Starting phenix.real_space_refine on Fri Aug 22 22:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqe_29385/08_2025/8fqe_29385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqe_29385/08_2025/8fqe_29385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fqe_29385/08_2025/8fqe_29385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqe_29385/08_2025/8fqe_29385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fqe_29385/08_2025/8fqe_29385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqe_29385/08_2025/8fqe_29385.map" } resolution = 3.14 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= 0.002 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 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 8386 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" 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} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.21 Number of scatterers: 8386 At special positions: 0 Unit cell: (118.755, 90.909, 84.357, 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 1602 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 356.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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 19 sheets defined 42.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.635A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.061A 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: 3.572A 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 488 removed outlier: 4.056A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.682A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.898A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.984A 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 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.899A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 705 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.504A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.808A 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 removed outlier: 3.628A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.578A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.705A 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 758 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.217A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 480 removed outlier: 9.619A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 480 removed outlier: 9.619A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.575A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.690A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.690A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.584A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 509 through 510 removed outlier: 3.716A pdb=" N ARG B 628 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.186A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.687A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 503 through 505 Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.560A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 475 through 480 removed outlier: 5.373A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 475 through 480 removed outlier: 5.373A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.695A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 332 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: 1.03 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2627 1.35 - 1.47: 2029 1.47 - 1.59: 3738 1.59 - 1.72: 40 1.72 - 1.84: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " 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 A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.575 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CYZ A1302 " pdb=" C6 CYZ A1302 " ideal model delta sigma weight residual 1.553 1.327 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11161 1.87 - 3.75: 253 3.75 - 5.62: 58 5.62 - 7.49: 29 7.49 - 9.36: 19 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C8 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" S1 CYZ A1302 " ideal model delta sigma weight residual 117.40 108.04 9.36 3.00e+00 1.11e-01 9.74e+00 angle pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sigma weight residual 117.40 108.44 8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.53 8.82 3.00e+00 1.11e-01 8.65e+00 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 109.69 8.66 3.00e+00 1.11e-01 8.34e+00 angle pdb=" C1 CYZ D1302 " pdb=" C6 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 102.82 111.01 -8.19 3.00e+00 1.11e-01 7.46e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 4710 23.65 - 47.31: 447 47.31 - 70.96: 59 70.96 - 94.61: 20 94.61 - 118.27: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: 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 93.00 178.40 -85.40 1 1.00e+01 1.00e-02 8.83e+01 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 -86.00 -155.20 69.20 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" N2 CYZ C1302 " pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sinusoidal sigma weight residual 55.73 -62.54 118.27 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1175 0.087 - 0.175: 93 0.175 - 0.262: 0 0.262 - 0.349: 2 0.349 - 0.437: 14 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.87 