Starting phenix.real_space_refine on Sat Feb 7 16:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ooi_17016/02_2026/8ooi_17016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooi_17016/02_2026/8ooi_17016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ooi_17016/02_2026/8ooi_17016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooi_17016/02_2026/8ooi_17016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ooi_17016/02_2026/8ooi_17016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooi_17016/02_2026/8ooi_17016.map" } resolution = 2.61 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= 0.001 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 P 42 5.49 5 Mg 18 5.21 5 S 180 5.16 5 C 21966 2.51 5 N 6210 2.21 5 O 6834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35256 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "F" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "B" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "D" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "C" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "E" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "A" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "F" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "B" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "D" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "C" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "E" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AHIS A 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 384 " occ=0.50 residue: pdb=" N AHIS F 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 384 " occ=0.50 residue: pdb=" N AHIS B 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 384 " occ=0.50 residue: pdb=" N AHIS D 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 384 " occ=0.50 residue: pdb=" N AHIS C 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 384 " occ=0.50 residue: pdb=" N AHIS E 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 384 " occ=0.50 residue: pdb="MG A MG A 904 " occ=0.50 pdb="MG B MG A 904 " occ=0.50 residue: pdb=" O1 APO4 A 906 " occ=0.50 ... (8 atoms not shown) pdb=" P BPO4 A 906 " occ=0.50 residue: pdb=" O1 APO4 F 901 " occ=0.50 ... (8 atoms not shown) pdb=" P BPO4 F 901 " occ=0.50 residue: pdb="MG A MG F 905 " occ=0.50 pdb="MG B MG F 905 " occ=0.50 residue: pdb="MG A MG B 904 " occ=0.50 pdb="MG B MG B 904 " occ=0.50 residue: pdb=" O1 APO4 B 906 " occ=0.50 ... (8 atoms not shown) pdb=" P BPO4 B 906 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 14.59, per 1000 atoms: 0.41 Number of scatterers: 35256 At special positions: 0 Unit cell: (170.64, 177.84, 100.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 6 19.00 S 180 16.00 P 42 15.00 Mg 18 11.99 O 6834 8.00 N 6210 7.00 C 21966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 695 " distance=2.06 Simple disulfide: pdb=" SG CYS F 691 " - pdb=" SG CYS F 695 " distance=2.06 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 695 " distance=2.06 Simple disulfide: pdb=" SG CYS D 691 " - pdb=" SG CYS D 695 " distance=2.06 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 695 " distance=2.06 Simple disulfide: pdb=" SG CYS E 691 " - pdb=" SG CYS E 695 " distance=2.06 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: 3.60 Conformation dependent library (CDL) restraints added in 3.1 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 36 sheets defined 46.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.683A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.557A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.452A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.838A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.755A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.616A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.698A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.716A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.542A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.854A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.549A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.769A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 710 removed outlier: 3.799A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 748 through 764 Processing helix chain 'F' and resid 42 through 48 removed outlier: 3.683A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 134 through 140 removed outlier: 3.558A pdb=" N TYR F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.452A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.838A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.755A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.616A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 444 removed outlier: 3.697A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.716A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 493 through 499 Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.542A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 554 Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.854A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.550A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.769A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 710 removed outlier: 3.800A pdb=" N LYS F 696 " --> pdb=" O GLN F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 Processing helix chain 'F' and resid 748 through 764 Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.684A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.557A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.452A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.839A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.754A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.616A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.698A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.716A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.543A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.855A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.549A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.768A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 710 removed outlier: 3.799A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 748 through 764 Processing helix chain 'D' and resid 42 through 48 removed outlier: 3.683A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.557A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.452A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.838A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.754A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.615A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.698A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.716A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.542A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.854A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.549A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.769A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 