Starting phenix.real_space_refine on Fri Aug 22 22:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqh_29388/08_2025/8fqh_29388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqh_29388/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fqh_29388/08_2025/8fqh_29388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqh_29388/08_2025/8fqh_29388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fqh_29388/08_2025/8fqh_29388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqh_29388/08_2025/8fqh_29388.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.23, per 1000 atoms: 0.27 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: 0.71 Conformation dependent library (CDL) restraints added in 434.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 18 sheets defined 42.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 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: 1.28 Time building geometry restraints manager: 0.93 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 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- 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 : 10.29 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (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 ARG 0.002 0.000 ARG D 684 TYR 0.018 0.001 TYR B 732 PHE 0.008 0.001 PHE D 495 TRP 0.007 0.001 TRP B 766 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.01463 ( 8538) covalent geometry : angle 0.76492 (11520) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.83566 ( 8) hydrogen bonds : bond 0.16280 ( 321) hydrogen bonds : angle 6.56755 ( 948) 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 : 0.210 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: 0.0848 time to fit residues: 17.8085 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 : 0.323 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.175006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152961 restraints weight = 12776.155| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.78 r_work: 0.3817 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 8543 Z= 0.276 Angle : 0.711 8.453 11528 Z= 0.354 Chirality : 0.051 0.208 1284 Planarity : 0.005 0.043 1422 Dihedral : 10.780 94.273 1268 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 5.15 % Allowed : 25.95 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.25), residues: 1044 helix: 0.09 (0.25), residues: 432 sheet: -0.64 (0.42), residues: 144 loop : -1.30 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 453 TYR 0.014 0.002 TYR A 405 PHE 0.016 0.002 PHE D 659 TRP 0.008 0.001 TRP D 671 HIS 0.007 0.002 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 8538) covalent geometry : angle 0.70979 (11520) SS BOND : bond 0.00504 ( 4) SS BOND : angle 1.55668 ( 8) hydrogen bonds : bond 0.04190 ( 321) hydrogen bonds : angle 5.30345 ( 948) Misc. bond : bond 0.01179 ( 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 194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.292 Fit side-chains REVERT: A 674 MET cc_start: 0.7004 (mpp) cc_final: 0.6457 (mpp) REVERT: A 742 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6369 (mt) REVERT: B 414 MET cc_start: 0.3867 (ppp) cc_final: 0.3620 (ppp) REVERT: C 674 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5480 (tpp) REVERT: C 675 ARG cc_start: 0.6218 (ptt180) cc_final: 0.5591 (tpm170) REVERT: C 751 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8337 (mm) REVERT: D 412 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6513 (p-80) outliers start: 46 outliers final: 23 residues processed: 179 average time/residue: 0.0840 time to fit residues: 20.9263 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 : 0.259 ------------------------------------------------------------------------------- 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 630 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.180831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159417 restraints weight = 12760.096| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.76 r_work: 0.3891 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8543 Z= 0.111 Angle : 0.535 7.878 11528 Z= 0.261 Chirality : 0.045 0.191 1284 Planarity : 0.004 0.052 1422 Dihedral : 9.340 88.847 1266 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.41 % Rotamer: Outliers : 3.36 % Allowed : 27.