Starting phenix.real_space_refine on Mon Aug 25 05:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqm_65260/08_2025/9vqm_65260_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqm_65260/08_2025/9vqm_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 { model { file = "/net/cci-nas-00/data/ceres_data/9vqm_65260/08_2025/9vqm_65260_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqm_65260/08_2025/9vqm_65260_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vqm_65260/08_2025/9vqm_65260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqm_65260/08_2025/9vqm_65260.map" } 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-2.0-5787/lib/python3.9/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, 44 Unusual residues: {' CU': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 43 Unusual residues: {' CU': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 5.70, per 1000 atoms: 0.23 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: 1.48 Conformation dependent library (CDL) restraints added in 820.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.04 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: 4.61 Time building geometry restraints manager: 2.09 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.410 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 aren 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 covalent geometry : bond 0.00340 (25162) covalent geometry : angle 0.73729 (34202) SS BOND : bond 0.00235 ( 99) SS BOND : angle 1.13414 ( 198) hydrogen bonds : bond 0.30253 ( 497) hydrogen bonds : angle 10.96714 ( 1242) link_BETA1-4 : bond 0.00464 ( 3) link_BETA1-4 : angle 0.79576 ( 9) link_NAG-ASN : bond 0.00810 ( 15) link_NAG-ASN : angle 3.31115 ( 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 : 0.627 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: 0.1577 time to fit residues: 113.3304 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 : 0.923 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.176603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.128202 restraints weight = 55325.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127758 restraints weight = 31526.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.128487 restraints weight = 23588.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129243 restraints weight = 21595.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.129453 restraints weight = 17287.348| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25279 Z= 0.163 Angle : 0.672 12.682 34454 Z= 0.341 Chirality : 0.046 0.353 3802 Planarity : 0.005 0.044 4375 Dihedral : 12.369 109.960 3768 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.47 % Allowed : 9.15 % Favored : 89.38 % 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 aren not related in a simple way. whole: -0.62 (0.15), residues: 3076 helix: -2.40 (0.63), residues: 40 sheet: -0.80 (0.17), residues: 890 loop : -0.12 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.019 0.002 TYR B 54 PHE 0.034 0.002 PHE D 696 TRP 0.025 0.002 TRP C 228 HIS 0.006 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00370 (25162) covalent geometry : angle 0.65316 (34202) SS BOND : bond 0.00503 ( 99) SS BOND : angle 1.39081 ( 198) hydrogen bonds : bond 0.04908 ( 497) hydrogen bonds : angle 7.82365 ( 1242) link_BETA1-4 : bond 0.00380 ( 3) link_BETA1-4 : angle 2.04806 ( 9) link_NAG-ASN : bond 0.00774 ( 15) link_NAG-ASN : angle 3.52961 ( 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 297 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 0.972 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: 0.8885 (m-10) cc_final: 0.8349 (m-10) REVERT: A 514 MET cc_start: 0.5672 (mtt) cc_final: 0.5230 (mtm) REVERT: A 534 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8888 (tmtt) REVERT: A 695 TYR cc_start: 0.8761 (p90) cc_final: 0.8488 (p90) REVERT: B 74 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7838 (t70) REVERT: B 99 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6913 (mm-30) REVERT: B 351 MET cc_start: 0.6697 (ptm) cc_final: 0.6162 (ptp) REVERT: B 514 MET cc_start: 0.7705 (mpp) cc_final: 0.7442 (mpp) REVERT: B 773 MET cc_start: 0.3263 (tpp) cc_final: 0.3000 (tpt) REVERT: C 166 ILE cc_start: 0.8996 (tp) cc_final: 0.8537 (tt) REVERT: C 496 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6638 (ttp-110) REVERT: C 499 PHE cc_start: 0.4761 (OUTLIER) cc_final: 0.4062 (m-10) REVERT: D 221 MET cc_start: 0.8007 (mmt) cc_final: 0.7490 (mmt) REVERT: D 587 TYR cc_start: 0.4411 (m-80) cc_final: 0.4171 (m-80) REVERT: D 775 LEU cc_start: 0.7132 (tp) cc_final: 0.6776 (tt) outliers start: 40 outliers final: 23 residues processed: 287 average time/residue: 0.1599 time to fit residues: 74.7831 Evaluate side-chains 239 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 130 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 307 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 467 ASN A 508 ASN C 432 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS D 263 ASN D 339 HIS D 410 HIS D 467 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.171735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.122516 restraints weight = 53875.