710 removed outlier: 3.799A pdb=" N LYS D 696 " --> pdb=" O GLN D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 748 through 764 Processing helix chain 'C' and resid 42 through 48 removed outlier: 3.683A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.558A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.452A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.839A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.755A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.617A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.698A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.716A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.542A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.855A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.549A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.769A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 710 removed outlier: 3.799A pdb=" N LYS C 696 " --> pdb=" O GLN C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 748 through 764 Processing helix chain 'E' and resid 42 through 48 removed outlier: 3.683A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 134 through 140 removed outlier: 3.557A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.452A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.840A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.755A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.615A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 444 removed outlier: 3.698A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.716A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 493 through 499 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.542A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 554 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.854A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.550A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.768A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 710 removed outlier: 3.799A pdb=" N LYS E 696 " --> pdb=" O GLN E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 741 Processing helix chain 'E' and resid 748 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 84 removed outlier: 5.685A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 118 removed outlier: 7.082A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.242A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.638A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 81 through 84 removed outlier: 5.685A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 41 Processing sheet with id=AA9, first strand: chain 'F' and resid 115 through 118 removed outlier: 7.083A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.242A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.638A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 81 through 84 removed outlier: 5.685A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.083A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.242A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.639A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 84 removed outlier: 5.685A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AC3, first strand: chain 'D' and resid 115 through 118 removed outlier: 7.083A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.242A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.638A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 81 through 84 removed outlier: 5.685A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 38 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 118 removed outlier: 7.082A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.242A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.638A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 81 through 84 removed outlier: 5.685A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 38 through 41 Processing sheet with id=AD6, first strand: chain 'E' and resid 115 through 118 removed outlier: 7.082A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.242A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.638A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) 1494 hydrogen bonds defined for protein. 4272 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: 8.08 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12060 1.36 - 1.49: 8150 1.49 - 1.63: 15202 1.63 - 1.77: 6 1.77 - 1.91: 282 Bond restraints: 35700 Sorted by residual: bond pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.27e-02 6.20e+03 1.54e+01 bond pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.27e-02 6.20e+03 1.53e+01 bond pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta sigma weight residual 1.528 1.478 0.049 1.27e-02 6.20e+03 1.52e+01 bond pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 1.528 1.478 0.049 1.27e-02 6.20e+03 1.52e+01 bond pdb=" CA ARG D 349 " pdb=" CB ARG D 349 " ideal model delta sigma weight residual 1.528 1.478 0.049 1.27e-02 6.20e+03 1.52e+01 ... (remaining 35695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 46985 1.91 - 3.82: 1066 3.82 - 5.73: 195 5.73 - 7.64: 18 7.64 - 9.55: 18 Bond angle restraints: 48282 Sorted by residual: angle pdb=" N ASN E 348 " pdb=" CA ASN E 348 " pdb=" C ASN E 348 " ideal model delta sigma weight residual 113.17 103.62 9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N ASN F 348 " pdb=" CA ASN F 348 " pdb=" C ASN F 348 " ideal model delta sigma weight residual 113.17 103.63 9.54 1.26e+00 6.30e-01 5.74e+01 angle pdb=" N ASN B 348 " pdb=" CA ASN B 348 " pdb=" C ASN B 348 " ideal model delta sigma weight residual 113.17 103.63 9.54 1.26e+00 6.30e-01 5.73e+01 angle pdb=" N ASN D 348 " pdb=" CA ASN D 348 " pdb=" C ASN D 348 " ideal model delta sigma weight residual 113.17 103.68 9.49 1.26e+00 6.30e-01 5.67e+01 angle pdb=" N ASN A 348 " pdb=" CA ASN A 348 " pdb=" C ASN A 348 " ideal model delta sigma weight residual 113.17 103.69 9.48 1.26e+00 6.30e-01 5.66e+01 ... (remaining 48277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 21480 33.37 - 66.75: 648 66.75 - 100.12: 54 100.12 - 133.50: 12 133.50 - 166.87: 6 Dihedral angle restraints: 22200 sinusoidal: 9474 harmonic: 12726 Sorted by residual: dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 106.88 -166.87 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP B 901 " pdb=" O5' ADP B 901 " pdb=" PA ADP B 901 " pdb=" O2A ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 