Starting phenix.real_space_refine on Sun Jul 5 04:12:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqm_65260/07_2026/9vqm_65260_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqm_65260/07_2026/9vqm_65260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vqm_65260/07_2026/9vqm_65260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqm_65260/07_2026/9vqm_65260.map" model { file = "/net/cci-nas-00/data/ceres_data/9vqm_65260/07_2026/9vqm_65260_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqm_65260/07_2026/9vqm_65260_neut.cif" } resolution = 3.5 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= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 3 5.60 5 S 256 5.16 5 C 15413 2.51 5 N 4095 2.21 5 O 4771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24538 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6122 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 748} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5904 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 721} Chain breaks: 12 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 6181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6181 Classifications: {'peptide': 807} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 757} Chain breaks: 8 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 6076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6076 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 47, 'TRANS': 744} Chain breaks: 10 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.35, per 1000 atoms: 0.22 Number of scatterers: 24538 At special positions: 0 Unit cell: (141.31, 155.441, 270.663, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 3 28.99 S 256 16.00 O 4771 8.00 N 4095 7.00 C 15413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=99, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 211 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 505 " - pdb=" SG CYS A 509 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 602 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 618 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 638 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 739 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 844 " distance=2.03 Simple disulfide: pdb=" SG CYS A 820 " - pdb=" SG CYS A 856 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS A 859 " - pdb=" SG CYS A 888 " distance=2.03 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 902 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 308 " distance=2.02 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 509 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS B 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 638 " distance=2.03 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 844 " distance=2.03 Simple disulfide: pdb=" SG CYS B 820 " - pdb=" SG CYS B 856 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 888 " distance=2.03 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 902 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 79 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 91 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 211 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 324 " distance=2.03 Simple disulfide: pdb=" SG CYS C 330 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 342 " - pdb=" SG CYS C 379 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 397 " - pdb=" SG CYS C 408 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 505 " - pdb=" SG CYS C 509 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 602 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS C 618 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 638 " distance=2.03 Simple disulfide: pdb=" SG CYS C 641 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 704 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 739 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 844 " distance=2.03 Simple disulfide: pdb=" SG CYS C 820 " - pdb=" SG CYS C 856 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 841 " distance=2.03 Simple disulfide: pdb=" SG CYS C 859 " - pdb=" SG CYS C 888 " distance=2.03 Simple disulfide: pdb=" SG CYS C 871 " - pdb=" SG CYS C 902 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 311 " - pdb=" SG CYS D 324 " distance=2.03 Simple disulfide: pdb=" SG CYS D 330 " - pdb=" SG CYS D 360 " distance=2.03 Simple disulfide: pdb=" SG CYS D 342 " - pdb=" SG CYS D 379 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 397 " - pdb=" SG CYS D 408 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 505 " - pdb=" SG CYS D 509 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS D 618 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 638 " distance=2.04 Simple disulfide: pdb=" SG CYS D 641 " - pdb=" SG CYS D 654 " distance=2.03 Simple disulfide: pdb=" SG CYS D 658 " - pdb=" SG CYS D 704 " distance=2.03 Simple disulfide: pdb=" SG CYS D 714 " - pdb=" SG CYS D 739 " distance=2.04 Simple disulfide: pdb=" SG CYS D 808 " - pdb=" SG CYS D 844 " distance=2.03 Simple disulfide: pdb=" SG CYS D 820 " - pdb=" SG CYS D 856 " distance=2.03 Simple disulfide: pdb=" SG CYS D 836 " - pdb=" SG CYS D 841 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 888 " distance=2.03 Simple disulfide: pdb=" SG CYS D 871 " - pdb=" SG CYS D 902 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1101 " - " ASN A 153 " " NAG A1102 " - " ASN A 576 " " NAG A1103 " - " ASN A 544 " " NAG B1101 " - " ASN B 153 " " NAG B1102 " - " ASN B 576 " " NAG B1103 " - " ASN B 544 " " NAG C1101 " - " ASN C 153 " " NAG C1102 " - " ASN C 576 " " NAG C1103 " - " ASN C 544 " " NAG D1101 " - " ASN D 153 " " NAG D1102 " - " ASN D 576 " " NAG D1103 " - " ASN D 544 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN D 717 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 915.4 milliseconds 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 101 sheets defined 3.6% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 517 through 520 Processing helix chain 'A' and resid 674 through 677 Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 860 through 862 No H-bonds generated for 'chain 'A' and resid 860 through 862' Processing helix chain 'B' and resid 517 through 520 Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 745 through 750 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 860 through 864 removed outlier: 3.526A pdb=" N ASP B 863 " --> pdb=" O SER B 860 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 864 " --> pdb=" O ALA B 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 860 through 864' Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 674 through 677 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 716 through 721 removed outlier: 3.522A pdb=" N ASP C 720 " --> pdb=" O ASP C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.782A pdb=" N TYR C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 677 removed outlier: 4.275A pdb=" N ALA D 677 " --> pdb=" O SER D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 674 through 677' Processing helix chain 'D' and resid 705 through 709 removed outlier: 3.763A pdb=" N GLY D 708 " --> pdb=" O GLY D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 721 removed outlier: 3.717A pdb=" N ASP D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 721 " --> pdb=" O ASN D 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 716 through 721' Processing helix chain 'D' and resid 781 through 785 Processing helix chain 'D' and resid 860 through 864 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 6.279A pdb=" N HIS A 47 " --> pdb=" O THR A 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.894A pdb=" N SER A 107 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA6, first strand: chain 'A' and resid 121 through 123 removed outlier: 5.806A pdb=" N VAL A 261 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR A 194 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN A 263 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 192 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 188 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 233 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 139 removed outlier: 3.660A pdb=" N GLN A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 205 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 247 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AB2, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.573A pdb=" N LYS A 353 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AB4, first