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121032 restraints weight = 32511.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.122534 restraints weight = 25665.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.122984 restraints weight = 21365.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123425 restraints weight = 17535.429| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 25279 Z= 0.244 Angle : 0.697 11.593 34454 Z= 0.354 Chirality : 0.047 0.355 3802 Planarity : 0.005 0.051 4375 Dihedral : 11.926 110.988 3753 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.57 % Allowed : 11.88 % Favored : 85.55 % 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 aren not related in a simple way. whole: -0.75 (0.15), residues: 3076 helix: -2.20 (0.72), residues: 40 sheet: -0.82 (0.18), residues: 860 loop : -0.26 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 245 TYR 0.033 0.002 TYR D 195 PHE 0.042 0.003 PHE C 499 TRP 0.021 0.002 TRP C 850 HIS 0.012 0.001 HIS C 847 Details of bonding type rmsd covalent geometry : bond 0.00559 (25162) covalent geometry : angle 0.68263 (34202) SS BOND : bond 0.00347 ( 99) SS BOND : angle 1.13901 ( 198) hydrogen bonds : bond 0.04442 ( 497) hydrogen bonds : angle 7.50601 ( 1242) link_BETA1-4 : bond 0.00509 ( 3) link_BETA1-4 : angle 1.96235 ( 9) link_NAG-ASN : bond 0.00777 ( 15) link_NAG-ASN : angle 3.41460 ( 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 283 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 213 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.5547 (p90) cc_final: 0.5307 (p90) REVERT: A 352 TYR cc_start: 0.8892 (m-10) cc_final: 0.8316 (m-10) REVERT: A 512 TYR cc_start: 0.7896 (m-80) cc_final: 0.7565 (m-10) REVERT: A 514 MET cc_start: 0.5692 (mtt) cc_final: 0.5264 (mtm) REVERT: A 517 MET cc_start: 0.6288 (mmm) cc_final: 0.5577 (mmt) REVERT: A 534 LYS cc_start: 0.9123 (ptpt) cc_final: 0.8819 (tmtt) REVERT: A 558 LEU cc_start: 0.8419 (tp) cc_final: 0.8199 (pp) REVERT: A 581 MET cc_start: 0.7303 (mtt) cc_final: 0.6559 (mtt) REVERT: A 695 TYR cc_start: 0.8772 (p90) cc_final: 0.8471 (p90) REVERT: B 53 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: B 351 MET cc_start: 0.6516 (ptm) cc_final: 0.6002 (ptp) REVERT: B 773 MET cc_start: 0.3602 (tpp) cc_final: 0.3071 (tpt) REVERT: B 881 MET cc_start: 0.6681 (mmm) cc_final: 0.5709 (mtt) REVERT: C 54 TYR cc_start: 0.9045 (p90) cc_final: 0.8677 (p90) REVERT: C 115 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8046 (mtp85) REVERT: C 351 MET cc_start: 0.7062 (ppp) cc_final: 0.6696 (ppp) REVERT: C 387 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5412 (p90) REVERT: C 496 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6605 (ttp-110) REVERT: C 499 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4185 (m-80) REVERT: C 846 PHE cc_start: 0.7902 (m-80) cc_final: 0.7625 (m-80) REVERT: D 221 MET cc_start: 0.8017 (mmt) cc_final: 0.7295 (mmt) REVERT: D 234 GLU cc_start: 0.8183 (mp0) cc_final: 0.7924 (mp0) REVERT: D 452 GLU cc_start: 0.7777 (mp0) cc_final: 0.7067 (mp0) REVERT: D 587 TYR cc_start: 0.4525 (m-80) cc_final: 0.4283 (m-80) REVERT: D 670 ASN cc_start: 0.8245 (t0) cc_final: 0.7673 (m-40) REVERT: D 671 TYR cc_start: 0.6835 (m-10) cc_final: 0.6565 (m-80) REVERT: D 775 LEU cc_start: 0.7245 (tp) cc_final: 0.6896 (tt) REVERT: D 823 MET cc_start: 0.7888 (tpp) cc_final: 0.7331 (tpt) outliers start: 70 outliers final: 48 residues processed: 264 average time/residue: 0.1664 time to fit residues: 70.8509 Evaluate side-chains 236 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 272 THR 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 189 VAL 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 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 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 359 ILE Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 584 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 296 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 118 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 284 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 865 HIS B 231 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.174155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.125902 restraints weight = 55257.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.124555 restraints weight = 33522.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.125167 restraints weight = 26473.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125922 restraints weight = 23184.