106.84 -166.84 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 106.84 -166.83 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 22197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4386 0.058 - 0.116: 862 0.116 - 0.174: 122 0.174 - 0.232: 0 0.232 - 0.290: 12 Chirality restraints: 5382 Sorted by residual: chirality pdb=" CA SER F 352 " pdb=" N SER F 352 " pdb=" C SER F 352 " pdb=" CB SER F 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA SER D 352 " pdb=" N SER D 352 " pdb=" C SER D 352 " pdb=" CB SER D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5379 not shown) Planarity restraints: 6324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO C 298 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 298 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 297 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO E 298 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " 0.034 5.00e-02 4.00e+02 ... (remaining 6321 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.23: 22 2.23 - 2.96: 16395 2.96 - 3.68: 63809 3.68 - 4.41: 106418 4.41 - 5.14: 172100 Nonbonded interactions: 358744 Sorted by model distance: nonbonded pdb=" SD MET A 427 " pdb=" OE2 GLU F 221 " model vdw 1.501 3.400 nonbonded pdb=" SD MET F 427 " pdb=" OE2 GLU E 221 " model vdw 1.501 3.400 nonbonded pdb=" SD MET D 427 " pdb=" OE2 GLU C 221 " model vdw 1.507 3.400 nonbonded pdb=" OE2 GLU B 221 " pdb=" SD MET C 427 " model vdw 1.534 3.400 nonbonded pdb=" OE2 GLU A 221 " pdb=" SD MET B 427 " model vdw 1.630 3.400 ... (remaining 358739 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'B' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'C' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'D' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'E' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'F' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) } 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=0.50 max=1.00 mean=0.99 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: 2.940 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 44.510 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.005 0.098 35706 Z= 0.260 Angle : 0.711 9.553 48294 Z= 0.385 Chirality : 0.048 0.290 5382 Planarity : 0.005 0.062 6324 Dihedral : 15.387 166.872 13938 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.53 % Favored : 95.05 % Rotamer: Outliers : 0.16 % Allowed : 11.66 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.61 (0.13), residues: 4398 helix: 0.23 (0.12), residues: 1908 sheet: -0.33 (0.21), residues: 576 loop : -0.99 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 453 TYR 0.024 0.002 TYR C 244 PHE 0.009 0.001 PHE D 736 TRP 0.024 0.003 TRP B 454 HIS 0.004 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00528 (35700) covalent geometry : angle 0.70392 (48282) SS BOND : bond 0.02593 ( 6) SS BOND : angle 6.41444 ( 12) hydrogen bonds : bond 0.13852 ( 1494) hydrogen bonds : angle 6.29947 ( 4272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7243 (mm) cc_final: 0.6857 (mp) REVERT: A 388 MET cc_start: 0.7640 (mtp) cc_final: 0.7310 (mtt) REVERT: A 670 VAL cc_start: 0.6916 (m) cc_final: 0.6712 (t) REVERT: F 26 LEU cc_start: 0.7050 (mm) cc_final: 0.6630 (mp) REVERT: F 388 MET cc_start: 0.7490 (mtp) cc_final: 0.7224 (mtt) REVERT: F 670 VAL cc_start: 0.6991 (m) cc_final: 0.6759 (t) REVERT: F 700 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7202 (ttp-170) REVERT: B 26 LEU cc_start: 0.7202 (mm) cc_final: 0.6892 (mp) REVERT: B 45 LYS cc_start: 0.5897 (tppt) cc_final: 0.5600 (tmtt) REVERT: B 288 LYS cc_start: 0.8267 (ttmp) cc_final: 0.8050 (tmmt) REVERT: B 388 MET cc_start: 0.7702 (mtp) cc_final: 0.7441 (mtt) REVERT: B 670 VAL cc_start: 0.6970 (m) cc_final: 0.6725 (t) REVERT: D 26 LEU cc_start: 0.7217 (mm) cc_final: 0.6903 (mp) REVERT: D 388 MET cc_start: 0.7733 (mtp) cc_final: 0.7396 (mtt) REVERT: C 26 LEU cc_start: 0.7137 (mm) cc_final: 0.6806 (mp) REVERT: C 388 MET cc_start: 0.7554 (mtp) cc_final: 0.7309 (mtt) REVERT: E 26 LEU cc_start: 0.7101 (mm) cc_final: 0.6749 (mp) REVERT: E 45 LYS cc_start: 0.5943 (tppt) cc_final: 0.5594 (tmtt) REVERT: E 63 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6964 (tppp) REVERT: E 288 LYS cc_start: 0.8279 (ttmp) cc_final: 0.8063 (tmmt) REVERT: E 388 MET cc_start: 0.7763 (mtp) cc_final: 0.7487 (mtt) REVERT: E 670 VAL cc_start: 0.6888 (m) cc_final: 0.6677 (t) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.7901 time to fit residues: 549.3535 Evaluate side-chains 396 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.0370 chunk 424 optimal weight: 4.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN F 351 ASN F 760 GLN B 404 HIS D 351 ASN C 351 ASN E 404 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.142067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109499 restraints weight = 160060.046| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.81 r_work: 0.3351 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 35706 Z= 0.175 Angle : 0.666 9.524 48294 Z= 0.340 Chirality : 0.046 0.151 5382 Planarity : 0.005 0.061 6324 Dihedral : 11.312 173.396 5094 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.56 % Favored : 94.16 % Rotamer: Outliers : 3.27 % Allowed : 15.63 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.39 (0.13), residues: 4398 helix: 0.49 (0.12), residues: 1944 sheet: -0.94 (0.18), residues: 750 loop : -0.64 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.009 0.002 TYR D 203 PHE 0.012 0.001 PHE B 163 TRP 0.021 0.002 TRP F 454 HIS 0.006 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00404 (35700) covalent geometry : angle 0.65935 (48282) SS BOND : bond 0.02515 ( 6) SS BOND : angle 5.85317 ( 12) hydrogen bonds : bond 0.04492 ( 1494) hydrogen bonds : angle 5.08037 ( 4272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 446 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7516 (mm) cc_final: 0.7128 (mp) REVERT: A 291 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: F 60 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6562 (mtmm) REVERT: F 268 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8684 (tt) REVERT: F 495 TYR cc_start: 0.8552 (m-10) cc_final: 0.8336 (m-10) REVERT: F 670 VAL cc_start: 0.6920 (m) cc_final: 0.6688 (t) REVERT: F 738 GLU cc_start: 0.7684 (tt0) cc_final: 0.7316 (tt0) REVERT: B 26 LEU cc_start: 0.7624 (mm) cc_final: 0.7228 (mt) REVERT: B 46 MET cc_start: 0.6615 (mtt) cc_final: 0.6274 (mtt) REVERT: B 268 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8803 (tt) REVERT: B 288 LYS cc_start: 0.8410 (ttmp) cc_final: 0.8000 (tmmt) REVERT: B 291 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: B 511 SER cc_start: 0.8586 (p) cc_final: 0.8333 (m) REVERT: D 26 LEU cc_start: 0.7548 (mm) cc_final: 0.7156 (mp) REVERT: D 291 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: C 26 LEU cc_start: 0.7602 (mm) cc_final: 0.7230 (mt) REVERT: C 60 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6662 (mtmm) REVERT: C 236 LYS cc_start: 0.7444 (mmmt) cc_final: 0.7173 (tttm) REVERT: C 268 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8657 (tt) REVERT: C 700 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7582 (ttp-170) REVERT: C 738 GLU cc_start: 0.7674 (tt0) cc_final: 0.7296 (tt0) REVERT: E 26 LEU cc_start: 0.7550 (mm) cc_final: 0.7125 (mt) REVERT: E 268 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8822 (tt) REVERT: E 288 LYS cc_start: 0.8390 (ttmp) cc_final: 0.7992 (tmmt) REVERT: E 335 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6641 (mt) REVERT: E 358 ARG cc_start: 0.8615 (mtp85) cc_final: 0.8363 (mtp85) REVERT: E 511 SER cc_start: 0.8644 (p) cc_final: 0.8388 (m) outliers start: 117 outliers final: 52 residues processed: 526 average time/residue: 0.7894 time to fit residues: 493.3352 Evaluate side-chains 431 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 368 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 180 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 430 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 HIS C 226 HIS E 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.140043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109368 restraints weight = 161402.220| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.82 r_work: 0.3310 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 35706 Z= 0.198 Angle : 0.669 9.108 48294 Z= 0.339 Chirality : 0.046 0.241 5382 Planarity : 0.005 0.058 6324 Dihedral : 11.280 179.627 5094 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.43 % Favored : 94.30 % Rotamer: Outliers : 3.04 % Allowed : 17.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.33 (0.13), residues: 4398 helix: 0.67 (0.12), residues: 1902 sheet: -0.98 (0.19), residues: 702 loop : -0.74 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 753 TYR 0.016 0.002 TYR B 203 PHE 0.013 0.002 PHE D 736 TRP 0.013 0.002 TRP E 454 HIS 0.005 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00472 (35700) covalent geometry : angle 0.66201 (48282) SS BOND : bond 0.02656 ( 6) SS BOND : angle 6.10752 ( 12) hydrogen bonds : bond 0.04582 ( 1494) hydrogen bonds : angle 4.97157 ( 4272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 397 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7560 (mm) cc_final: 0.7237 (mp) REVERT: A 148 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7537 (mmtt) REVERT: A 291 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 294 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6673 (tm-30) REVERT: A 364 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: A 388 MET cc_start: 0.6542 (mtt) cc_final: 0.6170 (mtp) REVERT: F 60 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6593 (mtmm) REVERT: F 268 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8669 (tt) REVERT: F 388 MET cc_start: 0.6572 (mtt) cc_final: 0.6274 (mtp) REVERT: F 670 VAL cc_start: 0.6935 (m) cc_final: 0.6683 (t) REVERT: F 738 GLU cc_start: 0.7688 (tt0) cc_final: 0.7272 (tt0) REVERT: B 26 LEU cc_start: 0.7704 (mm) cc_final: 0.7304 (mt) REVERT: B 268 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8800 (tt) REVERT: B 288 LYS cc_start: 0.8351 (ttmp) cc_final: 0.7954 (tmmt) REVERT: B 511 SER cc_start: 0.8623 (p) cc_final: 0.8374 (m) REVERT: B 670 VAL cc_start: 0.6927 (m) cc_final: 0.6688 (t) REVERT: D 26 LEU cc_start: 0.7564 (mm) cc_final: 0.7214 (mp) REVERT: D 120 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7201 (p0) REVERT: D 132 GLU cc_start: 0.7213 (mp0) cc_final: 0.6966 (mm-30) REVERT: D 148 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7547 (mmtt) REVERT: D 291 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: D 364 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: D 511 SER cc_start: 0.8653 (p) cc_final: 0.8435 (m) REVERT: C 26 LEU cc_start: 0.7549 (mm) cc_final: 0.7175 (mt) REVERT: C 60 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6645 (mtmm) REVERT: C 236 LYS cc_start: 0.7386 (mmmt) cc_final: 0.7157 (tttm) REVERT: C 268 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8634 (tt) REVERT: C 388 MET cc_start: 0.6664 (mtt) cc_final: 0.6348 (mtp) REVERT: C 700 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7504 (ttp-170) REVERT: C 738 GLU cc_start: 0.7650 (tt0) cc_final: 0.7265 (tt0) REVERT: E 268 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8806 (tt) REVERT: E 288 LYS cc_start: 0.8366 (ttmp) cc_final: 0.7966 (tmmt) REVERT: E 295 LYS cc_start: 0.7537 (mtmm) cc_final: 0.7299 (mmtm) REVERT: E 335 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6594 (mt) REVERT: E 511 SER cc_start: 0.8656 (p) cc_final: 0.8401 (m) outliers start: 108 outliers final: 74 residues processed: 479 average time/residue: 0.7789 time to fit residues: 443.2418 Evaluate side-chains 449 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 360 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 613 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 391 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 289 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 349 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN F 36 ASN F 85 ASN F 296 ASN F 404 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS C 296 ASN E 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105256 restraints weight = 138766.407| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.13 r_work: 0.3278 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 35706 Z= 0.307 Angle : 0.780 10.184 48294 Z= 0.399 Chirality : 0.051 0.244 5382 Planarity : 0.006 0.052 6324 Dihedral : 11.536 171.144 5094 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.27 % Favored : 93.45 % Rotamer: Outliers : 4.13 % Allowed : 16.43 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.75 (0.13), residues: 4398 helix: 0.28 (0.12), residues: 1914 sheet: -1.10 (0.18), residues: 702 loop : -0.95 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 89 TYR 0.017 0.003 TYR C 138 PHE 0.019 0.002 PHE D 736 TRP 0.010 0.002 TRP E 454 HIS 0.007 0.002 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00734 (35700) covalent geometry : angle 0.77133 (48282) SS BOND : bond 0.03288 ( 6) SS BOND : angle 7.50104 ( 12) hydrogen bonds : bond 0.05166 ( 1494) hydrogen bonds : angle 5.15554 ( 4272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 385 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7418 (mp0) cc_final: 0.7189 (mm-30) REVERT: A 148 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7556 (mmtt) REVERT: A 291 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 364 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: F 60 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6702 (mtmm) REVERT: F 158 MET cc_start: 0.7661 (mtp) cc_final: 0.7400 (mtt) REVERT: F 268 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8702 (tt) REVERT: F 288 LYS cc_start: 0.8442 (ttmp) cc_final: 0.7927 (tmmm) REVERT: F 670 VAL cc_start: 0.6874 (m) cc_final: 0.6615 (t) REVERT: F 738 GLU cc_start: 0.7702 (tt0) cc_final: 0.7295 (tt0) REVERT: B 26 LEU cc_start: 0.7671 (mm) cc_final: 0.7275 (mt) REVERT: B 148 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7625 (mmtt) REVERT: B 268 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8841 (tt) REVERT: B 288 LYS cc_start: 0.8370 (ttmp) cc_final: 0.7994 (tmmt) REVERT: B 295 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7148 (mmtm) REVERT: B 511 SER cc_start: 0.8672 (p) cc_final: 0.8379 (m) REVERT: B 670 VAL cc_start: 0.6960 (m) cc_final: 0.6723 (t) REVERT: D 148 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7616 (mtpt) REVERT: D 158 MET cc_start: 0.8094 (mtt) cc_final: 0.7864 (mtt) REVERT: D 239 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6649 (mmt-90) REVERT: D 291 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: D 364 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: D 511 SER cc_start: 0.8668 (p) cc_final: 0.8440 (m) REVERT: C 60 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6615 (mtmm) REVERT: C 132 GLU cc_start: 0.7678 (mp0) cc_final: 0.7453 (mm-30) REVERT: C 236 LYS cc_start: 0.7310 (mmmt) cc_final: 0.7105 (tttm) REVERT: C 268 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 738 GLU cc_start: 0.7678 (tt0) cc_final: 0.7266 (tt0) REVERT: E 132 GLU cc_start: 0.7409 (mp0) cc_final: 0.7181 (mm-30) REVERT: E 148 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7703 (mmtt) REVERT: E 268 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8824 (tt) REVERT: E 288 LYS cc_start: 0.8368 (ttmp) cc_final: 0.8002 (tmmt) REVERT: E 335 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6523 (mt) REVERT: E 511 SER cc_start: 0.8701 (p) cc_final: 0.8376 (m) outliers start: 149 outliers final: 89 residues processed: 493 average time/residue: 0.7653 time to fit residues: 450.0825 Evaluate side-chains 447 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 342 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 127 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 chunk 170 optimal weight: 0.0670 chunk 126 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN F 85 ASN F 351 ASN B 36 ASN B 404 HIS B 460 ASN D 36 ASN C 36 ASN C 351 ASN E 36 ASN E 404 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.138737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108257 restraints weight = 138417.004| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.09 r_work: 0.3332 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 35706 Z= 0.157 Angle : 0.639 7.321 48294 Z= 0.322 Chirality : 0.045 0.197 5382 Planarity : 0.005 0.061 6324 Dihedral : 10.918 174.140 5094 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.76 % Favored : 94.96 % Rotamer: Outliers : 2.96 % Allowed : 17.76 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.34 (0.13), residues: 4398 helix: 0.79 (0.12), residues: 1872 sheet: -1.15 (0.19), residues: 648 loop : -0.84 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 753 TYR 0.023 0.002 TYR B 203 PHE 0.009 0.001 PHE E 163 TRP 0.017 0.002 TRP A 454 HIS 0.005 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00372 (35700) covalent geometry : angle 0.63344 (48282) SS BOND : bond 0.02534 ( 6) SS BOND : angle 5.59050 ( 12) hydrogen bonds : bond 0.04108 ( 1494) hydrogen bonds : angle 4.90847 ( 4272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 368 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7689 (mm) cc_final: 0.7326 (mp) REVERT: A 291 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 761 THR cc_start: 0.7668 (p) cc_final: 0.7434 (t) REVERT: F 84 MET cc_start: 0.8238 (mtp) cc_final: 0.7931 (mtp) REVERT: F 236 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7156 (tttm) REVERT: F 268 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8660 (tt) REVERT: F 388 MET cc_start: 0.6639 (mtt) cc_final: 0.6420 (mtm) REVERT: F 670 VAL cc_start: 0.6883 (m) cc_final: 0.6577 (t) REVERT: F 738 GLU cc_start: 0.7695 (tt0) cc_final: 0.7322 (tt0) REVERT: B 26 LEU cc_start: 0.7590 (mm) cc_final: 0.7205 (mt) REVERT: B 148 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7577 (mmtt) REVERT: B 268 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8852 (tt) REVERT: B 511 SER cc_start: 0.8594 (p) cc_final: 0.8349 (m) REVERT: B 670 VAL cc_start: 0.6913 (m) cc_final: 0.6664 (t) REVERT: D 26 LEU cc_start: 0.7691 (mm) cc_final: 0.7317 (mp) REVERT: D 132 GLU cc_start: 0.7378 (mp0) cc_final: 0.7152 (mm-30) REVERT: D 158 MET cc_start: 0.8083 (mtt) cc_final: 0.7812 (mtt) REVERT: D 291 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: C 46 MET cc_start: 0.6886 (mtt) cc_final: 0.6576 (mtt) REVERT: C 236 LYS cc_start: 0.7321 (mmmt) cc_final: 0.7072 (tttm) REVERT: C 268 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 388 MET cc_start: 0.6640 (mtt) cc_final: 0.6380 (mtp) REVERT: C 738 GLU cc_start: 0.7669 (tt0) cc_final: 0.7319 (tt0) REVERT: E 190 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6550 (mppt) REVERT: E 236 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7266 (tttm) REVERT: E 288 LYS cc_start: 0.8327 (ttmp) cc_final: 0.7959 (tmmt) REVERT: E 335 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6384 (mt) REVERT: E 511 SER cc_start: 0.8631 (p) cc_final: 0.8367 (m) outliers start: 105 outliers final: 62 residues processed: 455 average time/residue: 0.7171 time to fit residues: 390.4932 Evaluate side-chains 411 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 342 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 652 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 81 optimal weight: 0.5980 chunk 436 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 64 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 460 ASN D 460 ASN C 296 ASN E 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.138981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107653 restraints weight = 162214.531| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.63 r_work: 0.3313 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 35706 Z= 0.148 Angle : 0.630 7.555 48294 Z= 0.315 Chirality : 0.045 0.184 5382 Planarity : 0.005 0.063 6324 Dihedral : 10.707 172.301 5094 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.79 % Favored : 93.93 % Rotamer: Outliers : 2.64 % Allowed : 18.45 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.18 (0.13), residues: 4398 helix: 0.98 (0.12), residues: 1872 sheet: -1.23 (0.20), residues: 576 loop : -0.78 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 753 TYR 0.022 0.002 TYR B 203 PHE 0.009 0.001 PHE D 736 TRP 0.019 0.002 TRP E 454 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00349 (35700) covalent geometry : angle 0.62399 (48282) SS BOND : bond 0.02425 ( 6) SS BOND : angle 5.50926 ( 12) hydrogen bonds : bond 0.04058 ( 1494) hydrogen bonds : angle 4.84900 ( 4272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 370 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7697 (mm) cc_final: 0.7313 (mp) REVERT: A 291 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: A 761 THR cc_start: 0.7673 (p) cc_final: 0.7469 (t) REVERT: F 38 VAL cc_start: 0.7940 (t) cc_final: 0.7655 (t) REVERT: F 60 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6500 (mtmm) REVERT: F 84 MET cc_start: 0.8240 (mtp) cc_final: 0.7951 (mtp) REVERT: F 222 LEU cc_start: 0.8250 (mt) cc_final: 0.7996 (tp) REVERT: F 236 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7146 (tttm) REVERT: F 268 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8655 (tt) REVERT: F 670 VAL cc_start: 0.6886 (m) cc_final: 0.6543 (t) REVERT: F 738 GLU cc_start: 0.7707 (tt0) cc_final: 0.7323 (tt0) REVERT: B 26 LEU cc_start: 0.7613 (mm) cc_final: 0.7215 (mt) REVERT: B 148 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7550 (mtpt) REVERT: B 291 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 511 SER cc_start: 0.8624 (p) cc_final: 0.8389 (m) REVERT: B 670 VAL cc_start: 0.6886 (m) cc_final: 0.6620 (t) REVERT: B 700 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7655 (ttm170) REVERT: B 738 GLU cc_start: 0.7762 (tt0) cc_final: 0.7452 (tt0) REVERT: D 26 LEU cc_start: 0.7708 (mm) cc_final: 0.7308 (mp) REVERT: D 120 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7135 (p0) REVERT: D 132 GLU cc_start: 0.7387 (mp0) cc_final: 0.7162 (mm-30) REVERT: D 158 MET cc_start: 0.8082 (mtt) cc_final: 0.7829 (mtt) REVERT: D 239 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6551 (mmt-90) REVERT: D 291 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: C 60 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6522 (mtmm) REVERT: C 222 LEU cc_start: 0.8207 (mt) cc_final: 0.8006 (tp) REVERT: C 268 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8633 (tt) REVERT: C 388 MET cc_start: 0.6705 (mtt) cc_final: 0.6463 (mtm) REVERT: C 738 GLU cc_start: 0.7661 (tt0) cc_final: 0.7277 (tt0) REVERT: E 189 ILE cc_start: 0.7140 (pt) cc_final: 0.6910 (pp) REVERT: E 190 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6521 (mppt) REVERT: E 288 LYS cc_start: 0.8303 (ttmp) cc_final: 0.7905 (tmmt) REVERT: E 335 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6393 (mt) REVERT: E 511 SER cc_start: 0.8649 (p) cc_final: 0.8382 (m) REVERT: E 738 GLU cc_start: 0.7779 (tt0) cc_final: 0.7500 (tt0) outliers start: 93 outliers final: 58 residues processed: 448 average time/residue: 0.7201 time to fit residues: 383.0083 Evaluate side-chains 417 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 652 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 222 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 427 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 0.0030 chunk 319 optimal weight: 9.9990 chunk 343 optimal weight: 4.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN D 460 ASN C 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106702 restraints weight = 147765.234| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.35 r_work: 0.3306 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 35706 Z= 0.202 Angle : 0.673 8.156 48294 Z= 0.339 Chirality : 0.047 0.217 5382 Planarity : 0.005 0.062 6324 Dihedral : 10.939 170.845 5094 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.18 % Favored : 93.54 % Rotamer: Outliers : 3.06 % Allowed : 18.10 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.26 (0.13), residues: 4398 helix: 0.89 (0.12), residues: 1866 sheet: -1.18 (0.19), residues: 642 loop : -0.80 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 753 TYR 0.022 0.002 TYR B 203 PHE 0.013 0.002 PHE D 736 TRP 0.019 0.002 TRP E 454 HIS 0.004 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00486 (35700) covalent geometry : angle 0.66540 (48282) SS BOND : bond 0.02717 ( 6) SS BOND : angle 6.29180 ( 12) hydrogen bonds : bond 0.04389 ( 1494) hydrogen bonds : angle 4.92207 ( 4272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 350 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7455 (mp0) cc_final: 0.7204 (mm-30) REVERT: A 239 ARG cc_start: 0.7103 (mmp-170) cc_final: 0.6899 (mmm160) REVERT: A 291 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: A 364 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: A 761 THR cc_start: 0.7637 (p) cc_final: 0.7434 (t) REVERT: F 30 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: F 84 MET cc_start: 0.8287 (mtp) cc_final: 0.7994 (mtp) REVERT: F 268 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8667 (tt) REVERT: F 442 MET cc_start: 0.7319 (tpp) cc_final: 0.7055 (mmm) REVERT: F 670 VAL cc_start: 0.6869 (m) cc_final: 0.6517 (t) REVERT: F 738 GLU cc_start: 0.7705 (tt0) cc_final: 0.7307 (tt0) REVERT: B 26 LEU cc_start: 0.7653 (mm) cc_final: 0.7227 (mt) REVERT: B 148 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7612 (mtpt) REVERT: B 292 GLU cc_start: 0.7708 (tp30) cc_final: 0.7497 (tp30) REVERT: B 511 SER cc_start: 0.8652 (p) cc_final: 0.8374 (m) REVERT: B 670 VAL cc_start: 0.6897 (m) cc_final: 0.6617 (t) REVERT: B 700 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7578 (ttm170) REVERT: D 26 LEU cc_start: 0.7733 (mm) cc_final: 0.7349 (mp) REVERT: D 158 MET cc_start: 0.8085 (mtt) cc_final: 0.7842 (mtt) REVERT: D 239 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6601 (mmt-90) REVERT: D 291 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: D 364 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: D 761 THR cc_start: 0.7697 (p) cc_final: 0.7473 (t) REVERT: C 60 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6531 (mtmm) REVERT: C 222 LEU cc_start: 0.8216 (mt) cc_final: 0.7998 (tp) REVERT: C 268 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8639 (tt) REVERT: C 388 MET cc_start: 0.6760 (mtt) cc_final: 0.6528 (mtm) REVERT: C 738 GLU cc_start: 0.7707 (tt0) cc_final: 0.7310 (tt0) REVERT: E 132 GLU cc_start: 0.7493 (mp0) cc_final: 0.7263 (mm-30) REVERT: E 189 ILE cc_start: 0.7226 (pt) cc_final: 0.6965 (pp) REVERT: E 190 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6558 (mppt) REVERT: E 288 LYS cc_start: 0.8314 (ttmp) cc_final: 0.7937 (tmmt) REVERT: E 335 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6497 (mt) REVERT: E 511 SER cc_start: 0.8669 (p) cc_final: 0.8390 (m) outliers start: 109 outliers final: 76 residues processed: 443 average time/residue: 0.7550 time to fit residues: 397.8309 Evaluate side-chains 426 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 339 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 69 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 395 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** E 340 HIS ** 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 = 0.3990 r_free = 0.3990 target = 0.136808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.105048 restraints weight = 156085.961| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.53 r_work: 0.3290 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 35706 Z= 0.239 Angle : 0.707 8.311 48294 Z= 0.358 Chirality : 0.048 0.209 5382 Planarity : 0.005 0.061 6324 Dihedral : 11.158 172.170 5094 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.57 % Favored : 93.15 % Rotamer: Outliers : 3.14 % Allowed : 18.45 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.41 (0.13), residues: 4398 helix: 0.73 (0.12), residues: 1866 sheet: -1.23 (0.19), residues: 630 loop : -0.86 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 753 TYR 0.018 0.002 TYR D 203 PHE 0.014 0.002 PHE D 736 TRP 0.008 0.002 TRP D 454 HIS 0.004 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00572 (35700) covalent geometry : angle 0.69907 (48282) SS BOND : bond 0.02886 ( 6) SS BOND : angle 6.77843 ( 12) hydrogen bonds : bond 0.04590 ( 1494) hydrogen bonds : angle 5.01129 ( 4272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 359 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7469 (mp0) cc_final: 0.7224 (mm-30) REVERT: A 288 LYS cc_start: 0.8394 (ttmp) cc_final: 0.7944 (tmmt) REVERT: A 291 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: A 364 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: F 30 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: F 84 MET cc_start: 0.8316 (mtp) cc_final: 0.8011 (mtp) REVERT: F 268 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8682 (tt) REVERT: F 442 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7164 (mmm) REVERT: F 670 VAL cc_start: 0.6889 (m) cc_final: 0.6525 (t) REVERT: F 738 GLU cc_start: 0.7711 (tt0) cc_final: 0.7329 (tt0) REVERT: B 26 LEU cc_start: 0.7668 (mm) cc_final: 0.7271 (mt) REVERT: B 53 ARG cc_start: 0.7291 (mmm-85) cc_final: 0.6969 (mmm-85) REVERT: B 148 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7644 (mmtt) REVERT: B 292 GLU cc_start: 0.7723 (tp30) cc_final: 0.7515 (tp30) REVERT: B 511 SER cc_start: 0.8668 (p) cc_final: 0.8382 (m) REVERT: B 670 VAL cc_start: 0.6912 (m) cc_final: 0.6654 (t) REVERT: B 700 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7549 (ttm170) REVERT: B 738 GLU cc_start: 0.7764 (tt0) cc_final: 0.7383 (tt0) REVERT: D 26 LEU cc_start: 0.7797 (mm) cc_final: 0.7434 (mp) REVERT: D 148 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7578 (mmmt) REVERT: D 158 MET cc_start: 0.8179 (mtt) cc_final: 0.7929 (mtt) REVERT: D 239 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6594 (mmt-90) REVERT: D 291 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: D 364 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: D 442 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.7011 (mmm) REVERT: D 761 THR cc_start: 0.7692 (p) cc_final: 0.7463 (t) REVERT: C 60 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6521 (mtmm) REVERT: C 222 LEU cc_start: 0.8240 (mt) cc_final: 0.7995 (tp) REVERT: C 268 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8645 (tt) REVERT: C 388 MET cc_start: 0.6767 (mtt) cc_final: 0.6518 (mtm) REVERT: C 442 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6997 (mmm) REVERT: C 738 GLU cc_start: 0.7708 (tt0) cc_final: 0.7329 (tt0) REVERT: E 53 ARG cc_start: 0.7272 (mmm-85) cc_final: 0.6932 (mmm-85) REVERT: E 132 GLU cc_start: 0.7578 (mp0) cc_final: 0.7377 (mm-30) REVERT: E 288 LYS cc_start: 0.8353 (ttmp) cc_final: 0.7963 (tmmt) REVERT: E 511 SER cc_start: 0.8676 (p) cc_final: 0.8370 (m) REVERT: E 738 GLU cc_start: 0.7810 (tt0) cc_final: 0.7418 (tt0) outliers start: 112 outliers final: 81 residues processed: 452 average time/residue: 0.7658 time to fit residues: 411.4852 Evaluate side-chains 437 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 342 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 379 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 391 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 369 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN D 460 ASN E 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106372 restraints weight = 167265.691| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.85 r_work: 0.3288 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 35706 Z= 0.170 Angle : 0.659 8.477 48294 Z= 0.330 Chirality : 0.046 0.214 5382 Planarity : 0.005 0.065 6324 Dihedral : 10.914 173.417 5094 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.02 % Favored : 93.70 % Rotamer: Outliers : 2.88 % Allowed : 18.93 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.27 (0.13), residues: 4398 helix: 0.91 (0.12), residues: 1866 sheet: -1.30 (0.19), residues: 630 loop : -0.79 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 753 TYR 0.018 0.002 TYR D 203 PHE 0.011 0.001 PHE D 736 TRP 0.016 0.002 TRP E 454 HIS 0.003 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00405 (35700) covalent geometry : angle 0.65209 (48282) SS BOND : bond 0.02610 ( 6) SS BOND : angle 5.85776 ( 12) hydrogen bonds : bond 0.04204 ( 1494) hydrogen bonds : angle 4.93507 ( 4272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 358 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7483 (mp0) cc_final: 0.7243 (mm-30) REVERT: A 288 LYS cc_start: 0.8383 (ttmp) cc_final: 0.7895 (tmmt) REVERT: A 291 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: A 364 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: F 30 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: F 84 MET cc_start: 0.8322 (mtp) cc_final: 0.8029 (mtp) REVERT: F 268 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8672 (tt) REVERT: F 442 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7164 (mmm) REVERT: F 670 VAL cc_start: 0.6836 (m) cc_final: 0.6466 (t) REVERT: F 738 GLU cc_start: 0.7719 (tt0) cc_final: 0.7337 (tt0) REVERT: B 26 LEU cc_start: 0.7630 (mm) cc_final: 0.7222 (mt) REVERT: B 53 ARG cc_start: 0.7264 (mmm-85) cc_final: 0.6974 (mmm-85) REVERT: B 148 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7608 (mmtt) REVERT: B 292 GLU cc_start: 0.7750 (tp30) cc_final: 0.7550 (tp30) REVERT: B 511 SER cc_start: 