strand: chain 'A' and resid 386 through 387 removed outlier: 3.672A pdb=" N PHE A 387 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 395 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AB6, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.706A pdb=" N TYR A 573 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 500 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 575 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 498 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL A 577 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG A 496 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 497 " --> pdb=" O TYR A 539 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 433 through 438 removed outlier: 3.702A pdb=" N LEU A 472 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP A 551 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 554 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A 510 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 511 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A 527 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE A 513 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 523 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB9, first strand: chain 'A' and resid 609 through 610 removed outlier: 3.905A pdb=" N HIS A 619 " --> pdb=" O TYR A 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 625 through 626 Processing sheet with id=AC2, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AC3, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AC4, first strand: chain 'A' and resid 680 through 683 removed outlier: 3.662A pdb=" N VAL A 680 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 701 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 682 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 680 through 683 removed outlier: 3.662A pdb=" N VAL A 680 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 701 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 682 " --> pdb=" O PHE A 699 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 696 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 742 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLN A 758 " --> pdb=" O VAL A 742 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.507A pdb=" N ALA A 712 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 765 through 770 removed outlier: 7.190A pdb=" N PHE A 798 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 769 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 796 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 846 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 848 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 852 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 864 through 866 Processing sheet with id=AC9, first strand: chain 'B' and resid 54 through 58 Processing sheet with id=AD1, first strand: chain 'B' and resid 100 through 102 removed outlier: 4.067A pdb=" N SER B 107 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=AD3, first strand: chain 'B' and resid 121 through 123 Processing sheet with id=AD4, first strand: chain 'B' and resid 121 through 123 removed outlier: 4.348A pdb=" N ILE B 264 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 190 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 266 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 188 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 233 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 134 through 139 removed outlier: 3.829A pdb=" N ALA B 175 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 134 through 139 removed outlier: 3.829A pdb=" N ALA B 175 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AD8, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AD9, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AE1, first strand: chain 'B' and resid 386 through 387 removed outlier: 3.813A pdb=" N PHE B 387 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 395 " --> pdb=" O PHE B 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AE3, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.575A pdb=" N TYR B 573 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B 500 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 575 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR B 498 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 577 " --> pdb=" O ARG B 496 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG B 496 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 497 " --> pdb=" O TYR B 539 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 433 through 438 removed outlier: 3.651A pdb=" N LEU B 472 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 551 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 510 " --> pdb=" O GLN B 554 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU B 511 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 527 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE B 513 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 523 " --> pdb=" O VAL B 515 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 609 through 610 removed outlier: 3.903A pdb=" N HIS B 619 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 625 through 627 Processing sheet with id=AE7, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AE8, first strand: chain 'B' and resid 659 through 663 Processing sheet with id=AE9, first strand: chain 'B' and resid 680 through 683 removed outlier: 3.684A pdb=" N VAL B 680 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 701 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 682 " --> pdb=" O PHE B 699 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 680 through 683 removed outlier: 3.684A pdb=" N VAL B 680 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 701 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 682 " --> pdb=" O PHE B 699 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 696 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 742 " --> pdb=" O GLN B 758 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN B 758 " --> pdb=" O VAL B 742 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 765 through 770 removed outlier: 7.176A pdb=" N PHE B 798 " --> pdb=" O VAL B 767 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL B 769 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL B 796 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 846 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 848 " --> pdb=" O THR B 815 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 852 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 865 through 866 Processing sheet with id=AF4, first strand: chain 'C' and resid 54 through 58 Processing sheet with id=AF5, first strand: chain 'C' and resid 100 through 102 removed outlier: 4.059A pdb=" N SER C 107 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=AF7, first strand: chain 'C' and resid 121 through 123 Processing sheet with id=AF8, first strand: chain 'C' and resid 121 through 123 removed outlier: 4.211A pdb=" N ILE C 264 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN C 190 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 266 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 188 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 187 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 189 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 233 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 134 through 139 removed outlier: 3.593A pdb=" N THR C 174 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 175 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 246 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 134 through 139 removed outlier: 3.593A pdb=" N THR C 174 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 175 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 246 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AG3, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AG4, first strand: chain 'C' and resid 315 through 316 Processing sheet with id=AG5, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.680A pdb=" N LYS C 353 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 347 through 348 Processing sheet with id=AG7, first strand: chain 'C' and resid 386 through 387 removed outlier: 3.732A pdb=" N PHE C 387 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 395 " --> pdb=" O PHE C 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'C' and resid 