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.126145 restraints weight = 19268.232| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25279 Z= 0.119 Angle : 0.612 11.419 34454 Z= 0.303 Chirality : 0.044 0.350 3802 Planarity : 0.004 0.046 4375 Dihedral : 11.169 108.072 3753 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.39 % Allowed : 13.38 % Favored : 84.23 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 3076 helix: -2.24 (0.71), residues: 40 sheet: -0.87 (0.18), residues: 873 loop : -0.16 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 245 TYR 0.022 0.001 TYR D 655 PHE 0.032 0.002 PHE C 499 TRP 0.016 0.001 TRP D 551 HIS 0.017 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00271 (25162) covalent geometry : angle 0.59453 (34202) SS BOND : bond 0.00211 ( 99) SS BOND : angle 1.01531 ( 198) hydrogen bonds : bond 0.03586 ( 497) hydrogen bonds : angle 6.95462 ( 1242) link_BETA1-4 : bond 0.00581 ( 3) link_BETA1-4 : angle 2.54491 ( 9) link_NAG-ASN : bond 0.00789 ( 15) link_NAG-ASN : angle 3.48644 ( 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 269 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8755 (mt) REVERT: A 337 TYR cc_start: 0.5554 (p90) cc_final: 0.5248 (p90) REVERT: A 352 TYR cc_start: 0.8826 (m-10) cc_final: 0.8254 (m-10) REVERT: A 512 TYR cc_start: 0.7879 (m-80) cc_final: 0.7529 (m-10) REVERT: A 514 MET cc_start: 0.5693 (mtt) cc_final: 0.5269 (mtm) REVERT: A 517 MET cc_start: 0.6246 (mmm) cc_final: 0.5472 (mmt) REVERT: A 534 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8813 (tmtt) REVERT: A 581 MET cc_start: 0.7381 (mtt) cc_final: 0.6565 (mtt) REVERT: B 53 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: B 351 MET cc_start: 0.6348 (ptm) cc_final: 0.5888 (ptp) REVERT: B 773 MET cc_start: 0.3868 (tpp) cc_final: 0.3198 (tpt) REVERT: B 881 MET cc_start: 0.6761 (mmm) cc_final: 0.5718 (mtt) REVERT: C 54 TYR cc_start: 0.9021 (p90) cc_final: 0.8701 (p90) REVERT: C 115 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8051 (mtp85) REVERT: C 351 MET cc_start: 0.6983 (ppp) cc_final: 0.6592 (ppp) REVERT: C 387 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.5549 (p90) REVERT: C 496 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6642 (ttp-110) REVERT: C 499 PHE cc_start: 0.4338 (OUTLIER) cc_final: 0.3779 (m-80) REVERT: C 846 PHE cc_start: 0.7981 (m-80) cc_final: 0.7732 (m-80) REVERT: D 221 MET cc_start: 0.8008 (mmt) cc_final: 0.7206 (mmt) REVERT: D 234 GLU cc_start: 0.8151 (mp0) cc_final: 0.7945 (mp0) REVERT: D 419 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7794 (m) REVERT: D 452 GLU cc_start: 0.7636 (mp0) cc_final: 0.7065 (mp0) REVERT: D 480 ARG cc_start: 0.8176 (tmt170) cc_final: 0.7747 (ptm160) REVERT: D 775 LEU cc_start: 0.7296 (tp) cc_final: 0.6945 (tt) outliers start: 65 outliers final: 41 residues processed: 259 average time/residue: 0.1653 time to fit residues: 69.7579 Evaluate side-chains 230 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS 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 242 LEU 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 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 234 GLU 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 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 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 391 ASN 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 550 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 419 VAL 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 735 THR 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: 4.9990 chunk 299 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 283 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.170147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120900 restraints weight = 53619.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119629 restraints weight = 29394.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.120713 restraints weight = 23072.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.121561 restraints weight = 19310.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.122436 restraints weight = 16613.662| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 25279 Z= 0.229 Angle : 0.666 10.696 34454 Z= 0.336 Chirality : 0.045 0.354 3802 Planarity : 0.005 0.046 4375 Dihedral : 11.052 111.485 3753 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.87 % Allowed : 14.67 % Favored : 82.46 % 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 aren not related in a simple way. whole: -0.84 (0.15), residues: 3076 helix: -1.87 (0.76), residues: 40 sheet: -0.99 (0.18), residues: 859 loop : -0.28 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 237 TYR 0.031 0.002 TYR D 195 PHE 0.040 0.002 PHE D 499 TRP 0.025 0.002 TRP D 551 HIS 0.035 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00523 (25162) covalent geometry : angle 0.65031 (34202) SS BOND : bond 0.00316 ( 99) SS BOND : angle 1.06063 ( 198) hydrogen bonds : bond 0.03639 ( 497) hydrogen bonds : angle 6.99778 ( 1242) link_BETA1-4 : bond 0.00221 ( 3) link_BETA1-4 : angle 2.98893 ( 9) link_NAG-ASN : bond 0.00681 ( 15) link_NAG-ASN : angle 3.40775 ( 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 262 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 1.003 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 242 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8747 (mp) REVERT: A 337 TYR cc_start: 0.5271 (p90) cc_final: 0.4958 (p90) REVERT: A 352 TYR cc_start: 0.8912 (m-10) cc_final: 0.8318 (m-10) REVERT: A 512 TYR cc_start: 