 Z= 0.107 Angle : 0.541 10.756 11528 Z= 0.264 Chirality : 0.045 0.243 1284 Planarity : 0.004 0.058 1422 Dihedral : 6.649 62.701 1266 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.80 % Allowed : 28.52 % Favored : 67.67 % 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: -0.30 (0.26), residues: 1044 helix: 0.85 (0.26), residues: 428 sheet: -0.26 (0.45), residues: 144 loop : -1.14 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 PHE 0.006 0.001 PHE A 667 TYR 0.009 0.001 TYR A 450 ARG 0.001 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02463 ( 321) hydrogen bonds : angle 4.57916 ( 948) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.93045 ( 8) covalent geometry : bond 0.00258 ( 8538) covalent geometry : angle 0.54075 (11520) Misc. bond : bond 0.00887 ( 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 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7466 (mtt-85) REVERT: A 661 ARG cc_start: 0.6170 (ptp-170) cc_final: 0.5802 (mpt-90) REVERT: A 748 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7646 (mp) REVERT: A 751 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8322 (mm) REVERT: B 414 MET cc_start: 0.3873 (ppp) cc_final: 0.3561 (ppp) REVERT: B 421 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: C 504 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5582 (pp) REVERT: C 674 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5651 (tpp) REVERT: C 675 ARG cc_start: 0.6016 (ptt180) cc_final: 0.5624 (tpm170) REVERT: C 708 MET cc_start: 0.7392 (ttp) cc_final: 0.6499 (tpt) REVERT: C 751 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8169 (mm) REVERT: D 486 GLU cc_start: 0.6711 (tt0) cc_final: 0.6475 (tt0) outliers start: 34 outliers final: 26 residues processed: 176 average time/residue: 0.2045 time to fit residues: 48.8956 Evaluate side-chains 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 674 MET 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 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 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 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 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: 1.9990 chunk 8 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.181642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160942 restraints weight = 12754.252| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.72 r_work: 0.3906 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8543 Z= 0.110 Angle : 0.541 10.552 11528 Z= 0.265 Chirality : 0.045 0.223 1284 Planarity : 0.004 0.058 1422 Dihedral : 6.554 67.598 1266 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.69 % Allowed : 28.75 % 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: -0.27 (0.26), residues: 1044 helix: 0.87 (0.26), residues: 428 sheet: -0.54 (0.41), residues: 170 loop : -1.01 (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 0.007 0.001 PHE D 495 TYR 0.011 0.001 TYR A 450 ARG 0.001 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02504 ( 321) hydrogen bonds : angle 4.56833 ( 948) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.99855 ( 8) covalent geometry : bond 0.00266 ( 8538) covalent geometry : angle 0.54081 (11520) Misc. bond : bond 0.00862 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.30 seconds wall clock time: 60 minutes 36.80 seconds (3636.80 seconds total)