401 through 403 Processing sheet with id=AG9, first strand: chain 'C' and resid 421 through 422 removed outlier: 3.758A pdb=" N TYR C 573 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C 500 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE C 575 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 498 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL C 577 " --> pdb=" O ARG C 496 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG C 496 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 535 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR C 503 " --> pdb=" O GLY C 533 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY C 533 " --> pdb=" O THR C 503 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 433 through 438 removed outlier: 3.596A pdb=" N PHE C 553 " --> pdb=" O MET C 470 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 472 " --> pdb=" O TRP C 551 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP C 551 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU C 511 " --> pdb=" O THR C 527 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR C 527 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE C 513 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 525 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 515 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 523 " --> pdb=" O VAL C 515 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.553A pdb=" N TYR C 459 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 609 through 610 removed outlier: 3.713A pdb=" N HIS C 619 " --> pdb=" O TYR C 610 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 625 through 626 Processing sheet with id=AH5, first strand: chain 'C' and resid 646 through 647 Processing sheet with id=AH6, first strand: chain 'C' and resid 659 through 663 Processing sheet with id=AH7, first strand: chain 'C' and resid 680 through 683 removed outlier: 3.761A pdb=" N LEU C 701 " --> pdb=" O VAL C 680 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 682 " --> pdb=" O PHE C 699 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 680 through 683 removed outlier: 3.761A pdb=" N LEU C 701 " --> pdb=" O VAL C 680 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 682 " --> pdb=" O PHE C 699 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 742 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN C 758 " --> pdb=" O VAL C 742 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 765 through 770 removed outlier: 7.126A pdb=" N PHE C 798 " --> pdb=" O VAL C 767 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL C 769 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL C 796 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 846 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 848 " --> pdb=" O THR C 815 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 865 through 866 Processing sheet with id=AI2, first strand: chain 'C' and resid 877 through 878 removed outlier: 3.971A pdb=" N THR C 878 " --> pdb=" O ARG C 898 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 898 " --> pdb=" O THR C 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'D' and resid 54 through 58 removed outlier: 3.766A pdb=" N VAL D 72 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.858A pdb=" N SER D 107 " --> pdb=" O ASP D 102 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=AI6, first strand: chain 'D' and resid 121 through 123 Processing sheet with id=AI7, first strand: chain 'D' and resid 121 through 123 removed outlier: 5.630A pdb=" N VAL D 261 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR D 194 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN D 263 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU D 192 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 188 " --> pdb=" O THR D 267 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 134 through 139 removed outlier: 3.627A pdb=" N ALA D 175 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 243 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE D 205 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 247 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 282 through 283 Processing sheet with id=AJ1, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AJ2, first strand: chain 'D' and resid 315 through 316 Processing sheet with id=AJ3, first strand: chain 'D' and resid 335 through 336 Processing sheet with id=AJ4, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AJ5, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AJ6, first strand: chain 'D' and resid 401 through 403 removed outlier: 3.506A pdb=" N TYR D 402 " --> pdb=" O THR D 409 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 420 through 423 Processing sheet with id=AJ8, first strand: chain 'D' and resid 434 through 438 removed outlier: 4.073A pdb=" N PHE D 553 " --> pdb=" O MET D 470 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 472 " --> pdb=" O TRP D 551 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 510 " --> pdb=" O GLN D 554 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 515 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.515A pdb=" N TYR D 459 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'D' and resid 495 through 498 removed outlier: 4.184A pdb=" N ALA D 495 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AK3, first strand: chain 'D' and resid 625 through 626 Processing sheet with id=AK4, first strand: chain 'D' and resid 646 through 647 Processing sheet with id=AK5, first strand: chain 'D' and resid 659 through 663 removed outlier: 3.989A pdb=" N ASN D 670 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 858 " --> pdb=" O ASN D 670 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 680 through 681 removed outlier: 3.716A pdb=" N PHE D 696 " --> pdb=" O ILE D 743 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 680 through 681 removed outlier: 4.709A pdb=" N VAL D 742 " --> pdb=" O GLN D 758 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLN D 758 " --> pdb=" O VAL D 742 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 712 through 715 removed outlier: 3.644A pdb=" N CYS D 714 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 734 " --> pdb=" O CYS D 714 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 765 through 770 removed outlier: 6.930A pdb=" N PHE D 798 " --> pdb=" O VAL D 767 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL D 769 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 796 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 852 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'D' and resid 774 through 775 removed outlier: 3.571A pdb=" N ILE D 778 " --> pdb=" O LEU D 775 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'D' and resid 865 through 866 533 hydrogen bonds defined for protein. 1242 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: 5.16 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4279 1.32 - 1.45: 7117 1.45 - 1.58: 13454 1.58 - 1.70: 0 1.70 - 1.83: 312 Bond restraints: 25162 Sorted by residual: bond pdb=" CA ALA B 71 " pdb=" CB ALA B 71 " ideal model delta sigma weight residual 1.529 1.443 0.086 1.38e-02 5.25e+03 3.89e+01 bond pdb=" CA PRO B 73 " pdb=" C PRO B 73 " ideal model delta sigma weight residual 1.521 1.448 0.073 1.27e-02 6.20e+03 3.32e+01 bond pdb=" CA SER B 75 " pdb=" CB SER B 75 " ideal model delta sigma weight residual 1.536 1.462 0.074 1.46e-02 4.69e+03 2.58e+01 bond pdb=" CA PRO B 73 " pdb=" CB PRO B 73 " ideal model delta sigma weight residual 1.532 1.475 0.057 1.34e-02 5.57e+03 1.79e+01 bond pdb=" CA PHE A 205 " pdb=" C PHE A 205 " ideal model delta sigma weight residual 1.520 1.470 0.050 1.21e-02 6.83e+03 1.72e+01 ... (remaining 25157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 34093 4.36 - 8.73: 88 8.73 - 13.09: 14 13.09 - 17.45: 4 17.45 - 21.81: 3 Bond angle restraints: 34202 Sorted by residual: angle pdb=" N VAL A 206 " pdb=" CA VAL A 206 " pdb=" CB VAL A 206 " ideal model delta sigma weight residual 111.31 97.40 13.91 1.23e+00 6.61e-01 1.28e+02 angle pdb=" N TYR B 243 " pdb=" CA TYR B 243 " pdb=" CB TYR B 243 " ideal model delta sigma weight residual 111.13 91.62 19.51 1.79e+00 3.12e-01 1.19e+02 angle pdb=" C HIS B 55 " pdb=" CA HIS B 55 " pdb=" CB HIS B 55 " ideal model delta sigma weight residual 109.79 87.98 21.81 2.05e+00 2.38e-01 1.13e+02 angle pdb=" C ASP B 209 " pdb=" CA ASP B 209 " pdb=" CB ASP B 209 " ideal model delta sigma weight residual 110.88 94.17 16.71 1.57e+00 4.06e-01 1.13e+02 