0.7967 (m-80) cc_final: 0.7581 (m-10) REVERT: A 514 MET cc_start: 0.5776 (mtt) cc_final: 0.5358 (mtm) REVERT: A 517 MET cc_start: 0.6163 (mmm) cc_final: 0.5410 (mmt) REVERT: A 534 LYS cc_start: 0.9082 (ptpt) cc_final: 0.8808 (tmtt) REVERT: A 555 ARG cc_start: 0.6801 (mtt180) cc_final: 0.6468 (mtt-85) REVERT: B 291 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5721 (t80) REVERT: B 351 MET cc_start: 0.6505 (ptm) cc_final: 0.5955 (ptp) REVERT: B 370 LEU cc_start: 0.5650 (tp) cc_final: 0.5176 (pp) REVERT: B 773 MET cc_start: 0.4181 (tpp) cc_final: 0.3598 (tpt) REVERT: B 881 MET cc_start: 0.6686 (mmm) cc_final: 0.5773 (mtt) REVERT: C 115 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7901 (mtp85) REVERT: C 351 MET cc_start: 0.6966 (ppp) cc_final: 0.6512 (ppp) REVERT: C 387 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.5643 (p90) REVERT: C 496 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6729 (ttp-110) REVERT: C 749 MET cc_start: 0.6520 (ppp) cc_final: 0.6292 (ppp) REVERT: C 846 PHE cc_start: 0.7928 (m-80) cc_final: 0.7697 (m-80) REVERT: D 221 MET cc_start: 0.8041 (mmt) cc_final: 0.7251 (mmt) REVERT: D 237 ARG cc_start: 0.7399 (tpp-160) cc_final: 0.6904 (tpp80) REVERT: D 282 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8412 (t) REVERT: D 419 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7972 (m) REVERT: D 452 GLU cc_start: 0.7866 (mp0) cc_final: 0.7506 (mp0) REVERT: D 480 ARG cc_start: 0.8188 (tmt170) cc_final: 0.7938 (ptm160) REVERT: D 775 LEU cc_start: 0.7263 (tp) cc_final: 0.6868 (tt) REVERT: D 823 MET cc_start: 0.7925 (tpp) cc_final: 0.7512 (tpt) outliers start: 78 outliers final: 57 residues processed: 252 average time/residue: 0.1635 time to fit residues: 68.5487 Evaluate side-chains 234 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 242 LEU 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 52 SER 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 178 MET Chi-restraints excluded: chain B residue 234 GLU 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 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 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 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 497 ILE 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: 7.9990 chunk 235 optimal weight: 3.9990 chunk 268 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 289 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 44 optimal weight: 0.0030 chunk 302 optimal weight: 0.1980 chunk 278 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 GLN ** 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 = 0.4549 r_free = 0.4549 target = 0.173873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.125949 restraints weight = 54812.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125150 restraints weight = 32757.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.126141 restraints weight = 24869.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.127061 restraints weight = 21712.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.127147 restraints weight = 17962.289| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25279 Z= 0.101 Angle : 0.596 10.326 34454 Z= 0.291 Chirality : 0.043 0.348 3802 Planarity : 0.004 0.045 4375 Dihedral : 10.126 108.020 3753 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.28 % Allowed : 15.92 % Favored : 81.80 % 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 aren not related in a simple way. whole: -0.64 (0.15), residues: 3076 helix: -2.03 (0.74), residues: 40 sheet: -0.86 (0.18), residues: 852 loop : -0.14 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 245 TYR 0.024 0.001 TYR D 655 PHE 0.027 0.001 PHE C 499 TRP 0.026 0.001 TRP D 551 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00229 (25162) covalent geometry : angle 0.57701 (34202) SS BOND : bond 0.00232 ( 99) SS BOND : angle 0.80639 ( 198) hydrogen bonds : bond 0.03088 ( 497) hydrogen bonds : angle 6.46354 ( 1242) link_BETA1-4 : bond 0.00450 ( 3) link_BETA1-4 : angle 3.63522 ( 9) link_NAG-ASN : bond 0.00771 ( 15) link_NAG-ASN : angle 3.65224 ( 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 256 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 1.052 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: 0.5251 (p90) cc_final: 0.4954 (p90) REVERT: A 352 TYR cc_start: 0.8810 (m-10) cc_final: 0.8217 (m-10) REVERT: A 512 TYR cc_start: 0.7927 (m-80) cc_final: 0.7590 (m-10) REVERT: A 514 MET cc_start: 0.5704 (mtt) cc_final: 0.5270 (mtm) REVERT: A 517 MET cc_start: 0.5936 (mmm) cc_final: 0.5170 (mmt) REVERT: A 534 LYS cc_start: 0.9032 (ptpt) cc_final: 0.8788 (tmtt) REVERT: B 351 MET cc_start: 0.6420 (ptm) cc_final: 0.5755 (ptp) REVERT: B 370 LEU cc_start: 0.5520 (tp) cc_final: 0.4883 (pp) REVERT: B 773 MET cc_start: 0.4573 (tpp) cc_final: 0.3948 (tpt) REVERT: B 881 MET cc_start: 0.6688 (mmm) cc_final: 0.5687 (mtt) REVERT: C 351 MET cc_start: 0.6870 (ppp) cc_final: 0.6240 (ppp) REVERT: C 387 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.5834 (p90) REVERT: C 434 GLU cc_start: 0.7097 (pm20) cc_final: 