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" C2 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" C3 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 2.87 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO D 494 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 506 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 507 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 507 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 507 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 737 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.021 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 174 2.67 - 3.23: 7921 3.23 - 3.78: 13124 3.78 - 4.34: 17849 4.34 - 4.90: 29650 Nonbonded interactions: 68718 Sorted by model distance: nonbonded pdb=" OE2 GLU D 705 " pdb=" O HOH D1401 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.208 3.040 nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C1302 " model vdw 2.221 3.040 nonbonded pdb=" NE2 GLN B 642 " pdb=" O ILE B 645 " model vdw 2.231 3.120 ... (remaining 68713 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 through 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.400 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.243 8542 Z= 0.745 Angle : 0.830 9.365 11528 Z= 0.376 Chirality : 0.064 0.437 1284 Planarity : 0.004 0.050 1422 Dihedral : 18.706 118.268 3288 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 0.22 % Allowed : 25.28 % Favored : 74.50 % 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: -1.27 (0.25), residues: 1044 helix: 0.31 (0.26), residues: 404 sheet: -1.73 (0.39), residues: 164 loop : -1.47 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 715 TYR 0.017 0.002 TYR B 647 PHE 0.016 0.002 PHE C 495 TRP 0.012 0.002 TRP C 767 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.01514 ( 8538) covalent geometry : angle 0.82965 (11520) SS BOND : bond 0.00410 ( 4) SS BOND : angle 1.44355 ( 8) hydrogen bonds : bond 0.19076 ( 325) hydrogen bonds : angle 7.45413 ( 948) *********************** 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 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: B 415 LEU cc_start: 0.7066 (mt) cc_final: 0.6838 (mt) REVERT: C 453 ARG cc_start: 0.5405 (mtt90) cc_final: 0.5110 (mtt90) outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.0928 time to fit residues: 18.4020 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.193425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168841 restraints weight = 10985.828| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.48 r_work: 0.3969 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8542 Z= 0.197 Angle : 0.610 6.460 11528 Z= 0.308 Chirality : 0.046 0.156 1284 Planarity : 0.004 0.042 1422 Dihedral : 11.258 106.155 1267 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 3.47 % Allowed : 21.92 % Favored : 74.61 % 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: -1.29 (0.25), residues: 1044 helix: 0.29 (0.26), residues: 414 sheet: -1.75 (0.37), residues: 162 loop : -1.51 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 715 TYR 0.018 0.002 TYR D 647 PHE 0.011 0.002 PHE C 495 TRP 0.013 0.002 TRP D 460 HIS 0.002 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 8538) covalent geometry : angle 0.60959 (11520) SS BOND : bond 0.00256 ( 4) SS BOND : angle 1.12595 ( 8) hydrogen bonds : bond 0.04201 ( 325) hydrogen bonds : angle 5.50845 ( 948) *********************** 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 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.292 Fit side-chains REVERT: B 410 LYS cc_start: 0.7391 (mppt) cc_final: 0.7116 (pttm) REVERT: B 642 GLN cc_start: 0.8178 (pp30) cc_final: 0.7903 (pp30) outliers start: 31 outliers final: 19 residues processed: 162 average time/residue: 0.0889 time to fit residues: 20.1046 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.197534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.173751 restraints weight = 10941.785| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.49 r_work: 0.4014 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8542 Z= 0.103 Angle : 0.509 6.325 11528 Z= 0.252 Chirality : 0.042 0.137 1284 Planarity : 0.003 0.038 1422 Dihedral : 10.160 100.532 1266 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 23.27 % Favored : 74.16 % 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: -1.01 (0.25), residues: 1044 helix: 0.59 (0.25), residues: 426 sheet: -1.53 (0.40), residues: 142 loop : -1.54 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.020 0.001 TYR A 647 PHE 0.007 0.001 PHE D 495 TRP 0.012 0.001 TRP D 460 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8538) covalent geometry : angle 0.50840 (11520) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.76621 ( 8) hydrogen bonds : bond 0.02848 ( 325) hydrogen bonds : angle 4.90852 ( 948) *********************** 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 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.208 Fit side-chains REVERT: A 498 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8670 (pt) REVERT: A 705 GLU cc_start: 0.7745 (mm-30) cc_final: 0.6773 (mm-30) REVERT: B 414 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.5815 (mmp) REVERT: B 460 TRP cc_start: 0.7107 (m100) cc_final: 0.6712 (m100) REVERT: B 503 MET cc_start: 0.7311 (ttt) cc_final: 0.7007 (ttp) REVERT: B 642 GLN cc_start: 0.8168 (pp30) cc_final: 0.7687 (pp30) REVERT: C 408 MET cc_start: 0.3303 (OUTLIER) cc_final: 0.3084 (mtm) REVERT: D 642 GLN cc_start: 0.8164 (pp30) cc_final: 0.7857 (pp30) outliers start: 23 outliers final: 12 residues processed: 162 average time/residue: 0.0854 time to fit residues: 19.1336 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 6 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.197133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.173129 restraints weight = 11193.480| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.53 r_work: 0.4003 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.111 Angle : 0.512 6.371 11528 Z= 0.252 Chirality : 0.042 0.149 1284 Planarity : 0.003 0.036 1422 Dihedral : 10.126 101.085 1266 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.91 % Allowed : 23.15 % Favored : 73.94 % 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: -0.90 (0.25), residues: 1044 helix: 0.69 (0.25), residues: 426 sheet: -1.54 (0.39), residues: 142 loop : -1.47 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 715 TYR 0.010 0.001 TYR C 421 PHE 0.007 0.001 PHE B 495 TRP 0.010 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8538) covalent geometry : angle 0.51174 (11520) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.73315 ( 8) hydrogen bonds : bond 0.02808 ( 325) hydrogen bonds : angle 4.80113 ( 948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.339 Fit side-chains REVERT: A 498 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8662 (pt) REVERT: A 705 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 414 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.5829 (mmp) REVERT: B 460 TRP cc_start: 0.7087 (m100) cc_final: 0.6735 (m100) REVERT: B 642 GLN cc_start: 0.8102 (pp30) cc_final: 0.7851 (pp30) REVERT: D 642 GLN cc_start: 0.8161 (pp30) cc_final: 0.7907 (pp30) outliers start: 26 outliers final: 19 residues processed: 162 average time/residue: 0.0927 time to fit residues: 20.6460 Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.0040 chunk 82 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.197193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.173683 restraints weight = 11093.696| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.47 r_work: 0.4009 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.105 Angle : 0.504 6.321 11528 Z= 0.248 Chirality : 0.042 0.161 1284 Planarity : 0.003 0.035 1422 Dihedral : 9.899 99.896 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.24 % Allowed : 23.15 % Favored : 73.60 % 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: -0.77 (0.25), residues: 1044 helix: 0.78 (0.25), residues: 428 sheet: -1.43 (0.39), residues: 142 loop : -1.40 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 715 TYR 0.019 0.001 TYR A 647 PHE 0.007 0.001 PHE D 495 TRP 0.010 0.001 TRP D 460 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8538) covalent geometry : angle 0.50376 (11520) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.67206 ( 8) hydrogen bonds : bond 0.02689 ( 325) hydrogen bonds : angle 4.69857 ( 948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.336 Fit side-chains REVERT: A 498 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8667 (pt) REVERT: A 705 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 414 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.5844 (mmp) REVERT: B 435 HIS cc_start: 0.6253 (t-90) cc_final: 0.6007 (t-90) REVERT: B 460 TRP cc_start: 0.7069 (m100) cc_final: 0.6748 (m100) REVERT: B 503 MET cc_start: 0.7295 (ttt) cc_final: 0.6988 (ttp) REVERT: B 642 GLN cc_start: 0.8134 (pp30) cc_final: 0.7647 (pp30) REVERT: C 408 MET cc_start: 0.3177 (OUTLIER) cc_final: 0.2929 (mtm) REVERT: D 642 GLN cc_start: 0.8129 (pp30) cc_final: 0.7812 (pp30) outliers start: 29 outliers final: 21 residues processed: 165 average time/residue: 0.0896 time to fit residues: 20.4309 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 16 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.199047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.175762 restraints weight = 10980.093| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.44 r_work: 0.4035 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8542 Z= 0.094 Angle : 0.504 6.881 11528 Z= 0.247 Chirality : 0.042 0.189 1284 Planarity : 0.003 0.034 1422 Dihedral : 9.292 97.433 1266 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.80 % Allowed : 23.60 % Favored : 73.60 % 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: -0.63 (0.25), residues: 1044 helix: 0.85 (0.25), residues: 434 sheet: -1.22 (0.42), residues: 128 loop : -1.36 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 453 TYR 0.011 0.001 TYR C 421 PHE 0.007 0.001 PHE D 495 TRP 0.010 0.001 TRP D 460 HIS 0.002 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8538) covalent geometry : angle 0.50371 (11520) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.58815 ( 8) hydrogen bonds : bond 0.02434 ( 325) hydrogen bonds : angle 4.55423 ( 948) *********************** 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 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.357 Fit side-chains REVERT: A 498 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8666 (pt) REVERT: A 705 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6751 (mm-30) REVERT: B 414 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.5884 (mmp) REVERT: B 435 HIS cc_start: 0.6180 (t-90) cc_final: 0.5910 (t-90) REVERT: B 460 TRP cc_start: 0.7028 (m100) cc_final: 0.6716 (m100) REVERT: B 629 MET cc_start: 0.5206 (tmm) cc_final: 0.4932 (ppp) REVERT: B 642 GLN cc_start: 0.8119 (pp30) cc_final: 0.7627 (pp30) REVERT: B 765 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6836 (ttpt) REVERT: C 408 MET cc_start: 0.3264 (OUTLIER) cc_final: 0.2985 (mtm) REVERT: C 421 TYR cc_start: 0.7251 (m-80) cc_final: 0.6955 (m-80) REVERT: D 642 GLN cc_start: 0.8090 (pp30) cc_final: 0.7798 (pp30) REVERT: D 772 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6482 (tm-30) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.0903 time to fit residues: 20.4010 Evaluate side-chains 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 0.0020 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.200863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.177444 restraints weight = 11181.870| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.48 r_work: 0.4058 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.088 Angle : 0.505 7.360 11528 Z= 0.244 Chirality : 0.041 0.238 1284 Planarity : 0.003 0.034 1422 Dihedral : 8.410 94.946 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.80 % Allowed : 24.05 % Favored : 73.15 % 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: -0.47 (0.25), residues: 1044 helix: 1.03 (0.25), residues: 434 sheet: -1.15 (0.42), residues: 128 loop : -1.31 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 453 TYR 0.014 0.001 TYR C 647 PHE 0.008 0.001 PHE B 495 TRP 0.009 0.001 TRP D 460 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8538) covalent geometry : angle 0.50480 (11520) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.69538 ( 8) hydrogen bonds : bond 0.02227 ( 325) hydrogen bonds : angle 4.46692 ( 948) *********************** 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 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.309 Fit side-chains REVERT: A 498 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8684 (pt) REVERT: A 705 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6784 (mm-30) REVERT: B 435 HIS cc_start: 0.6187 (t-90) cc_final: 0.5917 (t-90) REVERT: B 460 TRP cc_start: 0.6932 (m100) cc_final: 0.6616 (m100) REVERT: B 642 GLN cc_start: 0.8078 (pp30) cc_final: 0.7566 (pp30) REVERT: B 765 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6892 (ttpt) REVERT: C 408 MET cc_start: 0.3270 (OUTLIER) cc_final: 0.2964 (mtm) REVERT: C 421 TYR cc_start: 0.7325 (m-80) cc_final: 0.7011 (m-80) REVERT: C 634 GLU cc_start: 0.6400 (tp30) cc_final: 0.6004 (tp30) REVERT: D 642 GLN cc_start: 0.8041 (pp30) cc_final: 0.7748 (pp30) REVERT: D 772 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6493 (tm-30) outliers start: 25 outliers final: 16 residues processed: 169 average time/residue: 0.0950 time to fit residues: 21.9371 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.198524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.174730 restraints weight = 10990.651| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.47 r_work: 0.4029 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8542 Z= 0.109 Angle : 0.526 8.410 11528 Z= 0.255 Chirality : 0.043 0.257 1284 Planarity : 0.003 0.034 1422 Dihedral : 8.548 98.425 1266 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.80 % Allowed : 24.16 % Favored : 73.04 % 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: -0.48 (0.25), residues: 1044 helix: 0.99 (0.25), residues: 434 sheet: -1.13 (0.42), residues: 128 loop : -1.30 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 715 TYR 0.012 0.001 TYR C 421 PHE 0.007 0.001 PHE B 495 TRP 0.008 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8538) covalent geometry : angle 0.52536 (11520) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.75029 ( 8) hydrogen bonds : bond 0.02527 ( 325) hydrogen bonds : angle 4.54875 ( 948) *********************** 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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.334 Fit side-chains REVERT: A 498 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8689 (pt) REVERT: A 705 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6760 (mm-30) REVERT: B 435 HIS cc_start: 0.6201 (t-90) cc_final: 0.5934 (t-90) REVERT: B 460 TRP cc_start: 0.7028 (m100) cc_final: 0.6718 (m100) REVERT: B 642 GLN cc_start: 0.8121 (pp30) cc_final: 0.7831 (pp30) REVERT: B 765 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6898 (ttpt) REVERT: C 408 MET cc_start: 0.3233 (OUTLIER) cc_final: 0.2932 (mtm) REVERT: D 642 GLN cc_start: 0.8120 (pp30) cc_final: 0.7915 (pp30) REVERT: D 772 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6508 (tm-30) outliers start: 25 outliers final: 21 residues processed: 156 average time/residue: 0.0922 time to fit residues: 20.0284 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 59 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.199566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.175686 restraints weight = 11092.085| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.49 