angle pdb=" N TYR B 54 " pdb=" CA TYR B 54 " pdb=" CB TYR B 54 " ideal model delta sigma weight residual 111.55 95.41 16.14 1.74e+00 3.30e-01 8.60e+01 ... (remaining 34197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.93: 14571 23.93 - 47.85: 603 47.85 - 71.78: 107 71.78 - 95.71: 17 95.71 - 119.64: 51 Dihedral angle restraints: 15349 sinusoidal: 6222 harmonic: 9127 Sorted by residual: dihedral pdb=" C HIS B 55 " pdb=" N HIS B 55 " pdb=" CA HIS B 55 " pdb=" CB HIS B 55 " ideal model delta harmonic sigma weight residual -122.60 -92.54 -30.06 0 2.50e+00 1.60e-01 1.45e+02 dihedral pdb=" CB CYS D 111 " pdb=" SG CYS D 111 " pdb=" SG CYS D 275 " pdb=" CB CYS D 275 " ideal model delta sinusoidal sigma weight residual -86.00 -175.98 89.98 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS A 111 " pdb=" SG CYS A 111 " pdb=" SG CYS A 275 " pdb=" CB CYS A 275 " ideal model delta sinusoidal sigma weight residual 93.00 179.54 -86.54 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 15346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3562 0.091 - 0.182: 214 0.182 - 0.272: 17 0.272 - 0.363: 7 0.363 - 0.454: 2 Chirality restraints: 3802 Sorted by residual: chirality pdb=" CA HIS B 55 " pdb=" N HIS B 55 " pdb=" C HIS B 55 " pdb=" CB HIS B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.89 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" C1 NAG D1101 " pdb=" ND2 ASN D 153 " pdb=" C2 NAG D1101 " pdb=" O5 NAG D1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 3799 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 52 " 0.028 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C SER B 52 " -0.093 2.00e-02 2.50e+03 pdb=" O SER B 52 " 0.033 2.00e-02 2.50e+03 pdb=" N GLU B 53 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 204 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C PHE B 204 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE B 204 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE B 205 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 77 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C GLY B 77 " 0.064 2.00e-02 2.50e+03 pdb=" O GLY B 77 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 78 " -0.022 2.00e-02 2.50e+03 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 567 2.67 - 3.23: 23463 3.23 - 3.79: 36376 3.79 - 4.34: 50444 4.34 - 4.90: 81945 Nonbonded interactions: 192795 Sorted by model distance: nonbonded pdb=" O TYR B 337 " pdb=" OH TYR B 459 " model vdw 2.116 3.040 nonbonded pdb=" O TYR A 337 " pdb=" OH TYR A 459 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR D 195 " pdb=" O ILE D 200 " model vdw 2.127 3.040 nonbonded pdb=" O TYR C 337 " pdb=" OH TYR C 459 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR D 664 " pdb=" O ARG D 667 " model vdw 2.147 3.040 ... (remaining 192790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 141 or resid 153 through 221 or resid 228 throu \ gh 354 or resid 359 through 370 or resid 377 through 444 or resid 453 through 48 \ 1 or (resid 492 and (name N or name CA or name C or name O or name CB )) or resi \ d 493 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ me CB )) or resid 518 through 519 or (resid 520 through 521 and (name N or name \ CA or name C or name O or name CB )) or resid 522 through 541 or (resid 542 thro \ ugh 543 and (name N or name CA or name C or name O or name CB )) or resid 544 th \ rough 591 or resid 606 through 713 or resid 735 through 786 or resid 791 through \ 882 or resid 888 through 1103)) selection = (chain 'B' and (resid 46 through 141 or resid 153 through 214 or resid 219 throu \ gh 388 or resid 392 through 481 or (resid 492 and (name N or name CA or name C o \ r name O or name CB )) or resid 493 through 516 or (resid 517 and (name N or nam \ e CA or name C or name O or name CB )) or resid 518 through 519 or (resid 520 th \ rough 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 541 or (resid 542 through 543 and (name N or name CA or name C or name O \ or name CB )) or resid 544 through 591 or resid 606 through 745 or resid 755 th \ rough 786 or resid 791 through 882 or resid 888 through 1103)) selection = (chain 'C' and (resid 46 through 141 or resid 153 through 221 or resid 228 throu \ gh 251 or resid 256 through 354 or resid 359 through 370 or resid 377 through 38 \ 8 or resid 392 through 444 or resid 453 through 481 or resid 492 through 519 or \ (resid 520 through 521 and (name N or name CA or name C or name O or name CB )) \ or resid 522 through 591 or resid 606 through 713 or resid 735 through 745 or re \ sid 755 through 786 or resid 791 through 882 or resid 888 through 1103)) selection = (chain 'D' and (resid 46 through 214 or resid 219 through 221 or resid 228 throu \ gh 251 or resid 256 through 354 or resid 359 through 370 or resid 377 through 44 \ 4 or resid 453 through 481 or (resid 492 and (name N or name CA or name C or nam \ e O or name CB )) or resid 493 through 542 or (resid 543 and (name N or name CA \ or name C or name O or name CB )) or resid 544 through 713 or resid 735 through \ 882 or resid 888 through 1103)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.970 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.003 0.086 25279 Z= 0.205 Angle : 0.749 21.815 34454 Z= 0.433 Chirality : 0.046 0.454 3802 Planarity : 0.004 0.054 4375 Dihedral : 14.734 119.637 9188 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.37 % Allowed : 0.29 % Favored : 99.34 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.15), residues: 3076 helix: -3.19 (0.82), residues: 18 sheet: -0.90 (0.17), residues: 905 loop : -0.18 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 480 TYR 0.028 0.001 TYR B 54 PHE 0.031 0.001 PHE D 499 TRP 0.018 0.001 TRP C 551 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.21 (25162) covalent geometry : angle 0.73729 / 0.43 (34202) SS BOND : bond 0.00235 / 0.17 ( 99) SS BOND : angle 1.13414 / 0.78 ( 198) hydrogen bonds : bond 0.30253 / 20.58 ( 497) hydrogen bonds : angle 10.96714 / 7.63 ( 1242) link_BETA1-4 : bond 0.00464 / 0.23 ( 3) link_BETA1-4 : angle 0.79576 / 0.37 ( 9) link_NAG-ASN : bond 0.00810 / 0.47 ( 15) link_NAG-ASN : angle 3.31115 / 2.25 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 453 time to evaluate : 0.826 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7981 (p90) REVERT: A 210 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: A 352 TYR cc_start: 0.8613 (m-10) cc_final: 0.7787 (m-10) REVERT: A 459 TYR cc_start: 0.6205 (p90) cc_final: 0.5646 (p90) REVERT: A 514 MET cc_start: 0.5536 (mtt) cc_final: 0.5078 (mtm) REVERT: A 695 TYR cc_start: 0.8560 (p90) cc_final: 0.8291 (p90) REVERT: A 816 ILE cc_start: 0.7524 (mp) cc_final: 0.7316 (pt) REVERT: B 243 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: B 479 PHE cc_start: 0.3897 (m-80) cc_final: 0.3385 (m-80) REVERT: C 351 MET cc_start: 0.6990 (mmm) cc_final: 0.6682 (ppp) REVERT: C 511 LEU cc_start: 0.7724 (tp) cc_final: 0.7509 (mp) REVERT: C 796 VAL cc_start: 0.5712 (p) cc_final: 0.5452 (p) REVERT: C 846 PHE cc_start: 0.7483 (m-10) cc_final: 0.7281 (m-10) REVERT: D 439 SER cc_start: 0.8075 (t) cc_final: 0.7847 (m) REVERT: D 511 LEU cc_start: 0.8290 (tp) cc_final: 0.8081 (tt) outliers start: 10 outliers final: 4 residues processed: 461 average time/residue: 0.1568 time to fit residues: 112.9562 Evaluate side-chains 243 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 73 PRO Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 243 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 309 HIS A 339 HIS A 457 HIS A 508 ASN A 697 HIS B 806 GLN C 47 HIS C 339 HIS C 567 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS D 345 GLN ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 GLN D 821 ASN D 865 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.176617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.127220 restraints weight = 55263.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126872 restraints weight = 31679.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.128275 restraints weight = 22573.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129196 restraints weight = 18601.