0.6761 (pp20) REVERT: C 470 MET cc_start: 0.6426 (mmt) cc_final: 0.6083 (mmt) REVERT: C 496 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6651 (ttp-110) REVERT: C 773 MET cc_start: 0.7882 (tpp) cc_final: 0.7417 (tpp) REVERT: C 835 MET cc_start: 0.8298 (ppp) cc_final: 0.7946 (ppp) REVERT: D 221 MET cc_start: 0.7991 (mmt) cc_final: 0.7242 (mmt) REVERT: D 237 ARG cc_start: 0.6944 (tpp-160) cc_final: 0.6552 (tpp80) REVERT: D 419 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8049 (m) REVERT: D 480 ARG cc_start: 0.8035 (tmt170) cc_final: 0.7740 (ptm160) REVERT: D 573 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6776 (p90) REVERT: D 775 LEU cc_start: 0.7314 (tp) cc_final: 0.6912 (tt) REVERT: D 823 MET cc_start: 0.8050 (tpp) cc_final: 0.7507 (tpt) outliers start: 62 outliers final: 44 residues processed: 246 average time/residue: 0.1653 time to fit residues: 66.3495 Evaluate side-chains 222 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain A residue 233 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 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 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 617 THR Chi-restraints excluded: chain C residue 89 THR 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 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 504 ILE Chi-restraints excluded: chain C residue 505 CYS Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 786 HIS Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 573 TYR Chi-restraints excluded: chain D residue 587 TYR 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 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: 6.9990 chunk 269 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 206 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.170409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.122422 restraints weight = 54493.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.119252 restraints weight = 28758.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.120905 restraints weight = 25067.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121060 restraints weight = 21440.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121092 restraints weight = 18855.788| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 25279 Z= 0.216 Angle : 0.658 14.147 34454 Z= 0.330 Chirality : 0.045 0.371 3802 Planarity : 0.005 0.059 4375 Dihedral : 10.185 113.886 3753 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.72 % Allowed : 16.14 % Favored : 81.14 % 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 aren not related in a simple way. whole: -0.75 (0.15), residues: 3076 helix: -1.51 (0.89), residues: 34 sheet: -0.99 (0.18), residues: 865 loop : -0.20 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 237 TYR 0.026 0.002 TYR D 195 PHE 0.038 0.002 PHE C 499 TRP 0.026 0.002 TRP D 551 HIS 0.008 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00487 (25162) covalent geometry : angle 0.63722 (34202) SS BOND : bond 0.00491 ( 99) SS BOND : angle 1.21799 ( 198) hydrogen bonds : bond 0.03433 ( 497) hydrogen bonds : angle 6.68925 ( 1242) link_BETA1-4 : bond 0.00437 ( 3) link_BETA1-4 : angle 3.58267 ( 9) link_NAG-ASN : bond 0.00692 ( 15) link_NAG-ASN : angle 3.70092 ( 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 249 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 175 time to evaluate : 0.979 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: 0.5513 (p90) cc_final: 0.5213 (p90) REVERT: A 352 TYR cc_start: 0.9062 (m-10) cc_final: 0.8467 (m-10) REVERT: A 512 TYR cc_start: 0.7903 (m-80) cc_final: 0.7532 (m-10) REVERT: A 514 MET cc_start: 0.5706 (mtt) cc_final: 0.5318 (mtm) REVERT: A 517 MET cc_start: 0.6032 (mmm) cc_final: 0.5338 (mmt) REVERT: A 534 LYS cc_start: 0.9120 (ptpt) cc_final: 0.8823 (tmtt) REVERT: B 351 MET cc_start: 0.6316 (ptm) cc_final: 0.5766 (ptp) REVERT: B 609 HIS cc_start: 0.5799 (m-70) cc_final: 0.5548 (m-70) REVERT: B 773 MET cc_start: 0.4258 (tpp) cc_final: 0.3728 (tpt) REVERT: B 881 MET cc_start: 0.6452 (mmm) cc_final: 0.5506 (mtt) REVERT: C 496 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6073 (ttp-110) REVERT: C 581 MET cc_start: 0.4000 (ttm) cc_final: 0.3789 (ttp) REVERT: C 749 MET cc_start: 0.6480 (ppp) cc_final: 0.6251 (ppp) REVERT: C 773 MET cc_start: 0.7908 (tpp) cc_final: 0.7548 (tpp) REVERT: C 835 MET cc_start: 0.8338 (ppp) cc_final: 0.8055 (ppp) REVERT: D 221 MET cc_start: 0.7956 (mmt) cc_final: 0.7182 (mmt) REVERT: D 237 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.7136 (tpp80) REVERT: D 282 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8471 (t) REVERT: D 419 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8071 (m) REVERT: D 439 SER cc_start: 0.8434 (t) cc_final: 0.8123 (p) REVERT: D 452 GLU cc_start: 0.7808 (mp0) cc_final: 0.7568 (mp0) REVERT: D 480 ARG cc_start: 0.8172 (tmt170) cc_final: 0.7787 (ptm160) REVERT: D 775 LEU cc_start: 0.7237 (tp) cc_final: 0.6827 (tt) REVERT: D 823 MET cc_start: 0.7987 (tpp) cc_final: 0.7632 (tpp) outliers start: 74 outliers final: 57 residues processed: 239 average