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.25), residues: 1044 helix: 0.57 (0.26), residues: 430 sheet: -0.58 (0.40), residues: 170 loop : -1.17 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 694 TYR 0.010 0.001 TYR B 732 PHE 0.008 0.001 PHE D 659 TRP 0.008 0.001 TRP B 766 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8538) covalent geometry : angle 0.53473 (11520) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.56353 ( 8) hydrogen bonds : bond 0.02791 ( 321) hydrogen bonds : angle 4.80769 ( 948) Misc. bond : bond 0.00628 ( 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 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7408 (mtt-85) REVERT: A 660 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7468 (mtt180) REVERT: A 708 MET cc_start: 0.7279 (ttp) cc_final: 0.6500 (tpt) REVERT: A 772 GLU cc_start: 0.5202 (tt0) cc_final: 0.4495 (tm-30) REVERT: B 414 MET cc_start: 0.3906 (ppp) cc_final: 0.3652 (ppp) REVERT: B 421 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 705 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: C 674 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5539 (tpp) REVERT: C 675 ARG cc_start: 0.6138 (ptt180) cc_final: 0.5544 (tpm170) REVERT: C 751 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8201 (mm) REVERT: D 422 GLU cc_start: 0.6197 (mp0) cc_final: 0.5914 (mp0) outliers start: 30 outliers final: 16 residues processed: 175 average time/residue: 0.0948 time to fit residues: 22.8345 Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN C 764 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152126 restraints weight = 12917.092| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.75 r_work: 0.3798 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2481 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= 0.239 Angle : 0.647 8.067 11528 Z= 0.321 Chirality : 0.049 0.203 1284 Planarity : 0.005 0.055 1422 Dihedral : 9.750 87.520 1266 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 5.48 % Allowed : 27.74 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.25), residues: 1044 helix: 0.17 (0.25), residues: 432 sheet: -0.61 (0.43), residues: 144 loop : -1.32 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 453 TYR 0.018 0.002 TYR A 700 PHE 0.013 0.002 PHE B 659 TRP 0.007 0.001 TRP D 671 HIS 0.006 0.002 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 8538) covalent geometry : angle 0.64645 (11520) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.17242 ( 8) hydrogen bonds : bond 0.03830 ( 321) hydrogen bonds : angle 5.07568 ( 948) Misc. bond : bond 0.01072 ( 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 197 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.342 Fit side-chains REVERT: A 485 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7554 (mtt-85) REVERT: A 674 MET cc_start: 0.7073 (mpp) cc_final: 0.6725 (mpp) REVERT: A 772 GLU cc_start: 0.5356 (tt0) cc_final: 0.4732 (tm-30) REVERT: B 414 MET cc_start: 0.4073 (ppp) cc_final: 0.3852 (ppp) REVERT: C 504 ILE cc_start: 0.5727 (OUTLIER) cc_final: 0.5427 (pp) REVERT: C 674 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5436 (tpp) REVERT: C 675 ARG cc_start: 0.6324 (ptt180) cc_final: 0.5729 (tpm170) REVERT: C 751 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8274 (mm) REVERT: D 412 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6563 (p-80) outliers start: 49 outliers final: 31 residues processed: 184 average time/residue: 0.0837 time to fit residues: 21.2543 Evaluate side-chains 178 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 769 ASP 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 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 639 LEU 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 12 optimal weight: 0.0060 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN C 714 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158518 restraints weight = 12831.251| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.75 r_work: 0.3882 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8543 Z= 0.105 Angle : 0.525 8.816 11528 Z= 0.258 Chirality : 0.044 0.175 1284 Planarity : 0.004 0.057 1422 Dihedral : 8.605 90.716 1266 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.03 % Allowed : 28.52 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1044 helix: 0.64 (0.26), residues: 430 sheet: -0.72 (0.40), residues: 170 loop : -1.16 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 660 TYR 0.013 0.001 TYR A 700 PHE 0.007 0.001 PHE D 659 TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8538) covalent geometry : angle 0.52414 (11520) SS BOND : bond 0.00096 ( 4) SS BOND : angle 1.41155 ( 8) hydrogen bonds : bond 0.02578 ( 321) hydrogen bonds : angle 4.67235 ( 948) Misc. bond : bond 0.00600 ( 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 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.287 Fit side-chains REVERT: A 485 