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.129259 restraints weight = 16060.574| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25279 Z= 0.163 Angle : 0.670 12.405 34454 Z= 0.339 Chirality : 0.046 0.355 3802 Planarity : 0.005 0.042 4375 Dihedral : 12.366 110.039 3768 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.51 % Allowed : 9.08 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3076 helix: -2.38 (0.64), residues: 40 sheet: -0.79 (0.17), residues: 889 loop : -0.12 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 115 TYR 0.019 0.002 TYR B 864 PHE 0.034 0.002 PHE D 696 TRP 0.025 0.002 TRP C 228 HIS 0.011 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (25162) covalent geometry : angle 0.65107 / 0.33 (34202) SS BOND : bond 0.00548 / 0.41 ( 99) SS BOND : angle 1.44150 / 1.02 ( 198) hydrogen bonds : bond 0.05036 / 3.42 ( 497) hydrogen bonds : angle 7.81296 / 5.45 ( 1242) link_BETA1-4 : bond 0.00476 / 0.23 ( 3) link_BETA1-4 : angle 1.81689 / 0.90 ( 9) link_NAG-ASN : bond 0.00811 / 0.47 ( 15) link_NAG-ASN : angle 3.49142 / 2.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.8963 (m-10) cc_final: 0.8421 (m-10) REVERT: A 514 MET cc_start: 0.5592 (mtt) cc_final: 0.5172 (mtm) REVERT: A 534 LYS cc_start: 0.9166 (ptpt) cc_final: 0.8895 (tmtt) REVERT: A 695 TYR cc_start: 0.8762 (p90) cc_final: 0.8494 (p90) REVERT: B 74 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7837 (t70) REVERT: B 99 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6920 (mm-30) REVERT: B 351 MET cc_start: 0.6678 (ptm) cc_final: 0.6161 (ptp) REVERT: B 514 MET cc_start: 0.7633 (mpp) cc_final: 0.7383 (mpp) REVERT: B 773 MET cc_start: 0.3194 (tpp) cc_final: 0.2948 (tpt) REVERT: C 166 ILE cc_start: 0.8982 (tp) cc_final: 0.8531 (tt) REVERT: C 496 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6631 (ttp-110) REVERT: C 499 PHE cc_start: 0.4627 (OUTLIER) cc_final: 0.4020 (m-10) REVERT: D 221 MET cc_start: 0.7991 (mmt) cc_final: 0.7371 (mmt) REVERT: D 452 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7187 (mp0) REVERT: D 587 TYR cc_start: 0.4362 (m-80) cc_final: 0.4119 (m-80) REVERT: D 775 LEU cc_start: 0.7049 (tp) cc_final: 0.6696 (tt) outliers start: 41 outliers final: 24 residues processed: 289 average time/residue: 0.1422 time to fit residues: 67.2374 Evaluate side-chains 237 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 856 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 130 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS D 263 ASN D 410 HIS D 467 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.173478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.126445 restraints weight = 53933.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.125010 restraints weight = 29386.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.125194 restraints weight = 24949.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.125781 restraints weight = 22078.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.126352 restraints weight = 18320.107| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25279 Z= 0.192 Angle : 0.658 10.755 34454 Z= 0.332 Chirality : 0.045 0.351 3802 Planarity : 0.005 0.043 4375 Dihedral : 11.732 108.839 3755 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.43 % Allowed : 11.62 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -0.67 (0.15), residues: 3076 helix: -2.34 (0.68), residues: 40 sheet: -0.83 (0.18), residues: 880 loop : -0.16 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 245 TYR 0.027 0.002 TYR D 195 PHE 0.037 0.002 PHE D 499 TRP 0.019 0.002 TRP D 551 HIS 0.009 0.001 HIS C 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (25162) covalent geometry : angle 0.64212 / 0.33 (34202) SS BOND : bond 0.00318 / 0.24 ( 99) SS BOND : angle 1.12991 / 0.82 ( 198) hydrogen bonds : bond 0.04371 / 2.96 ( 497) hydrogen bonds : angle 7.34419 / 5.15 ( 1242) link_BETA1-4 : bond 0.00336 / 0.17 ( 3) link_BETA1-4 : angle 1.94729 / 0.96 ( 9) link_NAG-ASN : bond 0.00787 / 0.48 ( 15) link_NAG-ASN : angle 3.37662 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7665 (p-80) REVERT: A 337 TYR cc_start: 0.5530 (p90) cc_final: 0.5266 (p90) REVERT: A 352 TYR cc_start: 0.8908 (m-10) cc_final: 0.8293 (m-10) REVERT: A 514 MET cc_start: 0.5621 (mtt) cc_final: 0.5211 (mtm) REVERT: A 517 MET cc_start: 0.6273 (mmm) cc_final: 0.5574 (mmt) REVERT: A 534 LYS cc_start: 0.9121 (ptpt) cc_final: 0.8832 (tmtt) REVERT: A 558 LEU cc_start: 0.8457 (tp) cc_final: 0.8230 (pp) REVERT: A 581 MET cc_start: 0.7358 (mtt) cc_final: 0.6637 (mtt) REVERT: A 695 TYR cc_start: 0.8788 (p90) cc_final: 0.8473 (p90) REVERT: B 53 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: B 351 MET cc_start: 0.6533 (ptm) cc_final: 0.6053 (ptp) REVERT: B 773 MET cc_start: 0.3605 (tpp) cc_final: 0.3110 (tpt) REVERT: B 881 MET cc_start: 0.6730 (mmm) cc_final: 0.5854 (mtt) REVERT: C 54 TYR cc_start: 0.8945 (p90) cc_final: 0.8477 (p90) REVERT: C 115 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8096 (mtp85) REVERT: C 337 TYR cc_start: 0.6721 (p90) cc_final: 0.6486 (p90) REVERT: C 351 MET cc_start: 0.7044 (ppp) cc_final: 0.6700 (ppp) REVERT: C 387 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5440 (p90) REVERT: C 496 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6544 (ttp-110) REVERT: C 499 PHE cc_start: 0.4348 (OUTLIER) cc_final: 0.3560 (m-80) REVERT: C 830 LEU cc_start: 0.7269 (tp) cc_final: 0.6815 (mp) REVERT: C 846 PHE cc_start: 0.7963 (m-80) cc_final: 0.7636 (m-80) REVERT: D 221 MET cc_start: 0.7948 (mmt) cc_final: 0.7239 (mmt) REVERT: D 234 GLU cc_start: 0.8085 (mp0) cc_final: 0.7863 (mp0) REVERT: D 419 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7814 (m) REVERT: D 452 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: D 480 ARG cc_start: 0.8193 (tmt170) cc_final: 0.7902 (ptm160) REVERT: D 499 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6992 (m-10) REVERT: D 587 TYR cc_start: 0.4619 (m-80) cc_final: 0.4354 (m-80) REVERT: D 670 ASN cc_start: 0.8242 (t0) cc_final: 0.7628 (m-40) REVERT: D 775 LEU cc_start: 0.7248 (tp) cc_final: 0.6929 (tt) REVERT: D 823 MET cc_start: 0.7917 (tpp) cc_final: 0.7305 (tpt) outliers start: 66 outliers final: 43 residues processed: 265 average time/residue: 0.1500 time to fit residues: 64.7411 Evaluate side-chains 239 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 296 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 284 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 865 HIS B 231 HIS C 567 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.172828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.126010 restraints weight = 55075.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123699 restraints weight = 31202.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124222 restraints weight = 27787.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.124770 restraints weight = 23567.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.125572 restraints weight = 19520.430| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25279 Z= 0.170 Angle : 0.627 11.147 34454 Z= 0.314 Chirality : 0.044 0.353 3802 Planarity : 0.004 0.060 4375 Dihedral : 11.202 108.957 3755 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.87 % Allowed : 13.05 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -0.70 (0.15), residues: 3076 helix: -2.19 (0.72), residues: 40 sheet: -0.83 (0.18), residues: 868 loop : -0.21 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 555 TYR 0.028 0.002 TYR D 195 PHE 0.035 0.002 PHE C 499 TRP 0.018 0.002 TRP D 551 HIS 0.040 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (25162) covalent geometry : angle 0.61102 / 0.31 (34202) SS BOND : bond 0.00308 / 0.20 ( 99) SS BOND : angle 1.02953 / 0.77 ( 198) hydrogen bonds : bond 0.03675 / 2.50 ( 497) hydrogen bonds : angle 7.00285 / 4.92 ( 1242) link_BETA1-4 : bond 0.00591 / 0.30 ( 3) link_BETA1-4 : angle 2.61957 / 1.31 ( 9) link_NAG-ASN : bond 0.00731 / 0.42 ( 15) link_NAG-ASN : angle 3.41681 / 2.