time/residue: 0.1585 time to fit residues: 62.3507 Evaluate side-chains 227 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 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 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 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 391 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 439 SER 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 523 THR Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 659 THR 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 350 LEU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 419 VAL 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 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: 50.0000 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 192 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** 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 = 0.4566 r_free = 0.4566 target = 0.172097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.126378 restraints weight = 54712.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.122273 restraints weight = 31450.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.123755 restraints weight = 26701.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.124091 restraints weight = 21413.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.124465 restraints weight = 18753.771| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25279 Z= 0.133 Angle : 0.613 10.586 34454 Z= 0.305 Chirality : 0.044 0.349 3802 Planarity : 0.004 0.044 4375 Dihedral : 9.812 111.927 3753 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.79 % Allowed : 16.36 % Favored : 80.85 % 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 aren not related in a simple way. whole: -0.70 (0.15), residues: 3076 helix: -1.61 (0.88), residues: 34 sheet: -0.96 (0.18), residues: 855 loop : -0.17 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 237 TYR 0.030 0.001 TYR D 610 PHE 0.028 0.002 PHE D 699 TRP 0.026 0.002 TRP D 850 HIS 0.007 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00307 (25162) covalent geometry : angle 0.59171 (34202) SS BOND : bond 0.00228 ( 99) SS BOND : angle 1.13085 ( 198) hydrogen bonds : bond 0.03119 ( 497) hydrogen bonds : angle 6.48965 ( 1242) link_BETA1-4 : bond 0.00519 ( 3) link_BETA1-4 : angle 3.88133 ( 9) link_NAG-ASN : bond 0.00730 ( 15) link_NAG-ASN : angle 3.66131 ( 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 245 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 0.968 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: 0.5429 (p90) cc_final: 0.5099 (p90) REVERT: A 352 TYR cc_start: 0.8941 (m-10) cc_final: 0.8299 (m-10) REVERT: A 512 TYR cc_start: 0.7932 (m-80) cc_final: 0.7557 (m-10) REVERT: A 514 MET cc_start: 0.5705 (mtt) cc_final: 0.5290 (mtm) REVERT: A 534 LYS cc_start: 0.9062 (ptpt) cc_final: 0.8816 (tmtt) REVERT: B 351 MET cc_start: 0.6186 (ptm) cc_final: 0.5596 (ptp) REVERT: B 881 MET cc_start: 0.6195 (mmm) cc_final: 0.5418 (mtt) REVERT: C 378 ARG cc_start: 0.7471 (mmm-85) cc_final: 0.7264 (mmm160) REVERT: C 387 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.5863 (p90) REVERT: C 434 GLU cc_start: 0.7052 (pm20) cc_final: 0.6535 (pp20) REVERT: C 496 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6094 (ttp-110) REVERT: C 499 PHE cc_start: 0.5008 (OUTLIER) cc_final: 0.4399 (m-10) REVERT: C 773 MET cc_start: 0.7967 (tpp) cc_final: 0.7560 (tpp) REVERT: C 835 MET cc_start: 0.8343 (ppp) cc_final: 0.8048 (ppp) REVERT: D 221 MET cc_start: 0.7917 (mmt) cc_final: 0.7100 (mmt) REVERT: D 237 ARG cc_start: 0.7399 (tpp-160) cc_final: 0.7054 (tpp80) REVERT: D 282 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (t) REVERT: D 419 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8182 (m) REVERT: D 452 GLU cc_start: 0.7717 (mp0) cc_final: 0.7503 (mp0) REVERT: D 480 ARG cc_start: 0.8155 (tmt170) cc_final: 0.7660 (ptm160) REVERT: D 775 LEU cc_start: 0.7238 (tp) cc_final: 0.6841 (tt) REVERT: D 823 MET cc_start: 0.7926 (tpp) cc_final: 0.7414 (tpt) outliers start: 76 outliers final: 58 residues processed: 234 average time/residue: 0.1558 time to fit residues: 60.1516 Evaluate side-chains 226 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 52 SER 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 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 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 391 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 462 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 505 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 572 ILE 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 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 618 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 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=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: 4.9990 chunk 142 optimal weight: 40.0000 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** 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 = 0.4555 r_free = 0.4555 target = 0.171194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121904 restraints weight = 54614.