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7489 (mtt-85) REVERT: A 661 ARG cc_start: 0.6247 (ptp-170) cc_final: 0.5818 (mpt-90) REVERT: A 674 MET cc_start: 0.7182 (mpp) cc_final: 0.6906 (mpp) REVERT: A 751 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 414 MET cc_start: 0.3840 (ppp) cc_final: 0.3638 (ppp) REVERT: B 421 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: C 396 VAL cc_start: 0.7791 (t) cc_final: 0.7580 (t) REVERT: C 504 ILE cc_start: 0.5695 (OUTLIER) cc_final: 0.5399 (pp) REVERT: C 674 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.5685 (tpp) REVERT: C 675 ARG cc_start: 0.6085 (ptt180) cc_final: 0.5605 (tpm170) REVERT: C 751 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8195 (mm) REVERT: D 422 GLU cc_start: 0.6266 (mp0) cc_final: 0.5807 (mp0) outliers start: 36 outliers final: 19 residues processed: 179 average time/residue: 0.0868 time to fit residues: 21.5704 Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 681 VAL 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 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 719 ASP 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 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 102 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 0.0070 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.180997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.159619 restraints weight = 12804.774| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.75 r_work: 0.3895 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8543 Z= 0.105 Angle : 0.533 9.173 11528 Z= 0.260 Chirality : 0.045 0.334 1284 Planarity : 0.004 0.057 1422 Dihedral : 7.843 72.465 1266 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.03 % Allowed : 28.75 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.26), residues: 1044 helix: 0.78 (0.26), residues: 430 sheet: -0.62 (0.40), residues: 170 loop : -1.09 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 485 TYR 0.009 0.001 TYR D 732 PHE 0.008 0.001 PHE D 659 TRP 0.007 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8538) covalent geometry : angle 0.53208 (11520) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.08896 ( 8) hydrogen bonds : bond 0.02551 ( 321) hydrogen bonds : angle 4.59169 ( 948) Misc. bond : bond 0.01087 ( 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 194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.6202 (ptp-170) cc_final: 0.5776 (mpt-90) REVERT: A 674 MET cc_start: 0.7165 (mpp) cc_final: 0.6909 (mpp) REVERT: A 751 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8366 (mt) REVERT: B 421 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: C 396 VAL cc_start: 0.7802 (t) cc_final: 0.7597 (t) REVERT: C 504 ILE cc_start: 0.5782 (OUTLIER) cc_final: 0.5460 (pp) REVERT: C 674 MET cc_start: 0.5866 (OUTLIER) cc_final: 0.5570 (tpp) REVERT: C 675 ARG cc_start: 0.6034 (ptt180) cc_final: 0.5599 (tpm170) REVERT: C 751 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8156 (mm) REVERT: D 422 GLU cc_start: 0.6293 (mp0) cc_final: 0.5740 (mp0) outliers start: 36 outliers final: 28 residues processed: 183 average time/residue: 0.0842 time to fit residues: 21.3828 Evaluate side-chains 178 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 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 719 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.173221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151260 restraints weight = 12979.231| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.75 r_work: 0.3789 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 8543 Z= 0.263 Angle : 0.696 13.412 11528 Z= 0.344 Chirality : 0.051 0.296 1284 Planarity : 0.005 0.057 1422 Dihedral : 8.001 68.610 1266 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 6.04 % Allowed : 27.85 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.25), residues: 1044 helix: 0.19 (0.25), residues: 432 sheet: -0.70 (0.43), residues: 142 loop : -1.35 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 453 TYR 0.016 0.002 TYR D 732 PHE 0.016 0.002 PHE B 659 TRP 0.008 0.001 TRP B 767 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 8538) covalent geometry : angle 0.69405 (11520) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.96471 ( 8) hydrogen bonds : bond 0.03866 ( 321) hydrogen bonds : angle 5.00423 ( 948) Misc. bond : bond 0.01456 ( 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 202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7522 (mtt-85) REVERT: A 661 ARG cc_start: 0.6206 (ptp-170) cc_final: 0.5762 (mpt-90) REVERT: A 674 MET cc_start: 0.7142 (mpp) cc_final: 0.6913 (mpp) REVERT: A 751 