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.5644 (p90) cc_final: 0.5348 (p90) REVERT: A 352 TYR cc_start: 0.8987 (m-10) cc_final: 0.8408 (m-10) REVERT: A 512 TYR cc_start: 0.7930 (m-80) cc_final: 0.7539 (m-10) REVERT: A 514 MET cc_start: 0.5598 (mtt) cc_final: 0.5210 (mtm) REVERT: A 517 MET cc_start: 0.6248 (mmm) cc_final: 0.5515 (mmt) REVERT: A 534 LYS cc_start: 0.9117 (ptpt) cc_final: 0.8811 (tmtt) REVERT: A 581 MET cc_start: 0.7390 (mtt) cc_final: 0.6528 (mtt) REVERT: B 53 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: B 351 MET cc_start: 0.6438 (ptm) cc_final: 0.5921 (ptp) REVERT: B 520 ARG cc_start: 0.5978 (tpp-160) cc_final: 0.5576 (tpp-160) REVERT: B 773 MET cc_start: 0.3737 (tpp) cc_final: 0.3116 (tpt) REVERT: B 881 MET cc_start: 0.6689 (mmm) cc_final: 0.5687 (mtt) REVERT: C 54 TYR cc_start: 0.9175 (p90) cc_final: 0.8781 (p90) REVERT: C 115 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7971 (mtp85) REVERT: C 351 MET cc_start: 0.7103 (ppp) cc_final: 0.6670 (ppp) REVERT: C 387 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.5578 (p90) REVERT: C 496 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6650 (ttp-110) REVERT: C 499 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.3649 (m-80) REVERT: C 749 MET cc_start: 0.6505 (ppp) cc_final: 0.6300 (ppp) REVERT: C 830 LEU cc_start: 0.7284 (tp) cc_final: 0.6676 (mp) REVERT: C 846 PHE cc_start: 0.8034 (m-80) cc_final: 0.7752 (m-80) REVERT: D 221 MET cc_start: 0.8030 (mmt) cc_final: 0.7265 (mmt) REVERT: D 234 GLU cc_start: 0.8155 (mp0) cc_final: 0.7935 (mp0) REVERT: D 499 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: D 775 LEU cc_start: 0.7230 (tp) cc_final: 0.6869 (tt) outliers start: 78 outliers final: 53 residues processed: 269 average time/residue: 0.1453 time to fit residues: 63.3359 Evaluate side-chains 244 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 205 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.171340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124114 restraints weight = 53684.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.122255 restraints weight = 30674.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.122174 restraints weight = 26614.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.122795 restraints weight = 23691.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.123238 restraints weight = 19719.722| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25279 Z= 0.182 Angle : 0.632 10.452 34454 Z= 0.316 Chirality : 0.044 0.352 3802 Planarity : 0.004 0.045 4375 Dihedral : 10.823 109.586 3753 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.12 % Allowed : 14.52 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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 (0.15), residues: 3076 helix: -2.10 (0.75), residues: 40 sheet: -0.94 (0.18), residues: 863 loop : -0.20 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.028 0.002 TYR D 195 PHE 0.036 0.002 PHE D 499 TRP 0.018 0.002 TRP D 551 HIS 0.007 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (25162) covalent geometry : angle 0.61492 / 0.31 (34202) SS BOND : bond 0.00267 / 0.18 ( 99) SS BOND : angle 1.02623 / 0.77 ( 198) hydrogen bonds : bond 0.03484 / 2.37 ( 497) hydrogen bonds : angle 6.81670 / 4.77 ( 1242) link_BETA1-4 : bond 0.00563 / 0.29 ( 3) link_BETA1-4 : angle 2.95791 / 1.49 ( 9) link_NAG-ASN : bond 0.00703 / 0.41 ( 15) link_NAG-ASN : angle 3.46577 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 191 time to evaluate : 0.855 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: symmetry clash REVERT: A 337 TYR cc_start: 0.5302 (p90) cc_final: 0.4972 (p90) REVERT: A 352 TYR cc_start: 0.9027 (m-10) cc_final: 0.8377 (m-10) REVERT: A 512 TYR cc_start: 0.7926 (m-80) cc_final: 0.7539 (m-10) REVERT: A 514 MET cc_start: 0.5626 (mtt) cc_final: 0.5223 (mtm) REVERT: A 517 MET cc_start: 0.6222 (mmm) cc_final: 0.5518 (mmt) REVERT: A 534 LYS cc_start: 0.9099 (ptpt) cc_final: 0.8821 (tmtt) REVERT: A 581 MET cc_start: 0.7534 (mtt) cc_final: 0.6592 (mtt) REVERT: B 351 MET cc_start: 0.6395 (ptm) cc_final: 0.5901 (ptp) REVERT: B 370 LEU cc_start: 0.5613 (tp) cc_final: 0.5215 (pp) REVERT: B 773 MET cc_start: 0.4079 (tpp) cc_final: 0.3528 (tpt) REVERT: B 881 MET cc_start: 0.6724 (mmm) cc_final: 0.5781 (mtt) REVERT: C 54 TYR cc_start: 0.9261 (p90) cc_final: 0.8978 (p90) REVERT: C 115 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7928 (mtp85) REVERT: C 351 MET cc_start: 0.6995 (ppp) cc_final: 0.6564 (ppp) REVERT: C 387 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5725 (p90) REVERT: C 470 MET cc_start: 0.6715 (mmt) cc_final: 0.6118 (mmt) REVERT: C 496 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6689 (ttp-110) REVERT: C 846 PHE cc_start: 0.7930 (m-80) cc_final: 0.7690 (m-80) REVERT: D 221 MET cc_start: 0.7990 (mmt) cc_final: 0.7208 (mmt) REVERT: D 282 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8437 (t) REVERT: D 419 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7900 (m) REVERT: D 452 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: D 480 ARG cc_start: 0.8325 (tmt170) cc_final: 0.7792 (ptm160) REVERT: D 499 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: D 775 LEU cc_start: 0.7246 (tp) cc_final: 0.6860 (tt) REVERT: D 823 MET cc_start: 0.8008 (tpp) cc_final: 0.7649 (tpt) REVERT: D 835 MET cc_start: 0.7258 (tmm) cc_final: 0.7021 (ptm) outliers start: 85 outliers final: 59 residues processed: 263 average time/residue: 0.1400 time to fit residues: 61.1226 Evaluate side-chains 240 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 638 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 92 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 268 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 289 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 302 optimal weight: 0.5980 chunk 278 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.172532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.124546 restraints weight = 55190.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.122755 restraints weight = 36386.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123264 restraints weight = 26737.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.123848 restraints weight = 24523.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.124312 restraints weight = 20423.006| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25279 Z= 0.135 Angle : 0.616 10.756 34454 Z= 0.302 Chirality : 0.043 0.351 3802 Planarity : 0.004 0.045 4375 Dihedral : 10.282 108.926 3753 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.01 % Allowed : 15.22 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -0.66 (0.15), residues: 3076 helix: -2.11 (0.76), residues: 40 sheet: -0.88 (0.18), residues: 864 loop : -0.15 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 245 TYR 0.023 0.001 TYR D 655 PHE 0.031 0.002 PHE C 499 TRP 0.022 0.001 TRP C 850 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (25162) covalent geometry : angle 0.59392 / 0.30 (34202) SS BOND : bond 0.00265 / 0.20 ( 99) SS BOND : angle 1.19512 / 0.86 ( 198) hydrogen bonds : bond 0.03189 / 2.19 ( 497) hydrogen bonds : angle 6.53483 / 4.56 ( 1242) link_BETA1-4 : bond 0.00503 / 0.25 ( 3) link_BETA1-4 : angle 3.45815 / 1.73 ( 9) link_NAG-ASN : bond 0.00724 / 0.42 ( 15) link_NAG-ASN : angle 3.69142 / 2.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 186 time to evaluate : 0.932 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 337 TYR cc_start: 0.5352 (p90) cc_final: 0.5046 (p90) REVERT: A 352 TYR cc_start: 0.8914 (m-10) cc_final: 0.8312 (m-10) REVERT: A 512 TYR cc_start: 0.7948 (m-80) cc_final: 0.7568 (m-10) REVERT: A 514 MET cc_start: 0.5697 (mtt) cc_final: 0.5268 (mtm) REVERT: A 517 MET cc_start: 0.5861 (mmm) cc_final: 0.5079 (mmt) REVERT: A 534 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8792 (tmtt) REVERT: B 351 MET cc_start: 0.6283 (ptm) cc_final: 0.5701 (ptp) REVERT: B 370 LEU cc_start: 0.5650 (tp) cc_final: 0.5022 (pp) REVERT: B 378 ARG cc_start: 0.6841 (tpt90) cc_final: 0.6626 (tpm170) REVERT: B 773 MET cc_start: 0.4623 (tpp) cc_final: 0.3999 (tpt) REVERT: B 881 MET cc_start: 0.6633 (mmm) cc_final: 0.5626 (mtt) REVERT: C 54 TYR cc_start: 0.9208 (p90) cc_final: 0.8998 (p90) REVERT: C 115 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8018 (mtp85) REVERT: C 351 MET cc_start: 0.7005 (ppp) cc_final: 0.6576 (ppp) REVERT: C 387 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.5810 (p90) REVERT: C 434 GLU cc_start: 0.6996 (pm20) cc_final: 0.6527 (pp20) REVERT: C 480 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.5255 (tmm-80) REVERT: C 496 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6731 (ttp-110) REVERT: C 499 PHE cc_start: 0.4769 (OUTLIER) cc_final: 0.4425 (m-10) REVERT: C 749 MET cc_start: 0.6430 (ppp) cc_final: 0.6191 (ppp) REVERT: C 773 MET cc_start: 0.7827 (tpp) cc_final: 0.7512 (tpp) REVERT: C 775 LEU cc_start: 0.6062 (mt) cc_final: 0.5816 (mt) REVERT: C 835 MET cc_start: 0.8322 (ppp) cc_final: 0.8027 (ppp) REVERT: C 846 PHE cc_start: 0.7782 (m-80) cc_final: 0.7526 (m-80) REVERT: D 221 MET cc_start: 0.7964 (mmt) cc_final: 0.7223 (mmt) REVERT: D 282 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8472 (t) REVERT: D 419 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7979 (m) REVERT: D 452 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: D 480 ARG cc_start: 0.8294 (tmt170) cc_final: 0.7769 (ptm160) REVERT: D 775 LEU cc_start: 0.7282 (tp) cc_final: 0.6896 (tt) REVERT: D 823 MET cc_start: 0.8120 (tpp) cc_final: 0.7578 (tpt) REVERT: D 835 MET cc_start: 0.7300 (tmm) cc_final: 0.7042 (ptp) outliers start: 82 outliers final: 55 residues processed: 256 average time/residue: 0.1502 time to fit residues: 62.8316 Evaluate side-chains 234 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain D residue 638 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 150 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 432 ASN ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN D 698 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.166954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.115620 restraints weight = 54344.