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.120907 restraints weight = 30245.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122069 restraints weight = 21609.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122589 restraints weight = 19233.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122604 restraints weight = 17077.164| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25279 Z= 0.162 Angle : 0.627 12.587 34454 Z= 0.311 Chirality : 0.044 0.350 3802 Planarity : 0.004 0.044 4375 Dihedral : 9.659 114.689 3753 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.50 % Allowed : 16.95 % Favored : 80.55 % 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 aren not related in a simple way. whole: -0.79 (0.15), residues: 3076 helix: -1.81 (0.93), residues: 34 sheet: -1.10 (0.18), residues: 886 loop : -0.17 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 237 TYR 0.022 0.001 TYR C 195 PHE 0.031 0.002 PHE D 699 TRP 0.021 0.002 TRP D 551 HIS 0.007 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00373 (25162) covalent geometry : angle 0.60850 (34202) SS BOND : bond 0.00288 ( 99) SS BOND : angle 0.88240 ( 198) hydrogen bonds : bond 0.03142 ( 497) hydrogen bonds : angle 6.45181 ( 1242) link_BETA1-4 : bond 0.00586 ( 3) link_BETA1-4 : angle 3.92233 ( 9) link_NAG-ASN : bond 0.00709 ( 15) link_NAG-ASN : angle 3.61175 ( 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 243 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 1.014 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: 0.5458 (p90) cc_final: 0.5130 (p90) REVERT: A 352 TYR cc_start: 0.8897 (m-10) cc_final: 0.8233 (m-10) REVERT: A 512 TYR cc_start: 0.7942 (m-80) cc_final: 0.7567 (m-10) REVERT: A 514 MET cc_start: 0.5895 (mtt) cc_final: 0.5467 (mtm) REVERT: A 517 MET cc_start: 0.5639 (tpt) cc_final: 0.4351 (mmt) REVERT: A 534 LYS cc_start: 0.9051 (ptpt) cc_final: 0.8787 (tmtt) REVERT: B 162 ARG cc_start: 0.8657 (ttm110) cc_final: 0.7710 (ttp80) REVERT: B 351 MET cc_start: 0.6238 (ptm) cc_final: 0.5650 (ptp) REVERT: B 539 TYR cc_start: 0.2449 (t80) cc_final: 0.2234 (t80) REVERT: B 881 MET cc_start: 0.6133 (mmm) cc_final: 0.5369 (mtt) REVERT: C 378 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7369 (mmm160) REVERT: C 387 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.5879 (p90) REVERT: C 434 GLU cc_start: 0.7065 (pm20) cc_final: 0.6494 (pp20) REVERT: C 470 MET cc_start: 0.7014 (mmt) cc_final: 0.6448 (mmt) REVERT: C 496 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6101 (ttp-110) REVERT: C 499 PHE cc_start: 0.5048 (OUTLIER) cc_final: 0.4502 (m-10) REVERT: C 773 MET cc_start: 0.7953 (tpp) cc_final: 0.7588 (tpp) REVERT: C 835 MET cc_start: 0.8359 (ppp) cc_final: 0.8050 (ppp) REVERT: D 221 MET cc_start: 0.7967 (mmt) cc_final: 0.7152 (mmt) REVERT: D 237 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7178 (tpp80) REVERT: D 282 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8467 (t) REVERT: D 419 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8135 (m) REVERT: D 439 SER cc_start: 0.8469 (t) cc_final: 0.8145 (p) REVERT: D 452 GLU cc_start: 0.7776 (mp0) cc_final: 0.7544 (mp0) REVERT: D 480 ARG cc_start: 0.8183 (tmt170) cc_final: 0.7677 (ptm160) REVERT: D 775 LEU cc_start: 0.7186 (tp) cc_final: 0.6777 (tt) REVERT: D 823 MET cc_start: 0.7641 (tpp) cc_final: 0.7133 (tpt) REVERT: D 865 HIS cc_start: 0.7509 (t-90) cc_final: 0.7225 (t70) outliers start: 68 outliers final: 60 residues processed: 234 average time/residue: 0.1624 time to fit residues: 61.9167 Evaluate side-chains 229 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 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 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 52 SER 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 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 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 242 LEU 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 462 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 505 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 572 ILE 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 760 VAL 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 449 THR Chi-restraints excluded: chain D residue 587 TYR 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 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: 0.0050 chunk 244 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 306 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.171707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.123858 restraints weight = 54508.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.121005 restraints weight = 37308.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.121530 restraints weight = 28863.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.121867 restraints weight = 25838.