r_work: 0.4034 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8542 Z= 0.098 Angle : 0.520 7.879 11528 Z= 0.253 Chirality : 0.042 0.246 1284 Planarity : 0.003 0.034 1422 Dihedral : 8.182 96.498 1266 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.57 % Allowed : 24.61 % Favored : 72.82 % 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: -0.42 (0.25), residues: 1044 helix: 1.03 (0.25), residues: 434 sheet: -1.14 (0.43), residues: 128 loop : -1.24 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 715 TYR 0.013 0.001 TYR C 421 PHE 0.007 0.001 PHE C 495 TRP 0.009 0.001 TRP D 460 HIS 0.002 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8538) covalent geometry : angle 0.51936 (11520) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.72262 ( 8) hydrogen bonds : bond 0.02432 ( 325) hydrogen bonds : angle 4.52144 ( 948) *********************** 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 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7278 (m-80) cc_final: 0.6895 (m-80) REVERT: A 498 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8689 (pt) REVERT: A 674 MET cc_start: 0.6585 (mtm) cc_final: 0.6376 (mtm) REVERT: A 705 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6769 (mm-30) REVERT: B 435 HIS cc_start: 0.6161 (t-90) cc_final: 0.5917 (t-90) REVERT: B 460 TRP cc_start: 0.6974 (m100) cc_final: 0.6676 (m100) REVERT: B 503 MET cc_start: 0.7318 (ttm) cc_final: 0.7040 (ttp) REVERT: B 642 GLN cc_start: 0.8119 (pp30) cc_final: 0.7821 (pp30) REVERT: B 765 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6870 (ttpt) REVERT: C 408 MET cc_start: 0.3352 (mtt) cc_final: 0.3001 (mtm) REVERT: C 421 TYR cc_start: 0.7269 (m-80) cc_final: 0.6983 (m-80) REVERT: D 642 GLN cc_start: 0.8084 (pp30) cc_final: 0.7850 (pp30) REVERT: D 772 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6510 (tm-30) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.0904 time to fit residues: 20.2071 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 chunk 84 optimal weight: 0.0010 chunk 79 optimal weight: 3.9990 overall best weight: 0.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.199541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.175799 restraints weight = 11073.521| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.48 r_work: 0.4037 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8542 Z= 0.099 Angle : 0.520 7.780 11528 Z= 0.254 Chirality : 0.042 0.225 1284 Planarity : 0.003 0.034 1422 Dihedral : 8.018 96.518 1266 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.57 % Allowed : 24.83 % Favored : 72.60 % 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: 1.04 (0.25), residues: 434 sheet: -1.17 (0.42), residues: 128 loop : -1.22 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.013 0.001 TYR C 647 PHE 0.006 0.001 PHE B 495 TRP 0.009 0.001 TRP D 460 HIS 0.002 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8538) covalent geometry : angle 0.52016 (11520) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.70383 ( 8) hydrogen bonds : bond 0.02446 ( 325) hydrogen bonds : angle 4.51281 ( 948) ********************** 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 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7270 (m-80) cc_final: 0.6949 (m-80) REVERT: A 498 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8694 (pt) REVERT: A 705 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 435 HIS cc_start: 0.6198 (t-90) cc_final: 0.5954 (t-90) REVERT: B 460 TRP cc_start: 0.6972 (m100) cc_final: 0.6676 (m100) REVERT: B 503 MET cc_start: 0.7331 (ttm) cc_final: 0.7005 (ttp) REVERT: B 642 GLN cc_start: 0.8120 (pp30) cc_final: 0.7852 (pp30) REVERT: B 765 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6874 (ttpt) REVERT: C 408 MET cc_start: 0.3365 (mtt) cc_final: 0.3023 (mtm) REVERT: D 772 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6510 (tm-30) outliers start: 23 outliers final: 20 residues processed: 156 average time/residue: 0.0941 time to fit residues: 20.4589 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 57 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 0.0670 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.198212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.174241 restraints weight = 11140.985| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.50 r_work: 0.4013 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8542 Z= 0.112 Angle : 0.530 7.519 11528 Z= 0.261 Chirality : 0.043 0.218 1284 Planarity : 0.003 0.034 1422 Dihedral : 8.217 98.362 1266 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.68 % Allowed : 24.94 % Favored : 72.37 % 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: -0.47 (0.25), residues: 1044 helix: 0.96 (0.25), residues: 434 sheet: -1.01 (0.44), residues: 118 loop : -1.30 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.015 0.001 TYR C 421 PHE 0.007 0.001 PHE C 495 TRP 0.021 0.001 TRP D 671 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8538) covalent geometry : angle 0.53020 (11520) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.74662 ( 8) hydrogen bonds : bond 0.02657 ( 325) hydrogen bonds : angle 4.58400 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1958.50 seconds wall clock time: 34 minutes 27.27 seconds (2067.27 seconds total)