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113718 restraints weight = 33573.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.115032 restraints weight = 27066.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.115492 restraints weight = 22232.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.115743 restraints weight = 18940.981| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 25279 Z= 0.358 Angle : 0.795 12.931 34454 Z= 0.407 Chirality : 0.049 0.380 3802 Planarity : 0.006 0.078 4375 Dihedral : 10.838 117.211 3753 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.79 % Allowed : 15.29 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -1.15 (0.15), residues: 3076 helix: -1.55 (0.91), residues: 34 sheet: -1.27 (0.17), residues: 895 loop : -0.47 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 831 TYR 0.038 0.003 TYR C 195 PHE 0.042 0.003 PHE C 499 TRP 0.032 0.003 TRP D 551 HIS 0.010 0.002 HIS D 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.36 (25162) covalent geometry : angle 0.77536 / 0.40 (34202) SS BOND : bond 0.00494 / 0.35 ( 99) SS BOND : angle 1.51873 / 1.07 ( 198) hydrogen bonds : bond 0.04133 / 2.79 ( 497) hydrogen bonds : angle 7.32257 / 5.11 ( 1242) link_BETA1-4 : bond 0.00746 / 0.38 ( 3) link_BETA1-4 : angle 3.15900 / 1.53 ( 9) link_NAG-ASN : bond 0.00675 / 0.40 ( 15) link_NAG-ASN : angle 3.89122 / 2.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 169 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.6832 (m170) REVERT: A 352 TYR cc_start: 0.8997 (m-10) cc_final: 0.8385 (m-10) REVERT: A 512 TYR cc_start: 0.7984 (m-80) cc_final: 0.7670 (m-10) REVERT: A 514 MET cc_start: 0.6011 (mtt) cc_final: 0.5537 (mtm) REVERT: A 517 MET cc_start: 0.5777 (mmm) cc_final: 0.5063 (mmt) REVERT: B 291 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.6034 (t80) REVERT: B 351 MET cc_start: 0.6351 (ptm) cc_final: 0.5698 (ptp) REVERT: B 378 ARG cc_start: 0.6499 (tpt90) cc_final: 0.6293 (tpm170) REVERT: B 773 MET cc_start: 0.4363 (tpp) cc_final: 0.3788 (tpt) REVERT: B 881 MET cc_start: 0.6519 (mmm) cc_final: 0.5501 (mtt) REVERT: C 115 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7972 (mtp85) REVERT: C 387 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5405 (p90) REVERT: C 480 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5604 (tmm-80) REVERT: C 496 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6204 (ttp-110) REVERT: C 499 PHE cc_start: 0.5624 (OUTLIER) cc_final: 0.5424 (m-10) REVERT: C 749 MET cc_start: 0.6507 (ppp) cc_final: 0.6194 (ppp) REVERT: C 773 MET cc_start: 0.7901 (tpp) cc_final: 0.7372 (tpp) REVERT: C 835 MET cc_start: 0.8291 (ppp) cc_final: 0.8009 (ppp) REVERT: C 846 PHE cc_start: 0.7941 (m-80) cc_final: 0.7611 (m-80) REVERT: D 221 MET cc_start: 0.8061 (mmt) cc_final: 0.7299 (mmt) REVERT: D 282 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8416 (t) REVERT: D 419 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8135 (m) REVERT: D 439 SER cc_start: 0.8533 (t) cc_final: 0.8271 (p) REVERT: D 480 ARG cc_start: 0.8281 (tmt170) cc_final: 0.7766 (ptm160) REVERT: D 499 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: D 775 LEU cc_start: 0.7261 (tp) cc_final: 0.6842 (tt) REVERT: D 823 MET cc_start: 0.8148 (tpp) cc_final: 0.7809 (tpp) REVERT: D 835 MET cc_start: 0.7071 (tmm) cc_final: 0.6850 (ptp) outliers start: 103 outliers final: 70 residues processed: 256 average time/residue: 0.1401 time to fit residues: 58.7998 Evaluate side-chains 234 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 154 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 638 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 66 optimal weight: 40.0000 chunk 69 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 192 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.121296 restraints weight = 54884.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.120338 restraints weight = 33600.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.121895 restraints weight = 24381.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.122612 restraints weight = 20098.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.122574 restraints weight = 17392.292| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25279 Z= 0.131 Angle : 0.643 10.693 34454 Z= 0.319 Chirality : 0.044 0.350 3802 Planarity : 0.004 0.045 4375 Dihedral : 9.838 111.877 3751 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.46 % Allowed : 17.32 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -0.90 (0.15), residues: 3076 helix: -1.67 (0.89), residues: 34 sheet: -1.10 (0.18), residues: 879 loop : -0.30 (0.14), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 245 TYR 0.027 0.001 TYR D 283 PHE 0.031 0.002 PHE B 499 TRP 0.033 0.002 TRP D 551 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (25162) covalent geometry : angle 0.61892 / 0.31 (34202) SS BOND : bond 0.00275 / 0.19 ( 99) SS BOND : angle 1.27441 / 0.93 ( 198) hydrogen bonds : bond 0.03204 / 2.18 ( 497) hydrogen bonds : angle 6.61051 / 4.61 ( 1242) link_BETA1-4 : bond 0.00880 / 0.43 ( 3) link_BETA1-4 : angle 3.63424 / 1.78 ( 9) link_NAG-ASN : bond 0.00872 / 0.55 ( 15) link_NAG-ASN : angle 4.01041 / 2.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.5327 (p90) cc_final: 0.4993 (p90) REVERT: A 352 TYR cc_start: 0.8923 (m-10) cc_final: 0.8271 (m-10) REVERT: A 512 TYR cc_start: 0.7864 (m-80) cc_final: 0.7504 (m-10) REVERT: A 514 MET cc_start: 0.5857 (mtt) cc_final: 0.5380 (mtm) REVERT: A 534 LYS cc_start: 0.9067 (ptpt) cc_final: 0.8769 (tmtt) REVERT: B 162 ARG cc_start: 0.8673 (ttm110) cc_final: 0.7772 (ttp80) REVERT: B 351 MET cc_start: 0.6379 (ptm) cc_final: 0.5762 (ptp) REVERT: B 479 PHE cc_start: 0.3588 (m-80) cc_final: 0.3165 (m-10) REVERT: B 881 MET cc_start: 0.6349 (mmm) cc_final: 0.5466 (mtt) REVERT: C 115 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8028 (mtp85) REVERT: C 387 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.5831 (p90) REVERT: C 434 GLU cc_start: 0.7196 (pm20) cc_final: 0.6613 (pp20) REVERT: C 480 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5257 (tmm-80) REVERT: C 496 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6178 (ttp-110) REVERT: C 749 MET cc_start: 0.6482 (ppp) cc_final: 0.6152 (ppp) REVERT: C 773 MET cc_start: 0.7941 (tpp) cc_final: 0.7550 (tpp) REVERT: C 835 MET cc_start: 0.8337 (ppp) cc_final: 0.7966 (ppp) REVERT: C 846 PHE cc_start: 0.7909 (m-80) cc_final: 0.7628 (m-80) REVERT: D 221 MET cc_start: 0.7976 (mmt) cc_final: 0.7139 (mmt) REVERT: D 419 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8416 (m) REVERT: D 439 SER cc_start: 0.8417 (t) cc_final: 0.8183 (p) REVERT: D 480 ARG cc_start: 0.8272 (tmt170) cc_final: 0.7711 (ptm160) REVERT: D 775 LEU cc_start: 0.7229 (tp) cc_final: 0.6816 (tt) REVERT: D 823 MET cc_start: 0.7979 (tpp) cc_final: 0.7430 (tpt) REVERT: D 835 MET cc_start: 0.7371 (tmm) cc_final: 0.7106 (ptp) outliers start: 67 outliers final: 53 residues processed: 240 average time/residue: 0.1428 time to fit residues: 56.3751 Evaluate side-chains 228 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 638 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 245 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 142 optimal weight: 40.0000 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.170963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.124232 restraints weight = 54644.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.120573 restraints weight = 31271.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122122 restraints weight = 26708.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122562 restraints weight = 21437.