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123413 restraints weight = 20960.098| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25279 Z= 0.144 Angle : 0.612 9.050 34454 Z= 0.304 Chirality : 0.043 0.349 3802 Planarity : 0.004 0.044 4375 Dihedral : 9.471 115.434 3753 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.54 % Allowed : 17.17 % Favored : 80.29 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 3076 helix: -1.79 (0.94), residues: 34 sheet: -1.04 (0.18), residues: 863 loop : -0.19 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 237 TYR 0.022 0.001 TYR C 195 PHE 0.034 0.002 PHE D 699 TRP 0.027 0.002 TRP C 354 HIS 0.013 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00335 (25162) covalent geometry : angle 0.59311 (34202) SS BOND : bond 0.00233 ( 99) SS BOND : angle 0.90464 ( 198) hydrogen bonds : bond 0.03015 ( 497) hydrogen bonds : angle 6.29503 ( 1242) link_BETA1-4 : bond 0.00598 ( 3) link_BETA1-4 : angle 4.03519 ( 9) link_NAG-ASN : bond 0.00742 ( 15) link_NAG-ASN : angle 3.56715 ( 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 242 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.5577 (p90) cc_final: 0.5244 (p90) REVERT: A 352 TYR cc_start: 0.9064 (m-10) cc_final: 0.8392 (m-10) REVERT: A 512 TYR cc_start: 0.7858 (m-80) cc_final: 0.7470 (m-10) REVERT: A 514 MET cc_start: 0.5650 (mtt) cc_final: 0.5214 (mtm) REVERT: A 517 MET cc_start: 0.5856 (tpt) cc_final: 0.4748 (mmt) REVERT: A 534 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8834 (tmtt) REVERT: B 162 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8209 (tmt-80) REVERT: B 351 MET cc_start: 0.6371 (ptm) cc_final: 0.5785 (ptp) REVERT: B 881 MET cc_start: 0.6196 (mmm) cc_final: 0.5476 (mtt) REVERT: C 378 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7354 (mmm160) REVERT: C 387 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.5965 (p90) REVERT: C 434 GLU cc_start: 0.7098 (pm20) cc_final: 0.6578 (pp20) REVERT: C 470 MET cc_start: 0.6995 (mmt) cc_final: 0.6453 (mmt) REVERT: C 496 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5982 (ttp-110) REVERT: C 499 PHE cc_start: 0.5240 (OUTLIER) cc_final: 0.4672 (m-10) REVERT: C 773 MET cc_start: 0.7853 (tpp) cc_final: 0.7503 (tpp) REVERT: C 835 MET cc_start: 0.8371 (ppp) cc_final: 0.8050 (ppp) REVERT: D 221 MET cc_start: 0.7892 (mmt) cc_final: 0.7040 (mmt) REVERT: D 282 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8458 (t) REVERT: D 439 SER cc_start: 0.8494 (t) cc_final: 0.8200 (p) REVERT: D 480 ARG cc_start: 0.8208 (tmt170) cc_final: 0.7850 (ptm160) REVERT: D 573 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7241 (p90) REVERT: D 775 LEU cc_start: 0.7169 (tp) cc_final: 0.6873 (tt) REVERT: D 823 MET cc_start: 0.7685 (tpp) cc_final: 0.7140 (tpt) REVERT: D 865 HIS cc_start: 0.7635 (t-90) cc_final: 0.7298 (t70) outliers start: 69 outliers final: 57 residues processed: 234 average time/residue: 0.1677 time to fit residues: 64.0939 Evaluate side-chains 228 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 52 SER 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 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 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 242 LEU 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 462 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 505 CYS Chi-restraints excluded: chain C residue 523 THR 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 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 573 TYR Chi-restraints excluded: chain D residue 587 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 3 optimal weight: 0.0970 chunk 60 optimal weight: 0.0370 chunk 154 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.172830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.123657 restraints weight = 55429.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.123203 restraints weight = 31446.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124321 restraints weight = 23819.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.124976 restraints weight = 19784.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.125096 restraints weight = 17029.101| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25279 Z= 0.104 Angle : 0.598 13.000 34454 Z= 0.294 Chirality : 0.043 0.346 3802 Planarity : 0.004 0.044 4375 Dihedral : 9.106 116.218 3753 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.95 % Allowed : 17.98 % Favored : 80.07 % 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 aren not related in a simple way. whole: -0.62 (0.15), residues: 3076 helix: -1.78 (0.96), residues: 34 sheet: -0.83 (0.18), residues: 861 loop : -0.13 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 115 TYR 0.021 0.001 TYR D 655 PHE 0.038 0.001 PHE D 699 TRP 0.032 0.002 TRP D 551 HIS 0.010 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00243 (25162) covalent geometry : angle 0.57889 (34202) SS BOND : bond 0.00189 ( 99) SS BOND : angle 0.84341 ( 198) hydrogen bonds : bond 0.02960 ( 497) hydrogen bonds : angle 6.01666 ( 1242) link_BETA1-4 : bond 0.00709 ( 3) link_BETA1-4 : angle 4.27290 ( 9) link_NAG-ASN : bond 0.00794 ( 15) link_NAG-ASN : angle 3.51892 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5065.97 seconds wall clock time: 88 minutes 21.00 seconds (5301.00 seconds total)