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 772 GLU cc_start: 0.5477 (tt0) cc_final: 0.4517 (tm-30) REVERT: B 412 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.5353 (p-80) REVERT: B 421 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 755 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6604 (mt-10) REVERT: C 396 VAL cc_start: 0.7907 (t) cc_final: 0.7682 (t) REVERT: C 504 ILE cc_start: 0.5676 (OUTLIER) cc_final: 0.5379 (pp) REVERT: C 674 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5446 (tpp) REVERT: C 675 ARG cc_start: 0.6224 (ptt180) cc_final: 0.5837 (tpm170) REVERT: C 751 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8284 (mm) REVERT: D 412 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6627 (p-80) REVERT: D 422 GLU cc_start: 0.6450 (mp0) cc_final: 0.5010 (mm-30) outliers start: 54 outliers final: 38 residues processed: 185 average time/residue: 0.0938 time to fit residues: 23.8871 Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 708 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 A residue 769 ASP Chi-restraints excluded: chain B residue 412 HIS 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 463 MET 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 B residue 772 GLU Chi-restraints excluded: chain C residue 398 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 502 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 681 VAL 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 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 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.179904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158648 restraints weight = 12816.118| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.75 r_work: 0.3875 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8543 Z= 0.110 Angle : 0.555 10.320 11528 Z= 0.272 Chirality : 0.046 0.259 1284 Planarity : 0.004 0.058 1422 Dihedral : 7.244 65.484 1266 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 4.81 % Allowed : 28.64 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.25), residues: 1044 helix: 0.60 (0.26), residues: 432 sheet: -0.62 (0.43), residues: 142 loop : -1.19 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 684 TYR 0.013 0.001 TYR D 732 PHE 0.007 0.001 PHE B 659 TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8538) covalent geometry : angle 0.55436 (11520) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.99336 ( 8) hydrogen bonds : bond 0.02588 ( 321) hydrogen bonds : angle 4.68404 ( 948) Misc. bond : bond 0.00926 ( 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 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7466 (mtt-85) REVERT: A 661 ARG cc_start: 0.6172 (ptp-170) cc_final: 0.5738 (mpt-90) REVERT: A 751 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 772 GLU cc_start: 0.5578 (tt0) cc_final: 0.4675 (tm-30) REVERT: B 421 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 626 VAL cc_start: 0.6719 (p) cc_final: 0.6469 (m) REVERT: B 755 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6509 (mt-10) REVERT: C 504 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.5392 (pp) REVERT: C 661 ARG cc_start: 0.6084 (mpt-90) cc_final: 0.5313 (ptm160) REVERT: C 674 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5669 (tpp) REVERT: C 675 ARG cc_start: 0.6079 (ptt180) cc_final: 0.5763 (tpm170) REVERT: C 751 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8178 (mm) REVERT: D 422 GLU cc_start: 0.6235 (mp0) cc_final: 0.5710 (mp0) outliers start: 43 outliers final: 26 residues processed: 175 average time/residue: 0.0969 time to fit residues: 23.5456 Evaluate side-chains 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 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 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 719 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.179059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158318 restraints weight = 12530.886| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.68 r_work: 0.3875 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2701 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= 0.120 Angle : 0.559 10.617 11528 Z= 0.273 Chirality : 0.046 0.236 1284 Planarity : 0.004 0.057 1422 Dihedral : 6.998 65.767 1266 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.93 % Rotamer: Outliers : 4.25 % Allowed : 29.