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.122772 restraints weight = 18338.501| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25279 Z= 0.142 Angle : 0.633 9.353 34454 Z= 0.314 Chirality : 0.044 0.350 3802 Planarity : 0.004 0.044 4375 Dihedral : 9.681 115.074 3751 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.39 % Allowed : 17.57 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -0.86 (0.15), residues: 3076 helix: -1.82 (0.88), residues: 34 sheet: -1.08 (0.18), residues: 883 loop : -0.25 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 496 TYR 0.021 0.001 TYR C 195 PHE 0.028 0.002 PHE B 499 TRP 0.036 0.002 TRP D 551 HIS 0.007 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (25162) covalent geometry : angle 0.61084 / 0.31 (34202) SS BOND : bond 0.00253 / 0.18 ( 99) SS BOND : angle 1.12918 / 0.81 ( 198) hydrogen bonds : bond 0.03091 / 2.11 ( 497) hydrogen bonds : angle 6.35340 / 4.42 ( 1242) link_BETA1-4 : bond 0.00699 / 0.35 ( 3) link_BETA1-4 : angle 3.91261 / 1.93 ( 9) link_NAG-ASN : bond 0.00865 / 0.55 ( 15) link_NAG-ASN : angle 3.79471 / 2.75 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.5280 (p90) cc_final: 0.4971 (p90) REVERT: A 352 TYR cc_start: 0.8937 (m-10) cc_final: 0.8309 (m-10) REVERT: A 512 TYR cc_start: 0.7851 (m-80) cc_final: 0.7458 (m-10) REVERT: A 514 MET cc_start: 0.5830 (mtt) cc_final: 0.5360 (mtm) REVERT: A 517 MET cc_start: 0.5778 (tpt) cc_final: 0.4624 (mmt) REVERT: A 534 LYS cc_start: 0.9062 (ptpt) cc_final: 0.8773 (tmtt) REVERT: B 162 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8236 (tmt-80) REVERT: B 351 MET cc_start: 0.6355 (ptm) cc_final: 0.5749 (ptp) REVERT: B 479 PHE cc_start: 0.3594 (m-80) cc_final: 0.3115 (m-10) REVERT: B 881 MET cc_start: 0.6199 (mmm) cc_final: 0.5450 (mtt) REVERT: C 387 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.5806 (p90) REVERT: C 416 GLU cc_start: 0.5492 (pp20) cc_final: 0.5154 (pp20) REVERT: C 470 MET cc_start: 0.6975 (mmt) cc_final: 0.6504 (mmt) REVERT: C 480 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.5281 (tmm-80) REVERT: C 496 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6112 (ttp-110) REVERT: C 749 MET cc_start: 0.6518 (ppp) cc_final: 0.6288 (ppp) REVERT: C 773 MET cc_start: 0.7912 (tpp) cc_final: 0.7518 (tpp) REVERT: D 221 MET cc_start: 0.8010 (mmt) cc_final: 0.7244 (mmt) REVERT: D 439 SER cc_start: 0.8506 (t) cc_final: 0.8202 (p) REVERT: D 480 ARG cc_start: 0.8268 (tmt170) cc_final: 0.7762 (ptm160) REVERT: D 775 LEU cc_start: 0.7166 (tp) cc_final: 0.6918 (tt) REVERT: D 823 MET cc_start: 0.7810 (tpp) cc_final: 0.7275 (tpt) REVERT: D 835 MET cc_start: 0.7512 (tmm) cc_final: 0.7274 (ptp) REVERT: D 865 HIS cc_start: 0.7557 (t-90) cc_final: 0.7238 (t70) outliers start: 65 outliers final: 57 residues processed: 229 average time/residue: 0.1580 time to fit residues: 59.3505 Evaluate side-chains 225 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 638 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 267 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 299 optimal weight: 0.2980 chunk 306 optimal weight: 0.0870 chunk 77 optimal weight: 50.0000 chunk 164 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.125213 restraints weight = 54364.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.123807 restraints weight = 31885.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.124439 restraints weight = 23911.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.125369 restraints weight = 20698.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.125517 restraints weight = 17842.164| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25279 Z= 0.110 Angle : 0.611 9.696 34454 Z= 0.299 Chirality : 0.043 0.347 3802 Planarity : 0.004 0.042 4375 Dihedral : 9.340 114.840 3751 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.13 % Allowed : 17.94 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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 (0.15), residues: 3076 helix: -1.75 (0.89), residues: 34 sheet: -0.98 (0.18), residues: 867 loop : -0.20 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 555 TYR 0.022 0.001 TYR D 655 PHE 0.024 0.001 PHE B 499 TRP 0.039 0.002 TRP C 354 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (25162) covalent geometry : angle 0.59024 / 0.29 (34202) SS BOND : bond 0.00200 / 0.14 ( 99) SS BOND : angle 0.97604 / 0.70 ( 198) hydrogen bonds : bond 0.02920 / 1.99 ( 497) hydrogen bonds : angle 6.07917 / 4.23 ( 1242) link_BETA1-4 : bond 0.00714 / 0.36 ( 3) link_BETA1-4 : angle 4.15105 / 2.02 ( 9) link_NAG-ASN : bond 0.00769 / 0.44 ( 15) link_NAG-ASN : angle 3.60770 / 2.60 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.5159 (p90) cc_final: 0.4843 (p90) REVERT: A 352 TYR cc_start: 0.8843 (m-10) cc_final: 0.8199 (m-10) REVERT: A 512 TYR cc_start: 0.7880 (m-80) cc_final: 0.7472 (m-10) REVERT: A 514 MET cc_start: 0.5701 (mtt) cc_final: 0.5219 (mtm) REVERT: A 517 MET cc_start: 0.5969 (tpt) cc_final: 0.4802 (mmt) REVERT: B 162 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8190 (tmt-80) REVERT: B 351 MET cc_start: 0.6251 (ptm) cc_final: 0.5586 (ptp) REVERT: B 479 PHE cc_start: 0.3446 (m-80) cc_final: 0.3119 (m-80) REVERT: B 655 TYR cc_start: 0.5523 (t80) cc_final: 0.4660 (t80) REVERT: B 881 MET cc_start: 0.6151 (mmm) cc_final: 0.5435 (mtt) REVERT: C 387 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.5898 (p90) REVERT: C 434 GLU cc_start: 0.6924 (pm20) cc_final: 0.6661 (pp20) REVERT: C 470 MET cc_start: 0.6673 (mmt) cc_final: 0.6248 (mmt) REVERT: C 496 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.5953 (ttp-110) REVERT: C 749 MET cc_start: 0.6432 (ppp) cc_final: 0.6115 (ppp) REVERT: C 773 MET cc_start: 0.7988 (tpp) cc_final: 0.7674 (tpp) REVERT: D 221 MET cc_start: 0.7935 (mmt) cc_final: 0.7167 (mmt) REVERT: D 282 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (t) REVERT: D 439 SER cc_start: 0.8476 (t) cc_final: 0.8171 (p) REVERT: D 452 GLU cc_start: 0.7810 (mp0) cc_final: 0.7570 (mp0) REVERT: D 480 ARG cc_start: 0.8339 (tmt170) cc_final: 0.7662 (ptt90) REVERT: D 775 LEU cc_start: 0.7248 (tp) cc_final: 0.6924 (tt) REVERT: D 823 MET cc_start: 0.7610 (tpp) cc_final: 0.7106 (tpt) REVERT: D 865 HIS cc_start: 0.7521 (t-90) cc_final: 0.7214 (t70) outliers start: 58 outliers final: 52 residues processed: 227 average time/residue: 0.1516 time to fit residues: 57.4331 Evaluate side-chains 216 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 TYR Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 638 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 655 TYR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 3 optimal weight: 0.2980 chunk 60 optimal weight: 0.0030 chunk 154 optimal weight: 20.0000 chunk 284 optimal weight: 0.4980 chunk 272 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 31 optimal weight: 0.0010 chunk 193 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.172694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.123395 restraints weight = 54919.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.122410 restraints weight = 32558.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.123573 restraints weight = 25785.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.124174 restraints weight = 20808.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.124369 restraints weight = 17922.801| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25279 Z= 0.114 Angle : 0.594 8.914 34454 Z= 0.294 Chirality : 0.043 0.347 3802 Planarity : 0.004 0.043 4375 Dihedral : 9.139 117.200 3751 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.13 % Allowed : 18.27 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % 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: -0.70 (0.15), residues: 3076 helix: -1.65 (0.91), residues: 34 sheet: -0.91 (0.18), residues: 859 loop : -0.18 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 480 TYR 0.025 0.001 TYR C 655 PHE 0.044 0.002 PHE B 499 TRP 0.033 0.002 TRP C 354 HIS 0.005 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (25162) covalent geometry : angle 0.57512 / 0.29 (34202) SS BOND : bond 0.00207 / 0.14 ( 99) SS BOND : angle 0.82654 / 0.59 ( 198) hydrogen bonds : bond 0.02890 / 1.97 ( 497) hydrogen bonds : angle 5.97601 / 4.16 ( 1242) link_BETA1-4 : bond 0.00710 / 0.36 ( 3) link_BETA1-4 : angle 4.15627 / 1.99 ( 9) link_NAG-ASN : bond 0.00759 / 0.44 ( 15) link_NAG-ASN : angle 3.53557 / 2.55 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4585.57 seconds wall clock time: 80 minutes 4.78 seconds (4804.78 seconds total)