0.8654 (p) cc_final: 0.8385 (m) REVERT: B 670 VAL cc_start: 0.6914 (m) cc_final: 0.6658 (t) REVERT: B 700 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7548 (ttm170) REVERT: D 26 LEU cc_start: 0.7757 (mm) cc_final: 0.7382 (mp) REVERT: D 158 MET cc_start: 0.8168 (mtt) cc_final: 0.7925 (mtt) REVERT: D 239 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6580 (mmt-90) REVERT: D 291 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: D 442 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6982 (mmm) REVERT: D 761 THR cc_start: 0.7645 (p) cc_final: 0.7431 (t) REVERT: C 60 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6504 (mtmm) REVERT: C 222 LEU cc_start: 0.8195 (mt) cc_final: 0.7963 (tp) REVERT: C 268 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8643 (tt) REVERT: C 442 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7004 (mmm) REVERT: C 738 GLU cc_start: 0.7704 (tt0) cc_final: 0.7326 (tt0) REVERT: E 53 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.6962 (mmm-85) REVERT: E 132 GLU cc_start: 0.7544 (mp0) cc_final: 0.7334 (mm-30) REVERT: E 236 LYS cc_start: 0.7677 (mmmt) cc_final: 0.7269 (tttm) REVERT: E 288 LYS cc_start: 0.8351 (ttmp) cc_final: 0.7937 (tmmt) REVERT: E 508 MET cc_start: 0.4065 (OUTLIER) cc_final: 0.3484 (ttp) REVERT: E 511 SER cc_start: 0.8662 (p) cc_final: 0.8375 (m) outliers start: 102 outliers final: 74 residues processed: 441 average time/residue: 0.7485 time to fit residues: 392.3796 Evaluate side-chains 430 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 343 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 662 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 6.9990 chunk 336 optimal weight: 1.9990 chunk 166 optimal weight: 0.0570 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 364 optimal weight: 0.5980 chunk 372 optimal weight: 0.2980 chunk 212 optimal weight: 0.0770 chunk 43 optimal weight: 6.9990 chunk 348 optimal weight: 0.0000 overall best weight: 0.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 460 ASN F 285 ASN B 285 ASN B 460 ASN D 285 ASN D 460 ASN C 285 ASN E 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110552 restraints weight = 166575.294| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.92 r_work: 0.3364 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 35706 Z= 0.119 Angle : 0.619 9.693 48294 Z= 0.306 Chirality : 0.044 0.178 5382 Planarity : 0.005 0.074 6324 Dihedral : 10.139 173.884 5094 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.24 % Favored : 94.48 % Rotamer: Outliers : 1.78 % Allowed : 20.10 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.04 (0.13), residues: 4398 helix: 1.21 (0.13), residues: 1896 sheet: -1.28 (0.19), residues: 618 loop : -0.65 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 753 TYR 0.018 0.001 TYR D 203 PHE 0.013 0.001 PHE E 163 TRP 0.019 0.001 TRP D 454 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00264 (35700) covalent geometry : angle 0.61518 (48282) SS BOND : bond 0.01982 ( 6) SS BOND : angle 4.33701 ( 12) hydrogen bonds : bond 0.03611 ( 1494) hydrogen bonds : angle 4.76564 ( 4272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 407 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7699 (mm) cc_final: 0.7326 (mp) REVERT: A 132 GLU cc_start: 0.7340 (mp0) cc_final: 0.7077 (mm-30) REVERT: A 288 LYS cc_start: 0.8286 (ttmp) cc_final: 0.7758 (tmmt) REVERT: A 291 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: A 741 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7692 (ttm110) REVERT: A 761 THR cc_start: 0.7733 (p) cc_final: 0.7485 (t) REVERT: F 84 MET cc_start: 0.8204 (mtp) cc_final: 0.7965 (mtp) REVERT: F 222 LEU cc_start: 0.8136 (mt) cc_final: 0.7911 (tp) REVERT: F 268 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8598 (tt) REVERT: F 442 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7111 (mmm) REVERT: F 670 VAL cc_start: 0.6812 (m) cc_final: 0.6450 (t) REVERT: F 700 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7568 (ttp-170) REVERT: F 738 GLU cc_start: 0.7703 (tt0) cc_final: 0.7283 (tt0) REVERT: B 26 LEU cc_start: 0.7542 (mm) cc_final: 0.7167 (mt) REVERT: B 291 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: B 511 SER cc_start: 0.8565 (p) cc_final: 0.8361 (m) REVERT: B 670 VAL cc_start: 0.6758 (m) cc_final: 0.6464 (t) REVERT: B 700 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7445 (ttm170) REVERT: B 742 PHE cc_start: 0.7798 (m-80) cc_final: 0.7512 (m-80) REVERT: D 26 LEU cc_start: 0.7691 (mm) cc_final: 0.7305 (mp) REVERT: D 120 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7143 (p0) REVERT: D 158 MET cc_start: 0.8037 (mtt) cc_final: 0.7793 (mtt) REVERT: D 291 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: C 268 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8599 (tt) REVERT: C 738 GLU cc_start: 0.7641 (tt0) cc_final: 0.7223 (tt0) REVERT: E 190 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6450 (mppt) REVERT: E 236 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7227 (tttm) REVERT: E 291 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7301 (mp0) outliers start: 61 outliers final: 31 residues processed: 449 average time/residue: 0.7881 time to fit residues: 416.6245 Evaluate side-chains 391 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 352 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 113 optimal weight: 0.0020 chunk 267 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 316 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 460 ASN B 460 ASN D 460 ASN E 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.138338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107226 restraints weight = 142960.347| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.35 r_work: 0.3321 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 35706 Z= 0.190 Angle : 0.675 9.770 48294 Z= 0.338 Chirality : 0.046 0.151 5382 Planarity : 0.005 0.067 6324 Dihedral : 10.553 169.369 5094 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 1.62 % Allowed : 20.61 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: -0.15 (0.13), residues: 4398 helix: 0.91 (0.12), residues: 1938 sheet: -1.28 (0.20), residues: 564 loop : -0.69 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 753 TYR 0.023 0.002 TYR A 244 PHE 0.012 0.002 PHE B 230 TRP 0.014 0.002 TRP B 454 HIS 0.003 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00453 (35700) covalent geometry : angle 0.66867 (48282) SS BOND : bond 0.02320 ( 6) SS BOND : angle 5.70412 ( 12) hydrogen bonds : bond 0.04263 ( 1494) hydrogen bonds : angle 4.85707 ( 4272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14691.69 seconds wall clock time: 250 minutes 35.46 seconds (15035.46 seconds total)