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.25), residues: 1044 helix: 0.67 (0.26), residues: 432 sheet: -0.61 (0.44), residues: 142 loop : -1.16 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 660 TYR 0.011 0.001 TYR A 450 PHE 0.009 0.001 PHE B 659 TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8538) covalent geometry : angle 0.55883 (11520) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.00523 ( 8) hydrogen bonds : bond 0.02683 ( 321) hydrogen bonds : angle 4.63825 ( 948) Misc. bond : bond 0.00923 ( 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 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7436 (mtt-85) REVERT: A 661 ARG cc_start: 0.6219 (ptp-170) cc_final: 0.5788 (mpt-90) REVERT: A 751 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 772 GLU cc_start: 0.5618 (tt0) cc_final: 0.4789 (tm-30) REVERT: B 421 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: B 626 VAL cc_start: 0.6689 (p) cc_final: 0.6465 (m) REVERT: C 504 ILE cc_start: 0.5719 (OUTLIER) cc_final: 0.5395 (pp) REVERT: C 674 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5714 (tpp) REVERT: C 675 ARG cc_start: 0.6100 (ptt180) cc_final: 0.5740 (tpm170) REVERT: C 751 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8162 (mm) REVERT: D 422 GLU cc_start: 0.6248 (mp0) cc_final: 0.5035 (mm-30) outliers start: 38 outliers final: 29 residues processed: 175 average time/residue: 0.0799 time to fit residues: 19.5020 Evaluate side-chains 178 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 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 719 ASP Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 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 = 0.4220 r_free = 0.4220 target = 0.180565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159918 restraints weight = 12612.392| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.70 r_work: 0.3892 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8543 Z= 0.109 Angle : 0.544 11.177 11528 Z= 0.265 Chirality : 0.045 0.211 1284 Planarity : 0.004 0.057 1422 Dihedral : 6.679 67.938 1266 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.80 % Allowed : 29.87 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1044 helix: 0.77 (0.26), residues: 430 sheet: -0.56 (0.44), residues: 142 loop : -1.11 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.010 0.001 TYR A 450 PHE 0.008 0.001 PHE B 659 TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8538) covalent geometry : angle 0.54376 (11520) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.88592 ( 8) hydrogen bonds : bond 0.02536 ( 321) hydrogen bonds : angle 4.58252 ( 948) Misc. bond : bond 0.00817 ( 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 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7489 (mtt-85) REVERT: A 661 ARG cc_start: 0.6214 (ptp-170) cc_final: 0.5760 (mpt-90) REVERT: A 751 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8341 (mt) REVERT: B 421 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 626 VAL cc_start: 0.6753 (p) cc_final: 0.6543 (m) REVERT: C 504 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5423 (pp) REVERT: C 661 ARG cc_start: 0.6355 (mpt-90) cc_final: 0.5624 (ptm160) REVERT: C 674 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5762 (tpp) REVERT: C 675 ARG cc_start: 0.6088 (ptt180) cc_final: 0.5760 (tpm170) REVERT: C 751 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8161 (mm) REVERT: D 422 GLU cc_start: 0.6196 (mp0) cc_final: 0.5589 (mp0) outliers start: 34 outliers final: 26 residues processed: 178 average time/residue: 0.0880 time to fit residues: 21.8011 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 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 432 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.4442 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.178303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157128 restraints weight = 12755.468| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.73 r_work: 0.3861 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8543 Z= 0.141 Angle : 0.580 11.236 11528 Z= 0.284 Chirality : 0.046 0.204 1284 Planarity : 0.004 0.057 1422 Dihedral : 6.748 68.108 1266 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.25 % Allowed : 29.64 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.25), residues: 1044 helix: 0.66 (0.26), residues: 432 sheet: -0.52 (0.44), residues: 142 loop : -1.16 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.011 0.001 TYR A 450 PHE 0.010 0.001 PHE B 659 TRP 0.008 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8538) covalent geometry : angle 0.57901 (11520) SS BOND : bond 0.00204 ( 4) SS BOND : angle 1.16830 ( 8) hydrogen bonds : bond 0.02877 ( 321) hydrogen bonds : angle 4.65065 ( 948) Misc. bond : bond 0.00910 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.55 seconds wall clock time: 28 minutes 46.33 seconds (1726.33 seconds total)